Textual Embeddings for StarkQA-PrimeKG using nomic-embed-text¶
In this tutorial, we will perform textual (enrichment and) embeddings for StarkQA-PrimeKG and eventually construct a knowledge graph.
First of all, we need to import necessary libraries as follows:
In [1]:
Copied!
# Import necessary libraries
import os
from tqdm import tqdm
import networkx as nx
import pandas as pd
import pickle
from torch_geometric.data import Data, HeteroData
from torch_geometric.utils import from_networkx
import sys
sys.path.append('../../..')
from aiagents4pharma.talk2knowledgegraphs.datasets.primekg import PrimeKG
from aiagents4pharma.talk2knowledgegraphs.datasets.starkqa_primekg import StarkQAPrimeKG
from aiagents4pharma.talk2knowledgegraphs.utils.embeddings.sentence_transformer import EmbeddingWithSentenceTransformer
from aiagents4pharma.talk2knowledgegraphs.utils import kg_utils
# # Set the logging level for httpx to WARNING to suppress INFO messages
# import logging
# logging.getLogger("httpx").setLevel(logging.WARNING)
# Import necessary libraries
import os
from tqdm import tqdm
import networkx as nx
import pandas as pd
import pickle
from torch_geometric.data import Data, HeteroData
from torch_geometric.utils import from_networkx
import sys
sys.path.append('../../..')
from aiagents4pharma.talk2knowledgegraphs.datasets.primekg import PrimeKG
from aiagents4pharma.talk2knowledgegraphs.datasets.starkqa_primekg import StarkQAPrimeKG
from aiagents4pharma.talk2knowledgegraphs.utils.embeddings.sentence_transformer import EmbeddingWithSentenceTransformer
from aiagents4pharma.talk2knowledgegraphs.utils import kg_utils
# # Set the logging level for httpx to WARNING to suppress INFO messages
# import logging
# logging.getLogger("httpx").setLevel(logging.WARNING)
/home/awmulyadi/Repositories/office/AIAgents4Pharma/venv/lib/python3.12/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html from .autonotebook import tqdm as notebook_tqdm /home/awmulyadi/Repositories/office/AIAgents4Pharma/venv/lib/python3.12/site-packages/pydantic/_internal/_fields.py:132: UserWarning: Field "model_id" in SysBioModel has conflict with protected namespace "model_". You may be able to resolve this warning by setting `model_config['protected_namespaces'] = ()`. warnings.warn( /home/awmulyadi/Repositories/office/AIAgents4Pharma/venv/lib/python3.12/site-packages/pydantic/_internal/_fields.py:132: UserWarning: Field "model_id" in BasicoModel has conflict with protected namespace "model_". You may be able to resolve this warning by setting `model_config['protected_namespaces'] = ()`. warnings.warn( /home/awmulyadi/Repositories/office/AIAgents4Pharma/venv/lib/python3.12/site-packages/pydantic/_internal/_fields.py:132: UserWarning: Field "model_data" in SimulateModelInput has conflict with protected namespace "model_". You may be able to resolve this warning by setting `model_config['protected_namespaces'] = ()`. warnings.warn(
We need to load the PrimeKG and StarkQAPrimeKG datasets in order to construct the knowledge graph for later application.
Load PrimeKG¶
To load PrimeKG dataset, we can utilize the PrimeKG class from the aiagents4pharma/talk2knowledgegraphs library.
The PrimeKG needs to be initialized with the path to the PrimeKG dataset to be stored/loaded from the local directory.
In [2]:
Copied!
# Define primekg data by providing a local directory where the data is stored
primekg_data = PrimeKG(local_dir="../../../../data/primekg/")
# Invoke a method to load the data
primekg_data.load_data()
# Get primekg_nodes and primekg_edges
primekg_nodes = primekg_data.get_nodes()
primekg_edges = primekg_data.get_edges()
# Define primekg data by providing a local directory where the data is stored
primekg_data = PrimeKG(local_dir="../../../../data/primekg/")
# Invoke a method to load the data
primekg_data.load_data()
# Get primekg_nodes and primekg_edges
primekg_nodes = primekg_data.get_nodes()
primekg_edges = primekg_data.get_edges()
Loading nodes of PrimeKG dataset ... ../../../../data/primekg/primekg_nodes.tsv.gz already exists. Loading the data from the local directory. Loading edges of PrimeKG dataset ... ../../../../data/primekg/primekg_edges.tsv.gz already exists. Loading the data from the local directory.
We can check the dataframes of nodes and edges of PrimeKG as follows:
In [3]:
Copied!
# Check PrimeKG nodes
primekg_nodes.head()
# Check PrimeKG nodes
primekg_nodes.head()
Out[3]:
| node_index | node_name | node_source | node_id | node_type | |
|---|---|---|---|---|---|
| 0 | 0 | PHYHIP | NCBI | 9796 | gene/protein |
| 1 | 1 | GPANK1 | NCBI | 7918 | gene/protein |
| 2 | 2 | ZRSR2 | NCBI | 8233 | gene/protein |
| 3 | 3 | NRF1 | NCBI | 4899 | gene/protein |
| 4 | 4 | PI4KA | NCBI | 5297 | gene/protein |
In [4]:
Copied!
# Check PrimeKG edges
primekg_edges.head()
# Check PrimeKG edges
primekg_edges.head()
Out[4]:
| head_index | head_name | head_source | head_id | head_type | tail_index | tail_name | tail_source | tail_id | tail_type | display_relation | relation | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 0 | PHYHIP | NCBI | 9796 | gene/protein | 8889 | KIF15 | NCBI | 56992 | gene/protein | ppi | protein_protein |
| 1 | 1 | GPANK1 | NCBI | 7918 | gene/protein | 2798 | PNMA1 | NCBI | 9240 | gene/protein | ppi | protein_protein |
| 2 | 2 | ZRSR2 | NCBI | 8233 | gene/protein | 5646 | TTC33 | NCBI | 23548 | gene/protein | ppi | protein_protein |
| 3 | 3 | NRF1 | NCBI | 4899 | gene/protein | 11592 | MAN1B1 | NCBI | 11253 | gene/protein | ppi | protein_protein |
| 4 | 4 | PI4KA | NCBI | 5297 | gene/protein | 2122 | RGS20 | NCBI | 8601 | gene/protein | ppi | protein_protein |
Load StarkQA¶
In [5]:
Copied!
# Define starkqa primekg data by providing a local directory where the data is stored
starkqa_data = StarkQAPrimeKG(local_dir="../../../../data/starkqa_primekg/")
# Invoke a method to load the data
starkqa_data.load_data()
# Get the StarkQAPrimeKG data, which are the QA pairs, split indices, and the node information
starkqa_df = starkqa_data.get_starkqa()
starkqa_split_indices = starkqa_data.get_starkqa_split_indicies()
starkqa_node_info = starkqa_data.get_starkqa_node_info()
# Define starkqa primekg data by providing a local directory where the data is stored
starkqa_data = StarkQAPrimeKG(local_dir="../../../../data/starkqa_primekg/")
# Invoke a method to load the data
starkqa_data.load_data()
# Get the StarkQAPrimeKG data, which are the QA pairs, split indices, and the node information
starkqa_df = starkqa_data.get_starkqa()
starkqa_split_indices = starkqa_data.get_starkqa_split_indicies()
starkqa_node_info = starkqa_data.get_starkqa_node_info()
Loading StarkQAPrimeKG dataset... ../../../../data/starkqa_primekg/qa/prime/stark_qa/stark_qa.csv already exists. Loading the data from the local directory. Loading StarkQAPrimeKG embeddings...
/home/awmulyadi/Repositories/office/AIAgents4Pharma/docs/notebooks/talk2knowledgegraphs/../../../aiagents4pharma/talk2knowledgegraphs/datasets/starkqa_primekg.py:141: FutureWarning: You are using `torch.load` with `weights_only=False` (the current default value), which uses the default pickle module implicitly. It is possible to construct malicious pickle data which will execute arbitrary code during unpickling (See https://github.com/pytorch/pytorch/blob/main/SECURITY.md#untrusted-models for more details). In a future release, the default value for `weights_only` will be flipped to `True`. This limits the functions that could be executed during unpickling. Arbitrary objects will no longer be allowed to be loaded via this mode unless they are explicitly allowlisted by the user via `torch.serialization.add_safe_globals`. We recommend you start setting `weights_only=True` for any use case where you don't have full control of the loaded file. Please open an issue on GitHub for any issues related to this experimental feature. query_emb_dict = torch.load(query_emb_path) /home/awmulyadi/Repositories/office/AIAgents4Pharma/docs/notebooks/talk2knowledgegraphs/../../../aiagents4pharma/talk2knowledgegraphs/datasets/starkqa_primekg.py:142: FutureWarning: You are using `torch.load` with `weights_only=False` (the current default value), which uses the default pickle module implicitly. It is possible to construct malicious pickle data which will execute arbitrary code during unpickling (See https://github.com/pytorch/pytorch/blob/main/SECURITY.md#untrusted-models for more details). In a future release, the default value for `weights_only` will be flipped to `True`. This limits the functions that could be executed during unpickling. Arbitrary objects will no longer be allowed to be loaded via this mode unless they are explicitly allowlisted by the user via `torch.serialization.add_safe_globals`. We recommend you start setting `weights_only=True` for any use case where you don't have full control of the loaded file. Please open an issue on GitHub for any issues related to this experimental feature. node_emb_dict = torch.load(node_emb_path)
We can get a set of questions from the StarkQA dataset contained in starkqa_df
In [6]:
Copied!
# Check StarkQA data
starkqa_df.head()
# Check StarkQA data
starkqa_df.head()
Out[6]:
| id | query | answer_ids | |
|---|---|---|---|
| 0 | 0 | Could you identify any skin diseases associate... | [95886] |
| 1 | 1 | What drugs target the CYP3A4 enzyme and are us... | [15450] |
| 2 | 2 | What is the name of the condition characterize... | [98851, 98853] |
| 3 | 3 | What drugs are used to treat epithelioid sarco... | [15698] |
| 4 | 4 | Can you supply a compilation of genes and prot... | [7161, 22045] |
Within the starkqa_node_info dictionary, we can access additional information of the nodes in the PrimeKG dataset provided by StarkQA team.
In [7]:
Copied!
# We can obtain additional node information from StarkQAPrimeKG
starkqa_node_info[0]
# We can obtain additional node information from StarkQAPrimeKG
starkqa_node_info[0]
Out[7]:
{'id': 9796,
'type': 'gene/protein',
'name': 'PHYHIP',
'source': 'NCBI',
'details': {'query': 'PHYHIP',
'_id': '9796',
'_score': 17.934021,
'alias': ['DYRK1AP3', 'PAHX-AP', 'PAHXAP1'],
'genomic_pos': {'chr': '8',
'end': 22232101,
'ensemblgene': 'ENSG00000168490',
'start': 22219703,
'strand': -1},
'name': 'phytanoyl-CoA 2-hydroxylase interacting protein',
'summary': 'Enables protein tyrosine kinase binding activity. Involved in protein localization. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]'}}
Textual Enrichment over PrimeKG¶
We begin with the textual enrichment over the PrimeKG nodes by using the StarkQA node information.
Note that not all nodes in the PrimeKG have additional information. For this case, we provide a basic text enrichment for the nodes by simply specifying their node name and type.
In [8]:
Copied!
def enrich_node(data, node_info):
"""
Enrich the node with additional information from StarkQA-PrimeKG
Args:
data (dict): The node data from PrimeKG
node_info (dict): The node information from StarkQA-PrimeKG
"""
# Basic textual enrichment of the node
enriched_node = f"{data['node_name']} belongs to {data['node_type']} category. "
# Only enrich the node if the node type is gene/protein, drug, disease, or pathway, which
# has additional information in the node_info of StarkQA-PrimeKG
added_info = ''
if data['node_type'] == 'gene/protein':
added_info = node_info['details']['summary'] if 'summary' in node_info['details'] else ''
elif data['node_type'] == 'drug':
added_info = ' '.join([str(node_info['details']['description']).replace('nan', ''),
str(node_info['details']['mechanism_of_action']).replace('nan', ''),
str(node_info['details']['protein_binding']).replace('nan', ''),
str(node_info['details']['pharmacodynamics']).replace('nan', ''),
str(node_info['details']['indication']).replace('nan', '')])
elif data['node_type'] == 'disease':
added_info = ' '.join([str(node_info['details']['mondo_definition']).replace('nan', ''),
str(node_info['details']['mayo_symptoms']).replace('nan', ''),
str(node_info['details']['mayo_causes']).replace('nan', '')])
elif data['node_type'] == 'pathway':
added_info += f"This pathway found in {node_info['details']['speciesName']}. " + ' '.join([x['text'] for x in node_info['details']['summation']]) if 'details' in node_info else ''
# Append the additional information for enrichment
enriched_node += added_info
return enriched_node
def enrich_node(data, node_info):
"""
Enrich the node with additional information from StarkQA-PrimeKG
Args:
data (dict): The node data from PrimeKG
node_info (dict): The node information from StarkQA-PrimeKG
"""
# Basic textual enrichment of the node
enriched_node = f"{data['node_name']} belongs to {data['node_type']} category. "
# Only enrich the node if the node type is gene/protein, drug, disease, or pathway, which
# has additional information in the node_info of StarkQA-PrimeKG
added_info = ''
if data['node_type'] == 'gene/protein':
added_info = node_info['details']['summary'] if 'summary' in node_info['details'] else ''
elif data['node_type'] == 'drug':
added_info = ' '.join([str(node_info['details']['description']).replace('nan', ''),
str(node_info['details']['mechanism_of_action']).replace('nan', ''),
str(node_info['details']['protein_binding']).replace('nan', ''),
str(node_info['details']['pharmacodynamics']).replace('nan', ''),
str(node_info['details']['indication']).replace('nan', '')])
elif data['node_type'] == 'disease':
added_info = ' '.join([str(node_info['details']['mondo_definition']).replace('nan', ''),
str(node_info['details']['mayo_symptoms']).replace('nan', ''),
str(node_info['details']['mayo_causes']).replace('nan', '')])
elif data['node_type'] == 'pathway':
added_info += f"This pathway found in {node_info['details']['speciesName']}. " + ' '.join([x['text'] for x in node_info['details']['summation']]) if 'details' in node_info else ''
# Append the additional information for enrichment
enriched_node += added_info
return enriched_node
By using the above function, we can enrich the node information from PrimeKG with additional information from StarkQA-PrimeKG as shown below:
In [9]:
Copied!
# Perform node enrichment for each row in primekg_nodes
enriched_nodes = primekg_nodes.apply(lambda x: enrich_node(x, starkqa_node_info[x['node_index']]), axis=1).tolist()
primekg_nodes['enriched_node'] = enriched_nodes
primekg_nodes.head()
# Perform node enrichment for each row in primekg_nodes
enriched_nodes = primekg_nodes.apply(lambda x: enrich_node(x, starkqa_node_info[x['node_index']]), axis=1).tolist()
primekg_nodes['enriched_node'] = enriched_nodes
primekg_nodes.head()
Out[9]:
| node_index | node_name | node_source | node_id | node_type | enriched_node | |
|---|---|---|---|---|---|---|
| 0 | 0 | PHYHIP | NCBI | 9796 | gene/protein | PHYHIP belongs to gene/protein category. Enabl... |
| 1 | 1 | GPANK1 | NCBI | 7918 | gene/protein | GPANK1 belongs to gene/protein category. This ... |
| 2 | 2 | ZRSR2 | NCBI | 8233 | gene/protein | ZRSR2 belongs to gene/protein category. This g... |
| 3 | 3 | NRF1 | NCBI | 4899 | gene/protein | NRF1 belongs to gene/protein category. This ge... |
| 4 | 4 | PI4KA | NCBI | 5297 | gene/protein | PI4KA belongs to gene/protein category. This g... |
Subsequently, we can perform similar textual enrichment for the edges in PrimeKG.
Since StarkQA only provides node information, we can only enrich the edges with basic information of the triples in combination with the head and tail nodes.
In [10]:
Copied!
# Perform textual enrichment over the edges by simply concatenating the head and tail nodes with the relation followed by the enriched node information
enriched_edges = primekg_edges.apply(lambda x: f"{x['head_name']} ({x['head_type']}) has a direct relationship of {x['display_relation']} with {x['tail_name']} ({x['tail_type']}).", axis=1).tolist()
enriched_edges
# Perform textual enrichment over the edges by simply concatenating the head and tail nodes with the relation followed by the enriched node information
enriched_edges = primekg_edges.apply(lambda x: f"{x['head_name']} ({x['head_type']}) has a direct relationship of {x['display_relation']} with {x['tail_name']} ({x['tail_type']}).", axis=1).tolist()
enriched_edges
Out[10]:
['PHYHIP (gene/protein) has a direct relationship of ppi with KIF15 (gene/protein).', 'GPANK1 (gene/protein) has a direct relationship of ppi with PNMA1 (gene/protein).', 'ZRSR2 (gene/protein) has a direct relationship of ppi with TTC33 (gene/protein).', 'NRF1 (gene/protein) has a direct relationship of ppi with MAN1B1 (gene/protein).', 'PI4KA (gene/protein) has a direct relationship of ppi with RGS20 (gene/protein).', 'SLC15A1 (gene/protein) has a direct relationship of ppi with RTL8C (gene/protein).', 'EIF3I (gene/protein) has a direct relationship of ppi with PAXIP1 (gene/protein).', 'FAXDC2 (gene/protein) has a direct relationship of ppi with SLC10A6 (gene/protein).', 'MT1A (gene/protein) has a direct relationship of ppi with TP53 (gene/protein).', 'SORT1 (gene/protein) has a direct relationship of ppi with PALMD (gene/protein).', 'LRP5 (gene/protein) has a direct relationship of ppi with FOXP3 (gene/protein).', 'RPS8 (gene/protein) has a direct relationship of ppi with SART3 (gene/protein).', 'CD7 (gene/protein) has a direct relationship of ppi with SFXN5 (gene/protein).', 'MRPL9 (gene/protein) has a direct relationship of ppi with TMEM177 (gene/protein).', 'PSMC4 (gene/protein) has a direct relationship of ppi with AARSD1 (gene/protein).', 'EGR1 (gene/protein) has a direct relationship of ppi with PIGX (gene/protein).', 'SNRPD2 (gene/protein) has a direct relationship of ppi with PRPF4 (gene/protein).', 'KRTAP4-5 (gene/protein) has a direct relationship of ppi with KRTAP10-7 (gene/protein).', 'TAF1 (gene/protein) has a direct relationship of ppi with SNHG12 (gene/protein).', 'VAV3 (gene/protein) has a direct relationship of ppi with ZRANB1 (gene/protein).', 'KRTAP5-9 (gene/protein) has a direct relationship of ppi with KRTAP10-3 (gene/protein).', 'HMOX2 (gene/protein) has a direct relationship of ppi with LMF2 (gene/protein).', 'FOS (gene/protein) has a direct relationship of ppi with SIRT1 (gene/protein).', 'DNAJC3 (gene/protein) has a direct relationship of ppi with UBC (gene/protein).', 'LGALS9 (gene/protein) has a direct relationship of ppi with PDIA6 (gene/protein).', 'MYC (gene/protein) has a direct relationship of ppi with PQBP1 (gene/protein).', 'MAP3K6 (gene/protein) has a direct relationship of ppi with FOXP3 (gene/protein).', 'KRT20 (gene/protein) has a direct relationship of ppi with DDIT4L (gene/protein).', 'TUBGCP5 (gene/protein) has a direct relationship of ppi with MZT2A (gene/protein).', 'F2 (gene/protein) has a direct relationship of ppi with SPP1 (gene/protein).', 'SNRPD2 (gene/protein) has a direct relationship of ppi with NCSTN (gene/protein).', 'DNM1 (gene/protein) has a direct relationship of ppi with CABIN1 (gene/protein).', 'NUDC (gene/protein) has a direct relationship of ppi with IFT122 (gene/protein).', 'CD53 (gene/protein) has a direct relationship of ppi with SMAGP (gene/protein).', 'GSK3B (gene/protein) has a direct relationship of ppi with NOTCH2 (gene/protein).', 'NAXD (gene/protein) has a direct relationship of ppi with KRTAP10-9 (gene/protein).', 'SLC7A14 (gene/protein) has a direct relationship of ppi with MMGT1 (gene/protein).', 'PVR (gene/protein) has a direct relationship of ppi with SLC41A2 (gene/protein).', 'CLCN7 (gene/protein) has a direct relationship of ppi with MANSC1 (gene/protein).', 'CCNB1 (gene/protein) has a direct relationship of ppi with CCNB2 (gene/protein).', 'GSK3B (gene/protein) has a direct relationship of ppi with ADAP1 (gene/protein).', 'ATF5 (gene/protein) has a direct relationship of ppi with SYCE1L (gene/protein).', 'CDK2 (gene/protein) has a direct relationship of ppi with PRMT1 (gene/protein).', 'NDUFS8 (gene/protein) has a direct relationship of ppi with NDUFAF3 (gene/protein).', 'PITX1 (gene/protein) has a direct relationship of ppi with KRTAP19-7 (gene/protein).', 'PIK3R1 (gene/protein) has a direct relationship of ppi with SYK (gene/protein).', 'SRPK1 (gene/protein) has a direct relationship of ppi with UBE2E2 (gene/protein).', 'HOXD12 (gene/protein) has a direct relationship of ppi with MAFB (gene/protein).', 'BZW2 (gene/protein) has a direct relationship of ppi with PACC1 (gene/protein).', 'TAB1 (gene/protein) has a direct relationship of ppi with CORO1A (gene/protein).', 'CDKL4 (gene/protein) has a direct relationship of ppi with POTEI (gene/protein).', 'PPP1R16A (gene/protein) has a direct relationship of ppi with ATP23 (gene/protein).', 'ETS2 (gene/protein) has a direct relationship of ppi with ANKS6 (gene/protein).', 'SORT1 (gene/protein) has a direct relationship of ppi with NUDCD3 (gene/protein).', 'SP1 (gene/protein) has a direct relationship of ppi with NUP62 (gene/protein).', 'NKIRAS2 (gene/protein) has a direct relationship of ppi with MIRLET7A1 (gene/protein).', 'IFIT2 (gene/protein) has a direct relationship of ppi with STAT2 (gene/protein).', 'AURKA (gene/protein) has a direct relationship of ppi with COPRS (gene/protein).', 'TRA2B (gene/protein) has a direct relationship of ppi with U2AF1 (gene/protein).', 'KAT5 (gene/protein) has a direct relationship of ppi with ZBTB8A (gene/protein).', 'TLX3 (gene/protein) has a direct relationship of ppi with DDIT4L (gene/protein).', 'XRN2 (gene/protein) has a direct relationship of ppi with IWS1 (gene/protein).', 'RPL5 (gene/protein) has a direct relationship of ppi with RBM34 (gene/protein).', 'SNAP23 (gene/protein) has a direct relationship of ppi with WASH2P (gene/protein).', 'CALM1 (gene/protein) has a direct relationship of ppi with KRAS (gene/protein).', 'INPP1 (gene/protein) has a direct relationship of ppi with WDR12 (gene/protein).', 'PPP5C (gene/protein) has a direct relationship of ppi with FOXD4L6 (gene/protein).', 'PRPF3 (gene/protein) has a direct relationship of ppi with SUPT16H (gene/protein).', 'SF3A1 (gene/protein) has a direct relationship of ppi with MRPL22 (gene/protein).', 'SF1 (gene/protein) has a direct relationship of ppi with RBM10 (gene/protein).', 'MET (gene/protein) has a direct relationship of ppi with ACTRT3 (gene/protein).', 'E2F1 (gene/protein) has a direct relationship of ppi with IFI16 (gene/protein).', 'RAD1 (gene/protein) has a direct relationship of ppi with MAP1LC3B (gene/protein).', 'KRT15 (gene/protein) has a direct relationship of ppi with BEX2 (gene/protein).', 'CTCF (gene/protein) has a direct relationship of ppi with CNEP1R1 (gene/protein).', 'RABGGTA (gene/protein) has a direct relationship of ppi with STIP1 (gene/protein).', 'COPS3 (gene/protein) has a direct relationship of ppi with FBXL14 (gene/protein).', 'ADRA2B (gene/protein) has a direct relationship of ppi with ACKR3 (gene/protein).', 'MYL6 (gene/protein) has a direct relationship of ppi with PPP1R9A (gene/protein).', 'NUBP1 (gene/protein) has a direct relationship of ppi with RAD21 (gene/protein).', 'IHO1 (gene/protein) has a direct relationship of ppi with BOLA2 (gene/protein).', 'VHL (gene/protein) has a direct relationship of ppi with INHBE (gene/protein).', 'GHITM (gene/protein) has a direct relationship of ppi with SLTM (gene/protein).', 'BRCA2 (gene/protein) has a direct relationship of ppi with RAD51C (gene/protein).', 'TLE5 (gene/protein) has a direct relationship of ppi with ECT2 (gene/protein).', 'CHML (gene/protein) has a direct relationship of ppi with RAB6A (gene/protein).', 'AP2S1 (gene/protein) has a direct relationship of ppi with BMP2K (gene/protein).', 'SNU13 (gene/protein) has a direct relationship of ppi with SRSF7 (gene/protein).', 'DDOST (gene/protein) has a direct relationship of ppi with ILF2 (gene/protein).', 'SKP2 (gene/protein) has a direct relationship of ppi with SP1 (gene/protein).', 'HNRNPA2B1 (gene/protein) has a direct relationship of ppi with SUMO2 (gene/protein).', 'PRPF31 (gene/protein) has a direct relationship of ppi with RBMY1F (gene/protein).', 'TMEM139 (gene/protein) has a direct relationship of ppi with TMEM120B (gene/protein).', 'BSG (gene/protein) has a direct relationship of ppi with TBRG4 (gene/protein).', 'PTTG1IP (gene/protein) has a direct relationship of ppi with PAX5 (gene/protein).', 'CLN5 (gene/protein) has a direct relationship of ppi with TMEM31 (gene/protein).', 'DUSP5 (gene/protein) has a direct relationship of ppi with ELAVL1 (gene/protein).', 'RNF10 (gene/protein) has a direct relationship of ppi with MIS12 (gene/protein).', 'NDUFS6 (gene/protein) has a direct relationship of ppi with NNT (gene/protein).', 'SP1 (gene/protein) has a direct relationship of ppi with TAF4 (gene/protein).', 'NADK (gene/protein) has a direct relationship of ppi with FAM124B (gene/protein).', 'ATP6AP2 (gene/protein) has a direct relationship of ppi with CKAP4 (gene/protein).', 'CTSA (gene/protein) has a direct relationship of ppi with PSCA (gene/protein).', 'GNAI1 (gene/protein) has a direct relationship of ppi with NGB (gene/protein).', 'SEC23A (gene/protein) has a direct relationship of ppi with ZNF274 (gene/protein).', 'ECI2 (gene/protein) has a direct relationship of ppi with NEURL4 (gene/protein).', 'NR2C2 (gene/protein) has a direct relationship of ppi with NUP214 (gene/protein).', 'SETD7 (gene/protein) has a direct relationship of ppi with H4-16 (gene/protein).', 'SF3A3 (gene/protein) has a direct relationship of ppi with SNW1 (gene/protein).', 'ZNF32 (gene/protein) has a direct relationship of ppi with KRTAP10-7 (gene/protein).', 'FOXA1 (gene/protein) has a direct relationship of ppi with INTS1 (gene/protein).', 'SUMO1 (gene/protein) has a direct relationship of ppi with SLX4 (gene/protein).', 'CHEK1 (gene/protein) has a direct relationship of ppi with BAZ1A (gene/protein).', 'TERF2 (gene/protein) has a direct relationship of ppi with HDGFL2 (gene/protein).', 'SUV39H1 (gene/protein) has a direct relationship of ppi with SPATA24 (gene/protein).', 'TTR (gene/protein) has a direct relationship of ppi with DDX31 (gene/protein).', 'OXLD1 (gene/protein) has a direct relationship of ppi with NUDT19 (gene/protein).', 'DDX42 (gene/protein) has a direct relationship of ppi with NOSIP (gene/protein).', 'RABEP1 (gene/protein) has a direct relationship of ppi with ZNF438 (gene/protein).', 'DNAJC30 (gene/protein) has a direct relationship of ppi with KASH5 (gene/protein).', 'CASP8 (gene/protein) has a direct relationship of ppi with BFAR (gene/protein).', 'SMC5 (gene/protein) has a direct relationship of ppi with NSMCE3 (gene/protein).', 'AQP1 (gene/protein) has a direct relationship of ppi with BAALC-AS2 (gene/protein).', 'ETS1 (gene/protein) has a direct relationship of ppi with PTPRE (gene/protein).', 'TERF1 (gene/protein) has a direct relationship of ppi with TERT (gene/protein).', 'EXOSC2 (gene/protein) has a direct relationship of ppi with ZNF260 (gene/protein).', 'CHRD (gene/protein) has a direct relationship of ppi with KRTAP12-1 (gene/protein).', 'STK4 (gene/protein) has a direct relationship of ppi with COPS6 (gene/protein).', 'ERGIC3 (gene/protein) has a direct relationship of ppi with ZDHHC21 (gene/protein).', 'EGFR (gene/protein) has a direct relationship of ppi with SRC (gene/protein).', 'H1-1 (gene/protein) has a direct relationship of ppi with PRKCD (gene/protein).', 'IRF4 (gene/protein) has a direct relationship of ppi with WDR54 (gene/protein).', 'TMEM52B (gene/protein) has a direct relationship of ppi with CNIH3 (gene/protein).', 'H2AC4 (gene/protein) has a direct relationship of ppi with RUVBL1 (gene/protein).', 'CDK2 (gene/protein) has a direct relationship of ppi with PCNA (gene/protein).', 'GATA1 (gene/protein) has a direct relationship of ppi with YES1 (gene/protein).', 'CEBPE (gene/protein) has a direct relationship of ppi with IL7 (gene/protein).', 'LCE1B (gene/protein) has a direct relationship of ppi with NOTCH2NLA (gene/protein).', 'CSNK2B (gene/protein) has a direct relationship of ppi with CIPC (gene/protein).', 'SPEN (gene/protein) has a direct relationship of ppi with PCBP3 (gene/protein).', 'GATA1 (gene/protein) has a direct relationship of ppi with USP6NL (gene/protein).', 'PPP1CA (gene/protein) has a direct relationship of ppi with POLR3E (gene/protein).', 'USP4 (gene/protein) has a direct relationship of ppi with PRPF19 (gene/protein).', 'GPR137B (gene/protein) has a direct relationship of ppi with ZYG11B (gene/protein).', 'HSPA1A (gene/protein) has a direct relationship of ppi with PEX5 (gene/protein).', 'PCNA (gene/protein) has a direct relationship of ppi with PPP1CC (gene/protein).', 'SUMO2 (gene/protein) has a direct relationship of ppi with SAE1 (gene/protein).', 'MED16 (gene/protein) has a direct relationship of ppi with MED25 (gene/protein).', 'YTHDF1 (gene/protein) has a direct relationship of ppi with PRR32 (gene/protein).', 'PRKAR1A (gene/protein) has a direct relationship of ppi with RPS6KA1 (gene/protein).', 'SMAD3 (gene/protein) has a direct relationship of ppi with PPP2CA (gene/protein).', 'PLSCR1 (gene/protein) has a direct relationship of ppi with LCE2D (gene/protein).', 'MEOX1 (gene/protein) has a direct relationship of ppi with ZNF410 (gene/protein).', 'EFNA5 (gene/protein) has a direct relationship of ppi with OR1D4 (gene/protein).', 'PLP2 (gene/protein) has a direct relationship of ppi with DLGAP4 (gene/protein).', 'AK4 (gene/protein) has a direct relationship of ppi with CCL5 (gene/protein).', 'FGFR3 (gene/protein) has a direct relationship of ppi with GPSM3 (gene/protein).', 'CCN2 (gene/protein) has a direct relationship of ppi with KLHL23 (gene/protein).', 'MYC (gene/protein) has a direct relationship of ppi with SLC16A1 (gene/protein).', 'GRB2 (gene/protein) has a direct relationship of ppi with PIK3CA (gene/protein).', 'E2F4 (gene/protein) has a direct relationship of ppi with INCENP (gene/protein).', 'FMR1 (gene/protein) has a direct relationship of ppi with PNISR (gene/protein).', 'CHD3 (gene/protein) has a direct relationship of ppi with TNNT1 (gene/protein).', 'ADD2 (gene/protein) has a direct relationship of ppi with PRKCZ (gene/protein).', 'NEDD8 (gene/protein) has a direct relationship of ppi with H4C5 (gene/protein).', 'RNF181 (gene/protein) has a direct relationship of ppi with UBE2D4 (gene/protein).', 'HNRNPUL1 (gene/protein) has a direct relationship of ppi with KLHDC7B (gene/protein).', 'SYNCRIP (gene/protein) has a direct relationship of ppi with UVSSA (gene/protein).', 'E2F4 (gene/protein) has a direct relationship of ppi with THAP7 (gene/protein).', 'XPO1 (gene/protein) has a direct relationship of ppi with YAP1 (gene/protein).', 'SLC26A2 (gene/protein) has a direct relationship of ppi with FOS (gene/protein).', 'LMNA (gene/protein) has a direct relationship of ppi with TRIM26 (gene/protein).', 'UBE2I (gene/protein) has a direct relationship of ppi with RUSF1 (gene/protein).', 'PCDH20 (gene/protein) has a direct relationship of ppi with MAP7D3 (gene/protein).', 'TIAL1 (gene/protein) has a direct relationship of ppi with ZNF263 (gene/protein).', 'CD82 (gene/protein) has a direct relationship of ppi with SMIM3 (gene/protein).', 'E2F3 (gene/protein) has a direct relationship of ppi with HDAC1 (gene/protein).', 'PAX6 (gene/protein) has a direct relationship of ppi with NGLY1 (gene/protein).', 'UBE2I (gene/protein) has a direct relationship of ppi with PRKRA (gene/protein).', 'COL8A1 (gene/protein) has a direct relationship of ppi with CCN3 (gene/protein).', 'CAPZA2 (gene/protein) has a direct relationship of ppi with TWF2 (gene/protein).', 'NPPB (gene/protein) has a direct relationship of ppi with HDAC4 (gene/protein).', 'H1-1 (gene/protein) has a direct relationship of ppi with EGFL6 (gene/protein).', 'RAB11A (gene/protein) has a direct relationship of ppi with CYSTM1 (gene/protein).', 'SPI1 (gene/protein) has a direct relationship of ppi with RASSF2 (gene/protein).', 'PSMD2 (gene/protein) has a direct relationship of ppi with URI1 (gene/protein).', 'PPARD (gene/protein) has a direct relationship of ppi with HDAC3 (gene/protein).', 'PTEN (gene/protein) has a direct relationship of ppi with LRP8 (gene/protein).', 'EP300 (gene/protein) has a direct relationship of ppi with PROX1 (gene/protein).', 'IL10RB (gene/protein) has a direct relationship of ppi with ANKAR (gene/protein).', 'CORO1B (gene/protein) has a direct relationship of ppi with SRSF12 (gene/protein).', 'PABPC3 (gene/protein) has a direct relationship of ppi with UBC (gene/protein).', 'MS4A3 (gene/protein) has a direct relationship of ppi with PLPP6 (gene/protein).', 'NFE2 (gene/protein) has a direct relationship of ppi with QRFP (gene/protein).', 'STAT2 (gene/protein) has a direct relationship of ppi with USP1 (gene/protein).', 'CSTF1 (gene/protein) has a direct relationship of ppi with UBC (gene/protein).', 'KRT18 (gene/protein) has a direct relationship of ppi with PSTPIP2 (gene/protein).', 'CASP10 (gene/protein) has a direct relationship of ppi with CASP8AP2 (gene/protein).', 'FTH1 (gene/protein) has a direct relationship of ppi with TSC1 (gene/protein).', 'UBC (gene/protein) has a direct relationship of ppi with RNF186 (gene/protein).', 'CRCT1 (gene/protein) has a direct relationship of ppi with KRTAP4-11 (gene/protein).', 'DVL2 (gene/protein) has a direct relationship of ppi with LRRK2 (gene/protein).', 'GNA12 (gene/protein) has a direct relationship of ppi with GNB3 (gene/protein).', 'ISLR (gene/protein) has a direct relationship of ppi with TEX264 (gene/protein).', 'UBC (gene/protein) has a direct relationship of ppi with CCT2 (gene/protein).', 'PRKCB (gene/protein) has a direct relationship of ppi with TYR (gene/protein).', 'TNPO1 (gene/protein) has a direct relationship of ppi with TEPSIN (gene/protein).', 'DUSP7 (gene/protein) has a direct relationship of ppi with UBE2D2 (gene/protein).', 'MAPK14 (gene/protein) has a direct relationship of ppi with INTS6L (gene/protein).', 'SERPINI2 (gene/protein) has a direct relationship of ppi with UBQLN4 (gene/protein).', 'POLB (gene/protein) has a direct relationship of ppi with H2AC11 (gene/protein).', 'CREB3 (gene/protein) has a direct relationship of ppi with CLP1 (gene/protein).', 'CYP1A1 (gene/protein) has a direct relationship of ppi with NAA50 (gene/protein).', 'COPS5 (gene/protein) has a direct relationship of ppi with FBXO7 (gene/protein).', 'UBC (gene/protein) has a direct relationship of ppi with TRMT112 (gene/protein).', 'CLEC5A (gene/protein) has a direct relationship of ppi with PIGU (gene/protein).', 'SF1 (gene/protein) has a direct relationship of ppi with ZNF461 (gene/protein).', 'CEBPG (gene/protein) has a direct relationship of ppi with UBC (gene/protein).', 'SUMO2 (gene/protein) has a direct relationship of ppi with CNTN2 (gene/protein).', 'ZNF76 (gene/protein) has a direct relationship of ppi with TBC1D22B (gene/protein).', 'HNRNPR (gene/protein) has a direct relationship of ppi with NPLOC4 (gene/protein).', 'MAX (gene/protein) has a direct relationship of ppi with SERF2 (gene/protein).', 'GRB7 (gene/protein) has a direct relationship of ppi with PHAX (gene/protein).', 'MYH9 (gene/protein) has a direct relationship of ppi with MYL12A (gene/protein).', 'NDUFA8 (gene/protein) has a direct relationship of ppi with KLC3 (gene/protein).', 'NPPA (gene/protein) has a direct relationship of ppi with PMPCA (gene/protein).', 'E2F4 (gene/protein) has a direct relationship of ppi with TICRR (gene/protein).', 'SLC35A1 (gene/protein) has a direct relationship of ppi with KIR3DL3 (gene/protein).', 'INS (gene/protein) has a direct relationship of ppi with ARMC3 (gene/protein).', 'SHC1 (gene/protein) has a direct relationship of ppi with SHC2 (gene/protein).', 'DNAJC7 (gene/protein) has a direct relationship of ppi with CTC1 (gene/protein).', 'MYH9 (gene/protein) has a direct relationship of ppi with RAI14 (gene/protein).', 'EGFR (gene/protein) has a direct relationship of ppi with TLR4 (gene/protein).', 'NCSTN (gene/protein) has a direct relationship of ppi with AHNAK2 (gene/protein).', 'ZNF433 (gene/protein) has a direct relationship of ppi with KRTAP10-1 (gene/protein).', 'SF3A2 (gene/protein) has a direct relationship of ppi with DDX46 (gene/protein).', 'ID2 (gene/protein) has a direct relationship of ppi with TCHP (gene/protein).', 'CASP8 (gene/protein) has a direct relationship of ppi with NOD1 (gene/protein).', 'NUDC (gene/protein) has a direct relationship of ppi with DYNC2I1 (gene/protein).', 'NUDT6 (gene/protein) has a direct relationship of ppi with UBR2 (gene/protein).', 'ATXN7L2 (gene/protein) has a direct relationship of ppi with CYSRT1 (gene/protein).', 'IMPDH2 (gene/protein) has a direct relationship of ppi with RNASEH2A (gene/protein).', 'MAGEA1 (gene/protein) has a direct relationship of ppi with EID2 (gene/protein).', 'SMCO4 (gene/protein) has a direct relationship of ppi with FAM209A (gene/protein).', 'EGR1 (gene/protein) has a direct relationship of ppi with FRS3 (gene/protein).', 'DGKZ (gene/protein) has a direct relationship of ppi with PARD6A (gene/protein).', 'U2AF1 (gene/protein) has a direct relationship of ppi with PSIP1 (gene/protein).', 'IL1R1 (gene/protein) has a direct relationship of ppi with ANKAR (gene/protein).', 'PCNA (gene/protein) has a direct relationship of ppi with TRAIP (gene/protein).', 'EPHA1 (gene/protein) has a direct relationship of ppi with EIF2B5 (gene/protein).', 'FXR1 (gene/protein) has a direct relationship of ppi with PINX1 (gene/protein).', 'PMPCB (gene/protein) has a direct relationship of ppi with WTAP (gene/protein).', 'RPL8 (gene/protein) has a direct relationship of ppi with RPL29 (gene/protein).', 'TRIM37 (gene/protein) has a direct relationship of ppi with DISC1 (gene/protein).', 'UACA (gene/protein) has a direct relationship of ppi with CORO6 (gene/protein).', 'SNRPF (gene/protein) has a direct relationship of ppi with LSM10 (gene/protein).', 'GRB2 (gene/protein) has a direct relationship of ppi with WAS (gene/protein).', 'UBC (gene/protein) has a direct relationship of ppi with CPSF7 (gene/protein).', 'ARRB2 (gene/protein) has a direct relationship of ppi with ANKRD11 (gene/protein).', 'RPL5 (gene/protein) has a direct relationship of ppi with H2BU1 (gene/protein).', 'CDKN2A (gene/protein) has a direct relationship of ppi with GGA3 (gene/protein).', 'COPS3 (gene/protein) has a direct relationship of ppi with C17orf75 (gene/protein).', 'MEOX1 (gene/protein) has a direct relationship of ppi with PAX1 (gene/protein).', 'POLE2 (gene/protein) has a direct relationship of ppi with POLE3 (gene/protein).', 'ACTB (gene/protein) has a direct relationship of ppi with HNF1A (gene/protein).', 'ZNF414 (gene/protein) has a direct relationship of ppi with TRIM42 (gene/protein).', 'ACP2 (gene/protein) has a direct relationship of ppi with HTR2C (gene/protein).', 'H4C11 (gene/protein) has a direct relationship of ppi with HDAC6 (gene/protein).', 'AKAP9 (gene/protein) has a direct relationship of ppi with SSX2B (gene/protein).', 'PDE6A (gene/protein) has a direct relationship of ppi with STAT3 (gene/protein).', 'HSP90AB1 (gene/protein) has a direct relationship of ppi with IKBKE (gene/protein).', 'KLC2 (gene/protein) has a direct relationship of ppi with PATL1 (gene/protein).', 'ATP6V1B2 (gene/protein) has a direct relationship of ppi with EPRS1 (gene/protein).', 'FBXO34 (gene/protein) has a direct relationship of ppi with KRTAP4-5 (gene/protein).', 'JUND (gene/protein) has a direct relationship of ppi with RPL3 (gene/protein).', 'GRN (gene/protein) has a direct relationship of ppi with UTP23 (gene/protein).', 'PLXNB1 (gene/protein) has a direct relationship of ppi with RAC1 (gene/protein).', 'CCNA2 (gene/protein) has a direct relationship of ppi with RAD23A (gene/protein).', 'DHX57 (gene/protein) has a direct relationship of ppi with KRTAP10-7 (gene/protein).', 'GATA1 (gene/protein) has a direct relationship of ppi with RSPH14 (gene/protein).', 'APBB2 (gene/protein) has a direct relationship of ppi with SYDE2 (gene/protein).', 'ITPRIP (gene/protein) has a direct relationship of ppi with HTR3C (gene/protein).', 'KPNB1 (gene/protein) has a direct relationship of ppi with TSR1 (gene/protein).', 'SNRPB (gene/protein) has a direct relationship of ppi with OIP5 (gene/protein).', 'TMEM179B (gene/protein) has a direct relationship of ppi with TM4SF19-DYNLT2B (gene/protein).', 'DCAF1 (gene/protein) has a direct relationship of ppi with SLX4 (gene/protein).', 'ORMDL2 (gene/protein) has a direct relationship of ppi with TMEM120A (gene/protein).', 'DIS3 (gene/protein) has a direct relationship of ppi with IQCF1 (gene/protein).', 'SPI1 (gene/protein) has a direct relationship of ppi with PDCD4 (gene/protein).', 'EAPP (gene/protein) has a direct relationship of ppi with UBQLN4 (gene/protein).', 'UPF1 (gene/protein) has a direct relationship of ppi with UBC (gene/protein).', 'TRAF4 (gene/protein) has a direct relationship of ppi with NPIPA9 (gene/protein).', 'PLK1 (gene/protein) has a direct relationship of ppi with BICD2 (gene/protein).', 'KRTAP1-1 (gene/protein) has a direct relationship of ppi with FAM71C (gene/protein).', 'EIF3B (gene/protein) has a direct relationship of ppi with PBX4 (gene/protein).', 'HPCAL1 (gene/protein) has a direct relationship of ppi with TPSG1 (gene/protein).', 'E2F4 (gene/protein) has a direct relationship of ppi with ZWINT (gene/protein).', 'PPP2CB (gene/protein) has a direct relationship of ppi with DOCK7 (gene/protein).', 'CCNT1 (gene/protein) has a direct relationship of ppi with PIP4K2A (gene/protein).', 'ZBTB33 (gene/protein) has a direct relationship of ppi with KAT5 (gene/protein).', 'ERRFI1 (gene/protein) has a direct relationship of ppi with ARRDC5 (gene/protein).', 'FOS (gene/protein) has a direct relationship of ppi with TDRKH (gene/protein).', 'SEC24C (gene/protein) has a direct relationship of ppi with SEC31A (gene/protein).', 'PIR (gene/protein) has a direct relationship of ppi with KHDRBS1 (gene/protein).', 'SUPT3H (gene/protein) has a direct relationship of ppi with TADA1 (gene/protein).', 'ADAMTSL5 (gene/protein) has a direct relationship of ppi with KRTAP10-3 (gene/protein).', 'LAMA3 (gene/protein) has a direct relationship of ppi with SCGB1D4 (gene/protein).', 'COG6 (gene/protein) has a direct relationship of ppi with COG3 (gene/protein).', 'STOM (gene/protein) has a direct relationship of ppi with KCNK1 (gene/protein).', 'HNF4A (gene/protein) has a direct relationship of ppi with HDAC3 (gene/protein).', 'UBE4B (gene/protein) has a direct relationship of ppi with ZNRD2 (gene/protein).', 'MTNR1A (gene/protein) has a direct relationship of ppi with UBAP2L (gene/protein).', 'LGALS3 (gene/protein) has a direct relationship of ppi with AGPS (gene/protein).', 'TSTD2 (gene/protein) has a direct relationship of ppi with FLCN (gene/protein).', 'SH3GLB1 (gene/protein) has a direct relationship of ppi with SH3GLB2 (gene/protein).', 'ELAVL1 (gene/protein) has a direct relationship of ppi with SMAD2 (gene/protein).', 'NR4A2 (gene/protein) has a direct relationship of ppi with TCF4 (gene/protein).', 'PBX1 (gene/protein) has a direct relationship of ppi with CDCA7L (gene/protein).', 'EPB41L1 (gene/protein) has a direct relationship of ppi with YWHAB (gene/protein).', 'CLNS1A (gene/protein) has a direct relationship of ppi with UBC (gene/protein).', 'ROCK1 (gene/protein) has a direct relationship of ppi with ARMC7 (gene/protein).', 'PTPN11 (gene/protein) has a direct relationship of ppi with TLK1 (gene/protein).', 'S100A8 (gene/protein) has a direct relationship of ppi with IGSF21 (gene/protein).', 'BRAP (gene/protein) has a direct relationship of ppi with ZNF382 (gene/protein).', 'RIPK1 (gene/protein) has a direct relationship of ppi with SIRT2 (gene/protein).', 'TWNK (gene/protein) has a direct relationship of ppi with EPB41L5 (gene/protein).', 'DVL3 (gene/protein) has a direct relationship of ppi with SNX22 (gene/protein).', 'USP9X (gene/protein) has a direct relationship of ppi with SEC24C (gene/protein).', 'SMO (gene/protein) has a direct relationship of ppi with NIPA1 (gene/protein).', 'SQLE (gene/protein) has a direct relationship of ppi with REEP4 (gene/protein).', 'PIP4K2A (gene/protein) has a direct relationship of ppi with BRD2 (gene/protein).', 'CSNK2A1 (gene/protein) has a direct relationship of ppi with JPH4 (gene/protein).', 'DYNC1LI2 (gene/protein) has a direct relationship of ppi with DYNC1LI1 (gene/protein).', 'GSN (gene/protein) has a direct relationship of ppi with GAS2L1 (gene/protein).', 'PPP1R12A (gene/protein) has a direct relationship of ppi with HDAC7 (gene/protein).', 'HNRNPA2B1 (gene/protein) has a direct relationship of ppi with PARVB (gene/protein).', 'ZNF629 (gene/protein) has a direct relationship of ppi with GOLGA6L9 (gene/protein).', 'TMOD2 (gene/protein) has a direct relationship of ppi with MYDGF (gene/protein).', 'HBM (gene/protein) has a direct relationship of ppi with SCGB2A1 (gene/protein).', 'CUL2 (gene/protein) has a direct relationship of ppi with RNF7 (gene/protein).', 'PAX5 (gene/protein) has a direct relationship of ppi with ELAPOR1 (gene/protein).', 'CCT2 (gene/protein) has a direct relationship of ppi with TTLL9 (gene/protein).', 'PCP4 (gene/protein) has a direct relationship of ppi with CTCF (gene/protein).', 'DVL2 (gene/protein) has a direct relationship of ppi with ITCH (gene/protein).', 'TLE5 (gene/protein) has a direct relationship of ppi with GPATCH2L (gene/protein).', 'GBP2 (gene/protein) has a direct relationship of ppi with STAT3 (gene/protein).', 'YWHAG (gene/protein) has a direct relationship of ppi with CGNL1 (gene/protein).', 'BARD1 (gene/protein) has a direct relationship of ppi with CAP1 (gene/protein).', 'CTCF (gene/protein) has a direct relationship of ppi with MTRNR2L1 (gene/protein).', 'DYRK1A (gene/protein) has a direct relationship of ppi with PRDM14 (gene/protein).', 'CALCOCO2 (gene/protein) has a direct relationship of ppi with DICER1 (gene/protein).', 'CUL1 (gene/protein) has a direct relationship of ppi with KLF4 (gene/protein).', 'UTP11 (gene/protein) has a direct relationship of ppi with IKZF5 (gene/protein).', 'CAPZA2 (gene/protein) has a direct relationship of ppi with MPRIP (gene/protein).', 'KRTAP5-9 (gene/protein) has a direct relationship of ppi with NLK (gene/protein).', 'MTNR1A (gene/protein) has a direct relationship of ppi with PEX14 (gene/protein).', 'PRPF8 (gene/protein) has a direct relationship of ppi with BUD13 (gene/protein).', 'DHRS2 (gene/protein) has a direct relationship of ppi with TCERG1 (gene/protein).', 'OXT (gene/protein) has a direct relationship of ppi with NIF3L1 (gene/protein).', 'ESRRA (gene/protein) has a direct relationship of ppi with GPT (gene/protein).', 'RFX3 (gene/protein) has a direct relationship of ppi with TRIP6 (gene/protein).', 'GTSE1 (gene/protein) has a direct relationship of ppi with MYO19 (gene/protein).', 'GTF3C1 (gene/protein) has a direct relationship of ppi with RBM23 (gene/protein).', 'JUN (gene/protein) has a direct relationship of ppi with TSG101 (gene/protein).', 'RPS2 (gene/protein) has a direct relationship of ppi with RPS15A (gene/protein).', 'KANK2 (gene/protein) has a direct relationship of ppi with SCARA5 (gene/protein).', 'TERF1 (gene/protein) has a direct relationship of ppi with PAGE2 (gene/protein).', 'H2AC20 (gene/protein) has a direct relationship of ppi with H4C4 (gene/protein).', 'ZXDC (gene/protein) has a direct relationship of ppi with ZMYND19 (gene/protein).', 'UBC (gene/protein) has a direct relationship of ppi with VPS37B (gene/protein).', 'TMOD1 (gene/protein) has a direct relationship of ppi with TRPM7 (gene/protein).', 'CDK4 (gene/protein) has a direct relationship of ppi with NUP133 (gene/protein).', 'MTX1 (gene/protein) has a direct relationship of ppi with KCNIP4 (gene/protein).', 'NMI (gene/protein) has a direct relationship of ppi with MCPH1 (gene/protein).', 'IL1R1 (gene/protein) has a direct relationship of ppi with IL1RN (gene/protein).', 'POLR3D (gene/protein) has a direct relationship of ppi with HOXC9 (gene/protein).', 'CDC25B (gene/protein) has a direct relationship of ppi with CDC14A (gene/protein).', 'BTK (gene/protein) has a direct relationship of ppi with DCAF13 (gene/protein).', 'H2AC15 (gene/protein) has a direct relationship of ppi with H3C6 (gene/protein).', 'JUN (gene/protein) has a direct relationship of ppi with HIRA (gene/protein).', 'FANCA (gene/protein) has a direct relationship of ppi with NAMPT (gene/protein).', 'BEX2 (gene/protein) has a direct relationship of ppi with KRTAP10-8 (gene/protein).', 'BCHE (gene/protein) has a direct relationship of ppi with LOXL1 (gene/protein).', 'APEX2 (gene/protein) has a direct relationship of ppi with PDE12 (gene/protein).', 'ETS1 (gene/protein) has a direct relationship of ppi with H3C12 (gene/protein).', 'ZNF574 (gene/protein) has a direct relationship of ppi with ZNF526 (gene/protein).', 'LBR (gene/protein) has a direct relationship of ppi with EIF4A3 (gene/protein).', 'UBE2M (gene/protein) has a direct relationship of ppi with CUL7 (gene/protein).', 'IWS1 (gene/protein) has a direct relationship of ppi with SAMD1 (gene/protein).', 'BDH2 (gene/protein) has a direct relationship of ppi with CFAP36 (gene/protein).', 'ZNF319 (gene/protein) has a direct relationship of ppi with KRTAP10-9 (gene/protein).', 'RPL15 (gene/protein) has a direct relationship of ppi with RPL13A (gene/protein).', 'CEBPB (gene/protein) has a direct relationship of ppi with RBM45 (gene/protein).', 'DLX1 (gene/protein) has a direct relationship of ppi with SMAD4 (gene/protein).', 'HNRNPA1 (gene/protein) has a direct relationship of ppi with YWHAZ (gene/protein).', 'KRTAP4-12 (gene/protein) has a direct relationship of ppi with LCE3B (gene/protein).', 'HLA-F (gene/protein) has a direct relationship of ppi with IL17RB (gene/protein).', 'CELSR2 (gene/protein) has a direct relationship of ppi with PSG8 (gene/protein).', 'NAB2 (gene/protein) has a direct relationship of ppi with C9orf78 (gene/protein).', 'ARRB1 (gene/protein) has a direct relationship of ppi with POU2F1 (gene/protein).', 'MDFI (gene/protein) has a direct relationship of ppi with AURKB (gene/protein).', 'PHF23 (gene/protein) has a direct relationship of ppi with BRMS1L (gene/protein).', 'FAM50B (gene/protein) has a direct relationship of ppi with AGMAT (gene/protein).', 'CDK2 (gene/protein) has a direct relationship of ppi with CNOT7 (gene/protein).', 'SOD1 (gene/protein) has a direct relationship of ppi with MYBBP1A (gene/protein).', 'WAS (gene/protein) has a direct relationship of ppi with UBA2 (gene/protein).', 'AR (gene/protein) has a direct relationship of ppi with PURA (gene/protein).', 'EPS15 (gene/protein) has a direct relationship of ppi with GRB2 (gene/protein).', 'HSH2D (gene/protein) has a direct relationship of ppi with LDHAL6B (gene/protein).', 'LCE2B (gene/protein) has a direct relationship of ppi with KRTAP10-8 (gene/protein).', 'AIMP2 (gene/protein) has a direct relationship of ppi with PFDN6 (gene/protein).', 'HTRA1 (gene/protein) has a direct relationship of ppi with CDYL (gene/protein).', 'AKAP8L (gene/protein) has a direct relationship of ppi with TFAP2D (gene/protein).', 'HOXC4 (gene/protein) has a direct relationship of ppi with POU2F1 (gene/protein).', 'SIN3A (gene/protein) has a direct relationship of ppi with HBP1 (gene/protein).', 'POP4 (gene/protein) has a direct relationship of ppi with TOR1AIP2 (gene/protein).', 'NOS2 (gene/protein) has a direct relationship of ppi with PLA2G4A (gene/protein).', 'PKN2 (gene/protein) has a direct relationship of ppi with PPIAL4G (gene/protein).', 'ESR1 (gene/protein) has a direct relationship of ppi with TXNRD1 (gene/protein).', 'UHRF1 (gene/protein) has a direct relationship of ppi with WIPI1 (gene/protein).', 'MEOX2 (gene/protein) has a direct relationship of ppi with CCDC102B (gene/protein).', 'EPS8 (gene/protein) has a direct relationship of ppi with HOOK2 (gene/protein).', 'GAK (gene/protein) has a direct relationship of ppi with USO1 (gene/protein).', 'LZTS2 (gene/protein) has a direct relationship of ppi with YTHDC1 (gene/protein).', 'IL17A (gene/protein) has a direct relationship of ppi with TRAF3IP2 (gene/protein).', 'TPRX1 (gene/protein) has a direct relationship of ppi with INCA1 (gene/protein).', 'RPL10 (gene/protein) has a direct relationship of ppi with RPS8 (gene/protein).', 'SRSF8 (gene/protein) has a direct relationship of ppi with SUZ12 (gene/protein).', 'PDHA2 (gene/protein) has a direct relationship of ppi with APBA3 (gene/protein).', 'LCE1A (gene/protein) has a direct relationship of ppi with KRTAP4-11 (gene/protein).', 'ACTA1 (gene/protein) has a direct relationship of ppi with SRC (gene/protein).', 'BLK (gene/protein) has a direct relationship of ppi with PXN (gene/protein).', 'KRTAP1-1 (gene/protein) has a direct relationship of ppi with KRTAP2-3 (gene/protein).', 'CREB1 (gene/protein) has a direct relationship of ppi with H3C10 (gene/protein).', 'ALK (gene/protein) has a direct relationship of ppi with ARMC7 (gene/protein).', 'BCKDHA (gene/protein) has a direct relationship of ppi with PDLIM5 (gene/protein).', 'MYC (gene/protein) has a direct relationship of ppi with MRPL3 (gene/protein).', 'MTMR4 (gene/protein) has a direct relationship of ppi with ZNF684 (gene/protein).', 'EPB42 (gene/protein) has a direct relationship of ppi with GFI1 (gene/protein).', 'NRF1 (gene/protein) has a direct relationship of ppi with RBM7 (gene/protein).', 'LECT2 (gene/protein) has a direct relationship of ppi with RSL1D1 (gene/protein).', 'ATR (gene/protein) has a direct relationship of ppi with VSIG2 (gene/protein).', 'SLC4A8 (gene/protein) has a direct relationship of ppi with SNX14 (gene/protein).', 'AMFR (gene/protein) has a direct relationship of ppi with SARAF (gene/protein).', 'VCP (gene/protein) has a direct relationship of ppi with DCAF7 (gene/protein).', 'SP2 (gene/protein) has a direct relationship of ppi with ANKRD16 (gene/protein).', 'SMAD3 (gene/protein) has a direct relationship of ppi with FAM90A1 (gene/protein).', 'MCL1 (gene/protein) has a direct relationship of ppi with TP53 (gene/protein).', 'GUCD1 (gene/protein) has a direct relationship of ppi with PCBD2 (gene/protein).', 'DDR1 (gene/protein) has a direct relationship of ppi with MTA1 (gene/protein).', 'NBEAL1 (gene/protein) has a direct relationship of ppi with SPIRE2 (gene/protein).', 'TSPAN15 (gene/protein) has a direct relationship of ppi with SYNE4 (gene/protein).', 'FGB (gene/protein) has a direct relationship of ppi with SF3A1 (gene/protein).', 'CCNE1 (gene/protein) has a direct relationship of ppi with UBTF (gene/protein).', 'MATR3 (gene/protein) has a direct relationship of ppi with PAXIP1 (gene/protein).', 'TTF1 (gene/protein) has a direct relationship of ppi with RNASEH2A (gene/protein).', 'CALML3 (gene/protein) has a direct relationship of ppi with MYO6 (gene/protein).', 'GTF3C1 (gene/protein) has a direct relationship of ppi with ZNF785 (gene/protein).', 'KRT15 (gene/protein) has a direct relationship of ppi with HAUS1 (gene/protein).', 'BBS2 (gene/protein) has a direct relationship of ppi with BBS9 (gene/protein).', 'THAP12 (gene/protein) has a direct relationship of ppi with KIAA1958 (gene/protein).', 'SCN2B (gene/protein) has a direct relationship of ppi with SCN9A (gene/protein).', 'PCBD1 (gene/protein) has a direct relationship of ppi with LRP1B (gene/protein).', 'PXN (gene/protein) has a direct relationship of ppi with PKP4 (gene/protein).', 'RBL1 (gene/protein) has a direct relationship of ppi with TSC22D2 (gene/protein).', 'TMBIM6 (gene/protein) has a direct relationship of ppi with SIT1 (gene/protein).', 'VCAM1 (gene/protein) has a direct relationship of ppi with CHMP2A (gene/protein).', 'MAPK1 (gene/protein) has a direct relationship of ppi with BRF2 (gene/protein).', 'USHBP1 (gene/protein) has a direct relationship of ppi with KRT79 (gene/protein).', 'MECOM (gene/protein) has a direct relationship of ppi with RUVBL2 (gene/protein).', 'UBC (gene/protein) has a direct relationship of ppi with DCBLD2 (gene/protein).', 'SREBF1 (gene/protein) has a direct relationship of ppi with NOP9 (gene/protein).', 'YWHAB (gene/protein) has a direct relationship of ppi with CAMKK1 (gene/protein).', 'COX4I1 (gene/protein) has a direct relationship of ppi with VDAC1 (gene/protein).', 'CCNB1 (gene/protein) has a direct relationship of ppi with CDKN1B (gene/protein).', 'CDCA8 (gene/protein) has a direct relationship of ppi with CTCFL (gene/protein).', 'BIK (gene/protein) has a direct relationship of ppi with CYB561 (gene/protein).', 'E2F4 (gene/protein) has a direct relationship of ppi with BECN1 (gene/protein).', 'MSH2 (gene/protein) has a direct relationship of ppi with MYC (gene/protein).', 'FHL3 (gene/protein) has a direct relationship of ppi with MAPK1 (gene/protein).', 'EED (gene/protein) has a direct relationship of ppi with CPSF7 (gene/protein).', 'TRAF6 (gene/protein) has a direct relationship of ppi with TICAM1 (gene/protein).', 'RAP2A (gene/protein) has a direct relationship of ppi with UBC (gene/protein).', 'RAC1 (gene/protein) has a direct relationship of ppi with ARHGAP45 (gene/protein).', 'AR (gene/protein) has a direct relationship of ppi with PPP1CC (gene/protein).', 'PDLIM7 (gene/protein) has a direct relationship of ppi with ARPC5L (gene/protein).', 'PRDM14 (gene/protein) has a direct relationship of ppi with SIRPA (gene/protein).', 'BTG3 (gene/protein) has a direct relationship of ppi with RIBC1 (gene/protein).', 'MFAP1 (gene/protein) has a direct relationship of ppi with MID2 (gene/protein).', 'B4GALT4 (gene/protein) has a direct relationship of ppi with NGLY1 (gene/protein).', 'UBC (gene/protein) has a direct relationship of ppi with ADI1 (gene/protein).', 'SORD (gene/protein) has a direct relationship of ppi with PDLIM7 (gene/protein).', 'UBB (gene/protein) has a direct relationship of ppi with TAX1BP1 (gene/protein).', 'CNP (gene/protein) has a direct relationship of ppi with SIRT3 (gene/protein).', 'CD79A (gene/protein) has a direct relationship of ppi with MARCHF2 (gene/protein).', 'FGFR4 (gene/protein) has a direct relationship of ppi with PSMC3IP (gene/protein).', 'PRR20A (gene/protein) has a direct relationship of ppi with PRR35 (gene/protein).', 'E2F6 (gene/protein) has a direct relationship of ppi with CDC45 (gene/protein).', 'FAM107A (gene/protein) has a direct relationship of ppi with CCDC125 (gene/protein).', 'HSF2 (gene/protein) has a direct relationship of ppi with PRCC (gene/protein).', 'NACA (gene/protein) has a direct relationship of ppi with LRIF1 (gene/protein).', 'E2F1 (gene/protein) has a direct relationship of ppi with TP53BP2 (gene/protein).', 'GLP1R (gene/protein) has a direct relationship of ppi with TMBIM6 (gene/protein).', 'TBX1 (gene/protein) has a direct relationship of ppi with SUZ12 (gene/protein).', 'ZEB1 (gene/protein) has a direct relationship of ppi with ROCK1P1 (gene/protein).', 'PLPP1 (gene/protein) has a direct relationship of ppi with SSMEM1 (gene/protein).', 'GIT2 (gene/protein) has a direct relationship of ppi with CORO1A (gene/protein).', 'COMT (gene/protein) has a direct relationship of ppi with UBC (gene/protein).', 'HNRNPD (gene/protein) has a direct relationship of ppi with GTF2IRD1 (gene/protein).', 'GATA2 (gene/protein) has a direct relationship of ppi with HERC1 (gene/protein).', 'CHRM3 (gene/protein) has a direct relationship of ppi with PPP6R1 (gene/protein).', 'ESRRB (gene/protein) has a direct relationship of ppi with WASL (gene/protein).', 'CNR2 (gene/protein) has a direct relationship of ppi with RFT1 (gene/protein).', 'RHEB (gene/protein) has a direct relationship of ppi with RELL2 (gene/protein).', 'TPR (gene/protein) has a direct relationship of ppi with ZC3HC1 (gene/protein).', 'SOX2 (gene/protein) has a direct relationship of ppi with NCOR1 (gene/protein).', 'KPNA2 (gene/protein) has a direct relationship of ppi with UBR5 (gene/protein).', 'SPRED1 (gene/protein) has a direct relationship of ppi with C2orf68 (gene/protein).', 'LGALS3 (gene/protein) has a direct relationship of ppi with SLC38A9 (gene/protein).', 'PGRMC2 (gene/protein) has a direct relationship of ppi with ST6GAL2 (gene/protein).', 'EIF4A3 (gene/protein) has a direct relationship of ppi with MAGOHB (gene/protein).', 'PLEKHG4 (gene/protein) has a direct relationship of ppi with DTX2 (gene/protein).', 'SRSF5 (gene/protein) has a direct relationship of ppi with HNRNPR (gene/protein).', 'GTF2B (gene/protein) has a direct relationship of ppi with MAPK1 (gene/protein).', 'PIH1D2 (gene/protein) has a direct relationship of ppi with SPRED1 (gene/protein).', 'MAGOHB (gene/protein) has a direct relationship of ppi with ZBTB42 (gene/protein).', 'TCF4 (gene/protein) has a direct relationship of ppi with ZBED5 (gene/protein).', 'NTM (gene/protein) has a direct relationship of ppi with NEGR1 (gene/protein).', 'MRPL19 (gene/protein) has a direct relationship of ppi with MRPL42 (gene/protein).', 'TRIM23 (gene/protein) has a direct relationship of ppi with UBE2V2 (gene/protein).', 'RSRC1 (gene/protein) has a direct relationship of ppi with SMAP1 (gene/protein).', 'PBX1 (gene/protein) has a direct relationship of ppi with C5orf24 (gene/protein).', 'SRI (gene/protein) has a direct relationship of ppi with UBC (gene/protein).', 'F13A1 (gene/protein) has a direct relationship of ppi with FGA (gene/protein).', 'IL2RG (gene/protein) has a direct relationship of ppi with ERRFI1 (gene/protein).', 'FAM50B (gene/protein) has a direct relationship of ppi with CCDC89 (gene/protein).', 'H1-5 (gene/protein) has a direct relationship of ppi with MLLT10 (gene/protein).', 'ICE1 (gene/protein) has a direct relationship of ppi with ICE2 (gene/protein).', 'SNX1 (gene/protein) has a direct relationship of ppi with SNX8 (gene/protein).', 'GATA2 (gene/protein) has a direct relationship of ppi with MAD2L1BP (gene/protein).', 'RPGRIP1 (gene/protein) has a direct relationship of ppi with ZNF564 (gene/protein).', 'TAX1BP1 (gene/protein) has a direct relationship of ppi with RAD54L2 (gene/protein).', 'MRPL50 (gene/protein) has a direct relationship of ppi with RNF213 (gene/protein).', 'PTK2 (gene/protein) has a direct relationship of ppi with SH2D1B (gene/protein).', 'LRPAP1 (gene/protein) has a direct relationship of ppi with LRP1B (gene/protein).', 'OXA1L (gene/protein) has a direct relationship of ppi with IKBIP (gene/protein).', 'CLDN19 (gene/protein) has a direct relationship of ppi with GPX8 (gene/protein).', 'BTK (gene/protein) has a direct relationship of ppi with WDR87 (gene/protein).', 'ATG9A (gene/protein) has a direct relationship of ppi with KPRP (gene/protein).', 'CAV1 (gene/protein) has a direct relationship of ppi with SPAST (gene/protein).', 'PDGFRB (gene/protein) has a direct relationship of ppi with SLA (gene/protein).', 'CALM1 (gene/protein) has a direct relationship of ppi with RYR2 (gene/protein).', 'NXF1 (gene/protein) has a direct relationship of ppi with BACH2 (gene/protein).', 'SMARCA4 (gene/protein) has a direct relationship of ppi with DGCR8 (gene/protein).', 'GSC2 (gene/protein) has a direct relationship of ppi with ISX (gene/protein).', 'FARSA (gene/protein) has a direct relationship of ppi with YY1 (gene/protein).', 'H2BC14 (gene/protein) has a direct relationship of ppi with BCLAF1 (gene/protein).', 'ACADVL (gene/protein) has a direct relationship of ppi with SINHCAF (gene/protein).', 'CNR2 (gene/protein) has a direct relationship of ppi with FXYD3 (gene/protein).', 'HIF1A (gene/protein) has a direct relationship of ppi with CUL2 (gene/protein).', 'TOM1 (gene/protein) has a direct relationship of ppi with MYO19 (gene/protein).', 'IRAK2 (gene/protein) has a direct relationship of ppi with ZC3H12C (gene/protein).', 'NR1H2 (gene/protein) has a direct relationship of ppi with BAG6 (gene/protein).', 'NPHP3 (gene/protein) has a direct relationship of ppi with ZNF517 (gene/protein).', 'SRPK1 (gene/protein) has a direct relationship of ppi with EIF3M (gene/protein).', 'NCOA1 (gene/protein) has a direct relationship of ppi with ANKAR (gene/protein).', 'YBX1 (gene/protein) has a direct relationship of ppi with ACTR8 (gene/protein).', 'FH (gene/protein) has a direct relationship of ppi with H2AZ1 (gene/protein).', 'GLI1 (gene/protein) has a direct relationship of ppi with TMEM100 (gene/protein).', 'ILF3 (gene/protein) has a direct relationship of ppi with RPS23 (gene/protein).', 'FOSL2 (gene/protein) has a direct relationship of ppi with AJUBA (gene/protein).', 'SERTAD1 (gene/protein) has a direct relationship of ppi with KLHL42 (gene/protein).', 'NR3C1 (gene/protein) has a direct relationship of ppi with H2AC20 (gene/protein).', 'EP300 (gene/protein) has a direct relationship of ppi with CORO1C (gene/protein).', 'DNAJB2 (gene/protein) has a direct relationship of ppi with CYHR1 (gene/protein).', 'PDE4DIP (gene/protein) has a direct relationship of ppi with FCHSD2 (gene/protein).', 'NAP1L1 (gene/protein) has a direct relationship of ppi with SRP72 (gene/protein).', 'ANKRD26 (gene/protein) has a direct relationship of ppi with NDEL1 (gene/protein).', 'GOLGB1 (gene/protein) has a direct relationship of ppi with ECPAS (gene/protein).', 'BCL3 (gene/protein) has a direct relationship of ppi with RPL38 (gene/protein).', 'CTTN (gene/protein) has a direct relationship of ppi with FGFR1 (gene/protein).', 'TMEM38A (gene/protein) has a direct relationship of ppi with PCP2 (gene/protein).', 'CSNK1E (gene/protein) has a direct relationship of ppi with BTBD1 (gene/protein).', 'HSPA9 (gene/protein) has a direct relationship of ppi with LAMTOR5 (gene/protein).', 'HNRNPC (gene/protein) has a direct relationship of ppi with VCAM1 (gene/protein).', 'RDH14 (gene/protein) has a direct relationship of ppi with BRINP2 (gene/protein).', 'ACD (gene/protein) has a direct relationship of ppi with PAGE2 (gene/protein).', 'TMCC2 (gene/protein) has a direct relationship of ppi with CORO1A (gene/protein).', 'RPS3A (gene/protein) has a direct relationship of ppi with RACK1 (gene/protein).', 'EHHADH (gene/protein) has a direct relationship of ppi with TRIM41 (gene/protein).', 'GABRG2 (gene/protein) has a direct relationship of ppi with LCLAT1 (gene/protein).', 'GAPDH (gene/protein) has a direct relationship of ppi with SERPINB9 (gene/protein).', 'HOXB5 (gene/protein) has a direct relationship of ppi with PBX2 (gene/protein).', 'PSMC5 (gene/protein) has a direct relationship of ppi with TRIM5 (gene/protein).', 'COPS5 (gene/protein) has a direct relationship of ppi with NUPR1 (gene/protein).', 'CDK1 (gene/protein) has a direct relationship of ppi with H4C14 (gene/protein).', 'YY1 (gene/protein) has a direct relationship of ppi with PEF1 (gene/protein).', 'OPRM1 (gene/protein) has a direct relationship of ppi with XPO6 (gene/protein).', 'MTIF2 (gene/protein) has a direct relationship of ppi with TUFM (gene/protein).', 'NUTF2 (gene/protein) has a direct relationship of ppi with CHMP4A (gene/protein).', 'DKC1 (gene/protein) has a direct relationship of ppi with PPAN (gene/protein).', 'BCL2L2 (gene/protein) has a direct relationship of ppi with RHBDD2 (gene/protein).', 'SAP30BP (gene/protein) has a direct relationship of ppi with WDR83 (gene/protein).', 'PLAUR (gene/protein) has a direct relationship of ppi with DHFR2 (gene/protein).', 'LYPD3 (gene/protein) has a direct relationship of ppi with NCEH1 (gene/protein).', 'UNC119 (gene/protein) has a direct relationship of ppi with CYB561D2 (gene/protein).', 'TCF4 (gene/protein) has a direct relationship of ppi with ZNF142 (gene/protein).', 'CDK1 (gene/protein) has a direct relationship of ppi with EIF2B3 (gene/protein).', 'MCM6 (gene/protein) has a direct relationship of ppi with H3C4 (gene/protein).', 'SRSF7 (gene/protein) has a direct relationship of ppi with SF3A1 (gene/protein).', 'MAP3K7 (gene/protein) has a direct relationship of ppi with TAB2 (gene/protein).', 'FOXH1 (gene/protein) has a direct relationship of ppi with KRTAP19-7 (gene/protein).', 'SVIL (gene/protein) has a direct relationship of ppi with COA7 (gene/protein).', 'DYNC1H1 (gene/protein) has a direct relationship of ppi with PLOD3 (gene/protein).', 'NINJ2 (gene/protein) has a direct relationship of ppi with MMGT1 (gene/protein).', 'SERPINB4 (gene/protein) has a direct relationship of ppi with TBC1D22B (gene/protein).', 'LGALS3 (gene/protein) has a direct relationship of ppi with FCF1 (gene/protein).', 'ACTN4 (gene/protein) has a direct relationship of ppi with MYO18A (gene/protein).', 'PNRC1 (gene/protein) has a direct relationship of ppi with EDC4 (gene/protein).', 'RCL1 (gene/protein) has a direct relationship of ppi with TENT4B (gene/protein).', 'PDK3 (gene/protein) has a direct relationship of ppi with CCT5 (gene/protein).', 'NEK2 (gene/protein) has a direct relationship of ppi with ANAPC1 (gene/protein).', 'BRCA1 (gene/protein) has a direct relationship of ppi with CTNND1 (gene/protein).', 'RHOC (gene/protein) has a direct relationship of ppi with CTNNB1 (gene/protein).', 'TACC3 (gene/protein) has a direct relationship of ppi with CBY2 (gene/protein).', 'DDIT4 (gene/protein) has a direct relationship of ppi with RIF1 (gene/protein).', 'NME4 (gene/protein) has a direct relationship of ppi with UBL5 (gene/protein).', 'PPP1R12C (gene/protein) has a direct relationship of ppi with TNKS2 (gene/protein).', 'PLP1 (gene/protein) has a direct relationship of ppi with TMEM52B (gene/protein).', 'EGR1 (gene/protein) has a direct relationship of ppi with FAM20B (gene/protein).', 'RASD1 (gene/protein) has a direct relationship of ppi with KRTAP10-9 (gene/protein).', 'AATK (gene/protein) has a direct relationship of ppi with PPM1K (gene/protein).', 'ZMAT4 (gene/protein) has a direct relationship of ppi with HEPHL1 (gene/protein).', 'KDM1B (gene/protein) has a direct relationship of ppi with TAFA3 (gene/protein).', 'GLI1 (gene/protein) has a direct relationship of ppi with USH1G (gene/protein).', 'PFDN5 (gene/protein) has a direct relationship of ppi with SPAG8 (gene/protein).', 'PRKCA (gene/protein) has a direct relationship of ppi with NOXA1 (gene/protein).', 'UBE2L3 (gene/protein) has a direct relationship of ppi with VDAC2 (gene/protein).', 'PARP1 (gene/protein) has a direct relationship of ppi with CEBPA (gene/protein).', 'BHLHE40 (gene/protein) has a direct relationship of ppi with MCRS1 (gene/protein).', 'KLC1 (gene/protein) has a direct relationship of ppi with TRAK2 (gene/protein).', 'CCDC85B (gene/protein) has a direct relationship of ppi with GCC1 (gene/protein).', 'GSK3B (gene/protein) has a direct relationship of ppi with NRBP1 (gene/protein).', 'KPNA1 (gene/protein) has a direct relationship of ppi with RB1 (gene/protein).', 'NFKBIB (gene/protein) has a direct relationship of ppi with TSPAN1 (gene/protein).', 'CASR (gene/protein) has a direct relationship of ppi with PRKCG (gene/protein).', 'PBX2 (gene/protein) has a direct relationship of ppi with UBE2E1 (gene/protein).', 'NRF1 (gene/protein) has a direct relationship of ppi with TMEM143 (gene/protein).', 'PRDM5 (gene/protein) has a direct relationship of ppi with FAAP20 (gene/protein).', 'RB1 (gene/protein) has a direct relationship of ppi with PIK3R3 (gene/protein).', 'SGK1 (gene/protein) has a direct relationship of ppi with MTA1 (gene/protein).', 'BMI1 (gene/protein) has a direct relationship of ppi with H1-10 (gene/protein).', 'RAN (gene/protein) has a direct relationship of ppi with SON (gene/protein).', 'AKAP5 (gene/protein) has a direct relationship of ppi with OTUD6B (gene/protein).', 'MAPK1 (gene/protein) has a direct relationship of ppi with SHANK3 (gene/protein).', 'POGZ (gene/protein) has a direct relationship of ppi with ZNF410 (gene/protein).', 'H2BC5 (gene/protein) has a direct relationship of ppi with MEF2A (gene/protein).', 'LCE2A (gene/protein) has a direct relationship of ppi with KRTAP2-3 (gene/protein).', 'EBF1 (gene/protein) has a direct relationship of ppi with ARPC1A (gene/protein).', 'STX12 (gene/protein) has a direct relationship of ppi with TBK1 (gene/protein).', 'HDAC2 (gene/protein) has a direct relationship of ppi with LZTR1 (gene/protein).', 'ZNF707 (gene/protein) has a direct relationship of ppi with ZNF445 (gene/protein).', 'SLC25A6 (gene/protein) has a direct relationship of ppi with ISLR (gene/protein).', 'RPS14 (gene/protein) has a direct relationship of ppi with RPS26 (gene/protein).', 'ALDOB (gene/protein) has a direct relationship of ppi with MUC20 (gene/protein).', 'FANCD2 (gene/protein) has a direct relationship of ppi with MCM2 (gene/protein).', 'CDKN2D (gene/protein) has a direct relationship of ppi with THAP1 (gene/protein).', 'DNMT1 (gene/protein) has a direct relationship of ppi with USP7 (gene/protein).', 'TAL1 (gene/protein) has a direct relationship of ppi with PPP1R15A (gene/protein).', 'MYOM1 (gene/protein) has a direct relationship of ppi with KRTAP5-7 (gene/protein).', 'BARD1 (gene/protein) has a direct relationship of ppi with H3C2 (gene/protein).', 'SPI1 (gene/protein) has a direct relationship of ppi with KIF3B (gene/protein).', 'UBE2D3 (gene/protein) has a direct relationship of ppi with TRIM35 (gene/protein).', 'ZNF263 (gene/protein) has a direct relationship of ppi with CMC2 (gene/protein).', 'EIF3A (gene/protein) has a direct relationship of ppi with EIF3G (gene/protein).', 'FAM161A (gene/protein) has a direct relationship of ppi with TRIM41 (gene/protein).', 'ABL1 (gene/protein) has a direct relationship of ppi with EGFR (gene/protein).', 'WWOX (gene/protein) has a direct relationship of ppi with C19orf54 (gene/protein).', 'CYP4F22 (gene/protein) has a direct relationship of ppi with TLCD4 (gene/protein).', 'UBC (gene/protein) has a direct relationship of ppi with ANTXR2 (gene/protein).', 'YWHAZ (gene/protein) has a direct relationship of ppi with MSL2 (gene/protein).', 'TULP3 (gene/protein) has a direct relationship of ppi with GGPS1 (gene/protein).', 'TRIP12 (gene/protein) has a direct relationship of ppi with PIH1D1 (gene/protein).', 'CAV1 (gene/protein) has a direct relationship of ppi with IRAK1 (gene/protein).', 'ASPHD2 (gene/protein) has a direct relationship of ppi with LYPD4 (gene/protein).', 'VPS35 (gene/protein) has a direct relationship of ppi with PPP1R14C (gene/protein).', 'ROR1 (gene/protein) has a direct relationship of ppi with PPM1F (gene/protein).', 'FYN (gene/protein) has a direct relationship of ppi with SOS2 (gene/protein).', 'APP (gene/protein) has a direct relationship of ppi with SENP2 (gene/protein).', 'SEPTIN3 (gene/protein) has a direct relationship of ppi with PELI2 (gene/protein).', 'MRPL18 (gene/protein) has a direct relationship of ppi with MRPL39 (gene/protein).', 'KPNA2 (gene/protein) has a direct relationship of ppi with PLAG1 (gene/protein).', 'FAM107A (gene/protein) has a direct relationship of ppi with RNLS (gene/protein).', 'PSMC3 (gene/protein) has a direct relationship of ppi with PSMD5 (gene/protein).', 'PSMB5 (gene/protein) has a direct relationship of ppi with PSMD8 (gene/protein).', 'EHHADH (gene/protein) has a direct relationship of ppi with ERVFRD-1 (gene/protein).', 'TRAF5 (gene/protein) has a direct relationship of ppi with SUMO1P1 (gene/protein).', 'RRM2 (gene/protein) has a direct relationship of ppi with FAF2 (gene/protein).', 'ORC3 (gene/protein) has a direct relationship of ppi with TOR1AIP1 (gene/protein).', 'TSG101 (gene/protein) has a direct relationship of ppi with PRDM16 (gene/protein).', 'KAT2A (gene/protein) has a direct relationship of ppi with PPARGC1A (gene/protein).', 'PAAF1 (gene/protein) has a direct relationship of ppi with UBLCP1 (gene/protein).', 'GYS1 (gene/protein) has a direct relationship of ppi with ZNF552 (gene/protein).', 'AQP10 (gene/protein) has a direct relationship of ppi with GPR152 (gene/protein).', 'ZNF581 (gene/protein) has a direct relationship of ppi with ASB13 (gene/protein).', 'IL7R (gene/protein) has a direct relationship of ppi with YWHAZ (gene/protein).', 'CHD5 (gene/protein) has a direct relationship of ppi with MBD3 (gene/protein).', 'NCKAP1 (gene/protein) has a direct relationship of ppi with BRK1 (gene/protein).', 'KIF1C (gene/protein) has a direct relationship of ppi with ADNP2 (gene/protein).', 'CTCF (gene/protein) has a direct relationship of ppi with EXD1 (gene/protein).', 'ANXA9 (gene/protein) has a direct relationship of ppi with ARHGEF10L (gene/protein).', 'CALU (gene/protein) has a direct relationship of ppi with ZPBP (gene/protein).', 'RASSF1 (gene/protein) has a direct relationship of ppi with SAV1 (gene/protein).', 'IRF1 (gene/protein) has a direct relationship of ppi with YBX1 (gene/protein).', 'IRF2 (gene/protein) has a direct relationship of ppi with PPP3CA (gene/protein).', 'TMEM42 (gene/protein) has a direct relationship of ppi with MGAT5B (gene/protein).', 'VAPA (gene/protein) has a direct relationship of ppi with CAVIN3 (gene/protein).', 'MDC1 (gene/protein) has a direct relationship of ppi with HINFP (gene/protein).', 'PTBP1 (gene/protein) has a direct relationship of ppi with SNRPA (gene/protein).', 'PBX3 (gene/protein) has a direct relationship of ppi with CHCHD2 (gene/protein).', 'PTPRE (gene/protein) has a direct relationship of ppi with RAD21 (gene/protein).', 'MESD (gene/protein) has a direct relationship of ppi with MCM9 (gene/protein).', 'APOC4 (gene/protein) has a direct relationship of ppi with UBQLN1 (gene/protein).', 'GJB2 (gene/protein) has a direct relationship of ppi with GPR152 (gene/protein).', 'PEX14 (gene/protein) has a direct relationship of ppi with CCL4 (gene/protein).', 'PPP2R3A (gene/protein) has a direct relationship of ppi with CEP170 (gene/protein).', 'SMARCA5 (gene/protein) has a direct relationship of ppi with NELFB (gene/protein).', 'NAP1L1 (gene/protein) has a direct relationship of ppi with DISC1 (gene/protein).', 'MYC (gene/protein) has a direct relationship of ppi with NFE2L2 (gene/protein).', 'HSBP1 (gene/protein) has a direct relationship of ppi with KRTAP1-1 (gene/protein).', 'CSRP3 (gene/protein) has a direct relationship of ppi with MAPKAPK5 (gene/protein).', 'NFYB (gene/protein) has a direct relationship of ppi with ROGDI (gene/protein).', 'ACTR2 (gene/protein) has a direct relationship of ppi with PLK4 (gene/protein).', 'LDB2 (gene/protein) has a direct relationship of ppi with C14orf119 (gene/protein).', 'PRKACA (gene/protein) has a direct relationship of ppi with PSEN1 (gene/protein).', 'SMARCA4 (gene/protein) has a direct relationship of ppi with TPM4 (gene/protein).', 'ALDOA (gene/protein) has a direct relationship of ppi with FN1 (gene/protein).', 'WWP1 (gene/protein) has a direct relationship of ppi with SPART (gene/protein).', 'SMARCA4 (gene/protein) has a direct relationship of ppi with ZNF280A (gene/protein).', 'CDK1 (gene/protein) has a direct relationship of ppi with MYCN (gene/protein).', 'STAM (gene/protein) has a direct relationship of ppi with NCEH1 (gene/protein).', 'E2F1 (gene/protein) has a direct relationship of ppi with RNF138 (gene/protein).', 'UBC (gene/protein) has a direct relationship of ppi with ASB2 (gene/protein).', 'TUBGCP3 (gene/protein) has a direct relationship of ppi with MZT2A (gene/protein).', 'GNAL (gene/protein) has a direct relationship of ppi with CHIA (gene/protein).', 'DEFA6 (gene/protein) has a direct relationship of ppi with UBQLN2 (gene/protein).', 'ARMC8 (gene/protein) has a direct relationship of ppi with MRPL4 (gene/protein).', 'PTER (gene/protein) has a direct relationship of ppi with NPDC1 (gene/protein).', 'RPL17 (gene/protein) has a direct relationship of ppi with RPS15A (gene/protein).', 'HNF4A (gene/protein) has a direct relationship of ppi with GMPR2 (gene/protein).', 'GYG2 (gene/protein) has a direct relationship of ppi with OSTC (gene/protein).', 'RAD23A (gene/protein) has a direct relationship of ppi with NUTM2F (gene/protein).', 'TRIM27 (gene/protein) has a direct relationship of ppi with TSGA10IP (gene/protein).', 'RPL6 (gene/protein) has a direct relationship of ppi with RPLP0 (gene/protein).', 'TNFRSF1A (gene/protein) has a direct relationship of ppi with TPCN1 (gene/protein).', 'ERCC1 (gene/protein) has a direct relationship of ppi with USP45 (gene/protein).', 'FOXM1 (gene/protein) has a direct relationship of ppi with LIN9 (gene/protein).', 'ETS2 (gene/protein) has a direct relationship of ppi with STAT3 (gene/protein).', 'EP300 (gene/protein) has a direct relationship of ppi with PMVK (gene/protein).', 'NR5A1 (gene/protein) has a direct relationship of ppi with PPARGC1A (gene/protein).', 'RBM7 (gene/protein) has a direct relationship of ppi with DCTN3 (gene/protein).', 'KTN1 (gene/protein) has a direct relationship of ppi with RPL13A (gene/protein).', 'TTLL12 (gene/protein) has a direct relationship of ppi with OTUD6B (gene/protein).', 'CUL1 (gene/protein) has a direct relationship of ppi with FBXO6 (gene/protein).', 'NKX3-1 (gene/protein) has a direct relationship of ppi with SLC22A18 (gene/protein).', 'COPS3 (gene/protein) has a direct relationship of ppi with COPS6 (gene/protein).', 'LPCAT2 (gene/protein) has a direct relationship of ppi with HSD17B13 (gene/protein).', 'HDGF (gene/protein) has a direct relationship of ppi with SRF (gene/protein).', 'HSD17B6 (gene/protein) has a direct relationship of ppi with TATDN1 (gene/protein).', 'RAC1 (gene/protein) has a direct relationship of ppi with HACE1 (gene/protein).', 'RAN (gene/protein) has a direct relationship of ppi with ISG15 (gene/protein).', 'GRB2 (gene/protein) has a direct relationship of ppi with SYK (gene/protein).', 'PTK2B (gene/protein) has a direct relationship of ppi with GAPDH (gene/protein).', 'COMMD3 (gene/protein) has a direct relationship of ppi with COMMD9 (gene/protein).', 'UBC (gene/protein) has a direct relationship of ppi with FEZ1 (gene/protein).', 'TINAGL1 (gene/protein) has a direct relationship of ppi with NBPF19 (gene/protein).', 'AIFM1 (gene/protein) has a direct relationship of ppi with AMZ1 (gene/protein).', 'FECH (gene/protein) has a direct relationship of ppi with CLUH (gene/protein).', 'TLE1 (gene/protein) has a direct relationship of ppi with SIX2 (gene/protein).', 'ATXN1 (gene/protein) has a direct relationship of ppi with TCTA (gene/protein).', 'NR4A1 (gene/protein) has a direct relationship of ppi with CHD1L (gene/protein).', 'PHLPP2 (gene/protein) has a direct relationship of ppi with USP46 (gene/protein).', 'KRTAP17-1 (gene/protein) has a direct relationship of ppi with LCE3C (gene/protein).', 'UBC (gene/protein) has a direct relationship of ppi with TRAM1 (gene/protein).', 'CISH (gene/protein) has a direct relationship of ppi with EP300 (gene/protein).', 'CEBPB (gene/protein) has a direct relationship of ppi with MST1P2 (gene/protein).', 'DEK (gene/protein) has a direct relationship of ppi with DHX16 (gene/protein).', 'IST1 (gene/protein) has a direct relationship of ppi with ANAPC2 (gene/protein).', 'PCDHGB1 (gene/protein) has a direct relationship of ppi with C3orf33 (gene/protein).', 'NFYA (gene/protein) has a direct relationship of ppi with YBX1 (gene/protein).', 'CD81 (gene/protein) has a direct relationship of ppi with PDIA4 (gene/protein).', 'YWHAB (gene/protein) has a direct relationship of ppi with CRTC2 (gene/protein).', 'PSMB9 (gene/protein) has a direct relationship of ppi with NCOA1 (gene/protein).', 'WASL (gene/protein) has a direct relationship of ppi with PAK4 (gene/protein).', 'CCNT2 (gene/protein) has a direct relationship of ppi with PRKAR2B (gene/protein).', 'ERCC6 (gene/protein) has a direct relationship of ppi with EIF3A (gene/protein).', 'ATP2B2 (gene/protein) has a direct relationship of ppi with SNTA1 (gene/protein).', 'YBX1 (gene/protein) has a direct relationship of ppi with FADD (gene/protein).', 'TMOD1 (gene/protein) has a direct relationship of ppi with PLEKHG6 (gene/protein).', 'CSNK1E (gene/protein) has a direct relationship of ppi with CSNK2B (gene/protein).', 'CYP2C8 (gene/protein) has a direct relationship of ppi with RIN3 (gene/protein).', 'ACO1 (gene/protein) has a direct relationship of ppi with CCDC69 (gene/protein).', 'XIAP (gene/protein) has a direct relationship of ppi with LATS1 (gene/protein).', 'PRKAR1A (gene/protein) has a direct relationship of ppi with CAPN11 (gene/protein).', 'P4HA2 (gene/protein) has a direct relationship of ppi with CCT7 (gene/protein).', 'GOLGA2 (gene/protein) has a direct relationship of ppi with FAM193B (gene/protein).', 'PSEN2 (gene/protein) has a direct relationship of ppi with UBC (gene/protein).', 'RPL27A (gene/protein) has a direct relationship of ppi with RACK1 (gene/protein).', 'DYNLL1 (gene/protein) has a direct relationship of ppi with UFL1 (gene/protein).', 'MYBPC2 (gene/protein) has a direct relationship of ppi with CMYA5 (gene/protein).', 'RARG (gene/protein) has a direct relationship of ppi with MRPL12 (gene/protein).', 'CXADR (gene/protein) has a direct relationship of ppi with NCOR1 (gene/protein).', 'NFYA (gene/protein) has a direct relationship of ppi with FBXO5 (gene/protein).', 'MITF (gene/protein) has a direct relationship of ppi with MAPK1 (gene/protein).', 'TFRC (gene/protein) has a direct relationship of ppi with CHMP4B (gene/protein).', 'DCTN2 (gene/protein) has a direct relationship of ppi with MARCKSL1 (gene/protein).', 'PICK1 (gene/protein) has a direct relationship of ppi with LRRC73 (gene/protein).', 'LCE3A (gene/protein) has a direct relationship of ppi with KRTAP5-2 (gene/protein).', 'MED7 (gene/protein) has a direct relationship of ppi with MED24 (gene/protein).', 'TGFBR1 (gene/protein) has a direct relationship of ppi with SMURF1 (gene/protein).', 'ETS1 (gene/protein) has a direct relationship of ppi with STK39 (gene/protein).', 'MYH11 (gene/protein) has a direct relationship of ppi with SMC3 (gene/protein).', 'NR3C1 (gene/protein) has a direct relationship of ppi with ZNF718 (gene/protein).', 'SOX2 (gene/protein) has a direct relationship of ppi with ENPP4 (gene/protein).', 'BMI1 (gene/protein) has a direct relationship of ppi with MAP2K1 (gene/protein).', 'EEF1G (gene/protein) has a direct relationship of ppi with HLTF (gene/protein).', 'RPL9 (gene/protein) has a direct relationship of ppi with SORBS2 (gene/protein).', 'PTPRJ (gene/protein) has a direct relationship of ppi with BAP1 (gene/protein).', 'HSF4 (gene/protein) has a direct relationship of ppi with YTHDF1 (gene/protein).', 'YY1 (gene/protein) has a direct relationship of ppi with YIPF6 (gene/protein).', 'PTGIR (gene/protein) has a direct relationship of ppi with XPR1 (gene/protein).', 'PSAP (gene/protein) has a direct relationship of ppi with U2AF1 (gene/protein).', 'EIF2B1 (gene/protein) has a direct relationship of ppi with SIGLECL1 (gene/protein).', 'RETREG3 (gene/protein) has a direct relationship of ppi with TSPO2 (gene/protein).', 'BDH1 (gene/protein) has a direct relationship of ppi with IL13RA2 (gene/protein).', 'SH3YL1 (gene/protein) has a direct relationship of ppi with ERRFI1 (gene/protein).', 'DAXX (gene/protein) has a direct relationship of ppi with FTH1 (gene/protein).', 'FGFR4 (gene/protein) has a direct relationship of ppi with LRATD2 (gene/protein).', 'HCCS (gene/protein) has a direct relationship of ppi with METTL16 (gene/protein).', 'RB1CC1 (gene/protein) has a direct relationship of ppi with DISC1 (gene/protein).', 'STAT3 (gene/protein) has a direct relationship of ppi with FANK1 (gene/protein).', 'SYNGAP1 (gene/protein) has a direct relationship of ppi with OPTN (gene/protein).', 'SIGLEC6 (gene/protein) has a direct relationship of ppi with TCF4 (gene/protein).', 'MAPK14 (gene/protein) has a direct relationship of ppi with MAP2K6 (gene/protein).', 'ZNF2 (gene/protein) has a direct relationship of ppi with IMP4 (gene/protein).', 'HDAC7 (gene/protein) has a direct relationship of ppi with BCORL1 (gene/protein).', 'CEP170 (gene/protein) has a direct relationship of ppi with FAM83D (gene/protein).', 'ZBTB33 (gene/protein) has a direct relationship of ppi with CDK12 (gene/protein).', 'IHH (gene/protein) has a direct relationship of ppi with JUP (gene/protein).', 'GTF2B (gene/protein) has a direct relationship of ppi with ANKRD30BL (gene/protein).', 'TEKT3 (gene/protein) has a direct relationship of ppi with KRTAP3-1 (gene/protein).', 'MEAF6 (gene/protein) has a direct relationship of ppi with H2BC1 (gene/protein).', 'SNRPB2 (gene/protein) has a direct relationship of ppi with PNMA1 (gene/protein).', 'FYN (gene/protein) has a direct relationship of ppi with MAP4K5 (gene/protein).', 'CCT6A (gene/protein) has a direct relationship of ppi with WDR37 (gene/protein).', 'BARD1 (gene/protein) has a direct relationship of ppi with FKBP2 (gene/protein).', 'RARA (gene/protein) has a direct relationship of ppi with TNFRSF10B (gene/protein).', 'CDK7 (gene/protein) has a direct relationship of ppi with MBNL3 (gene/protein).', 'UBC (gene/protein) has a direct relationship of ppi with RHOT2 (gene/protein).', 'MYOD1 (gene/protein) has a direct relationship of ppi with SIRT2 (gene/protein).', 'PSEN1 (gene/protein) has a direct relationship of ppi with ARMC1 (gene/protein).', 'C1D (gene/protein) has a direct relationship of ppi with ZCCHC8 (gene/protein).', 'ETS1 (gene/protein) has a direct relationship of ppi with DENND3 (gene/protein).', 'ATP5F1B (gene/protein) has a direct relationship of ppi with LNX2 (gene/protein).', 'CHD4 (gene/protein) has a direct relationship of ppi with HDAC2 (gene/protein).', 'KRT24 (gene/protein) has a direct relationship of ppi with KRT6C (gene/protein).', 'YWHAB (gene/protein) has a direct relationship of ppi with TFEB (gene/protein).', 'AKR1C4 (gene/protein) has a direct relationship of ppi with AKR1C3 (gene/protein).', 'MYH9 (gene/protein) has a direct relationship of ppi with ARHGEF28 (gene/protein).', 'FTH1 (gene/protein) has a direct relationship of ppi with GPR35 (gene/protein).', 'VEGFA (gene/protein) has a direct relationship of ppi with VEGFB (gene/protein).', 'LCK (gene/protein) has a direct relationship of ppi with SH2D2A (gene/protein).', 'DNAL4 (gene/protein) has a direct relationship of ppi with TRIM54 (gene/protein).', 'E2F6 (gene/protein) has a direct relationship of ppi with RING1 (gene/protein).', 'LUZP4 (gene/protein) has a direct relationship of ppi with KRTAP10-11 (gene/protein).', 'SH3BP4 (gene/protein) has a direct relationship of ppi with TOR1AIP2 (gene/protein).', 'IGBP1 (gene/protein) has a direct relationship of ppi with STAM (gene/protein).', 'FBXO9 (gene/protein) has a direct relationship of ppi with GFOD1 (gene/protein).', 'SHOC2 (gene/protein) has a direct relationship of ppi with MRAS (gene/protein).', 'FDXR (gene/protein) has a direct relationship of ppi with NIT1 (gene/protein).', 'CYB5R3 (gene/protein) has a direct relationship of ppi with WFDC2 (gene/protein).', 'BCL3 (gene/protein) has a direct relationship of ppi with GTF2B (gene/protein).', 'EIF2B4 (gene/protein) has a direct relationship of ppi with CA14 (gene/protein).', 'POU5F1 (gene/protein) has a direct relationship of ppi with ZNF281 (gene/protein).', 'RPL37A (gene/protein) has a direct relationship of ppi with MYBBP1A (gene/protein).', 'THOC2 (gene/protein) has a direct relationship of ppi with BUD23 (gene/protein).', 'MAPK9 (gene/protein) has a direct relationship of ppi with KPNA6 (gene/protein).', 'B4GALT4 (gene/protein) has a direct relationship of ppi with CLDND1 (gene/protein).', 'CDK7 (gene/protein) has a direct relationship of ppi with CDC37 (gene/protein).', 'CD38 (gene/protein) has a direct relationship of ppi with LCK (gene/protein).', 'YWHAG (gene/protein) has a direct relationship of ppi with DACT1 (gene/protein).', 'DVL3 (gene/protein) has a direct relationship of ppi with KLHL12 (gene/protein).', 'RPS27A (gene/protein) has a direct relationship of ppi with TRIM25 (gene/protein).', 'MUC1 (gene/protein) has a direct relationship of ppi with TRAM1L1 (gene/protein).', 'BOLA1 (gene/protein) has a direct relationship of ppi with GLRX5 (gene/protein).', 'HNRNPH2 (gene/protein) has a direct relationship of ppi with PLOD3 (gene/protein).', 'UBB (gene/protein) has a direct relationship of ppi with RIDA (gene/protein).', 'EP300 (gene/protein) has a direct relationship of ppi with CFLAR (gene/protein).', 'CTNNB1 (gene/protein) has a direct relationship of ppi with PSTPIP1 (gene/protein).', 'RAI14 (gene/protein) has a direct relationship of ppi with MYO18A (gene/protein).', 'MAFK (gene/protein) has a direct relationship of ppi with PRPF40A (gene/protein).', 'RAC1 (gene/protein) has a direct relationship of ppi with TRAF7 (gene/protein).', 'APP (gene/protein) has a direct relationship of ppi with EEPD1 (gene/protein).', 'RELA (gene/protein) has a direct relationship of ppi with MYBBP1A (gene/protein).', 'SRSF1 (gene/protein) has a direct relationship of ppi with MAPKAPK5 (gene/protein).', 'CTBP2 (gene/protein) has a direct relationship of ppi with FOXP2 (gene/protein).', 'ORC6 (gene/protein) has a direct relationship of ppi with LRWD1 (gene/protein).', 'SLC22A9 (gene/protein) has a direct relationship of ppi with SLC35B2 (gene/protein).', 'RPL15 (gene/protein) has a direct relationship of ppi with MAP3K20 (gene/protein).', 'MCL1 (gene/protein) has a direct relationship of ppi with PIN1 (gene/protein).', 'ZNF18 (gene/protein) has a direct relationship of ppi with ZNF483 (gene/protein).', 'ZNF24 (gene/protein) has a direct relationship of ppi with ERG28 (gene/protein).', 'AMOTL2 (gene/protein) has a direct relationship of ppi with L3MBTL2 (gene/protein).', 'SNRPE (gene/protein) has a direct relationship of ppi with PRPF31 (gene/protein).', 'CAMK2D (gene/protein) has a direct relationship of ppi with HSF1 (gene/protein).', 'RBX1 (gene/protein) has a direct relationship of ppi with RIPK4 (gene/protein).', 'FMR1 (gene/protein) has a direct relationship of ppi with RPL15 (gene/protein).', 'FAAP100 (gene/protein) has a direct relationship of ppi with PTGES3L-AARSD1 (gene/protein).', 'HNRNPA1 (gene/protein) has a direct relationship of ppi with NCL (gene/protein).', 'CDK16 (gene/protein) has a direct relationship of ppi with PRKAR1A (gene/protein).', 'CDK1 (gene/protein) has a direct relationship of ppi with TAF12 (gene/protein).', 'PCBD1 (gene/protein) has a direct relationship of ppi with DIP2C (gene/protein).', 'MYOD1 (gene/protein) has a direct relationship of ppi with NCOR1 (gene/protein).', 'BARD1 (gene/protein) has a direct relationship of ppi with RABEP1 (gene/protein).', 'ATXN1 (gene/protein) has a direct relationship of ppi with TCAP (gene/protein).', 'PDE3B (gene/protein) has a direct relationship of ppi with ARMC1 (gene/protein).', 'CD109 (gene/protein) has a direct relationship of ppi with GJB7 (gene/protein).', 'MYH10 (gene/protein) has a direct relationship of ppi with PRKCZ (gene/protein).', 'ANXA2 (gene/protein) has a direct relationship of ppi with RPS2 (gene/protein).', 'CHEK1 (gene/protein) has a direct relationship of ppi with YWHAG (gene/protein).', 'NEK2 (gene/protein) has a direct relationship of ppi with PPP1R13L (gene/protein).', 'PTH (gene/protein) has a direct relationship of ppi with BAG6 (gene/protein).', 'APOB (gene/protein) has a direct relationship of ppi with P2RY12 (gene/protein).', 'SP1 (gene/protein) has a direct relationship of ppi with SWSAP1 (gene/protein).', 'ESR1 (gene/protein) has a direct relationship of ppi with FOXP3 (gene/protein).', 'COX15 (gene/protein) has a direct relationship of ppi with RBBP4 (gene/protein).', 'TSC22D3 (gene/protein) has a direct relationship of ppi with TSC22D1 (gene/protein).', 'MEA1 (gene/protein) has a direct relationship of ppi with RAD21 (gene/protein).', 'MKRN3 (gene/protein) has a direct relationship of ppi with TXNDC11 (gene/protein).', 'TCF4 (gene/protein) has a direct relationship of ppi with LRMDA (gene/protein).', 'STAT1 (gene/protein) has a direct relationship of ppi with TP73 (gene/protein).', 'CNIH1 (gene/protein) has a direct relationship of ppi with ERGIC3 (gene/protein).', 'HDLBP (gene/protein) has a direct relationship of ppi with XRCC5 (gene/protein).', 'ETS1 (gene/protein) has a direct relationship of ppi with SP100 (gene/protein).', 'UBC (gene/protein) has a direct relationship of ppi with GINS1 (gene/protein).', 'ERC1 (gene/protein) has a direct relationship of ppi with GFOD1 (gene/protein).', 'JUND (gene/protein) has a direct relationship of ppi with KRT80 (gene/protein).', 'FGF2 (gene/protein) has a direct relationship of ppi with JUP (gene/protein).', 'HNRNPF (gene/protein) has a direct relationship of ppi with PRR22 (gene/protein).', 'RNF34 (gene/protein) has a direct relationship of ppi with KLHL15 (gene/protein).', 'CDK6 (gene/protein) has a direct relationship of ppi with PKM (gene/protein).', 'SMN1 (gene/protein) has a direct relationship of ppi with BAG6 (gene/protein).', 'CREB1 (gene/protein) has a direct relationship of ppi with CCL3 (gene/protein).', 'FBRSL1 (gene/protein) has a direct relationship of ppi with PCGF5 (gene/protein).', 'CEBPA (gene/protein) has a direct relationship of ppi with UBTF (gene/protein).', 'HMGN3 (gene/protein) has a direct relationship of ppi with RTL10 (gene/protein).', 'SGTA (gene/protein) has a direct relationship of ppi with TXNDC12 (gene/protein).', 'MECOM (gene/protein) has a direct relationship of ppi with RBBP4 (gene/protein).', 'RAP1GDS1 (gene/protein) has a direct relationship of ppi with RET (gene/protein).', 'BRF1 (gene/protein) has a direct relationship of ppi with SDF2L1 (gene/protein).', 'C10orf88 (gene/protein) has a direct relationship of ppi with NEDD1 (gene/protein).', 'NDUFB1 (gene/protein) has a direct relationship of ppi with SPPL2B (gene/protein).', 'ZNF668 (gene/protein) has a direct relationship of ppi with ZNF792 (gene/protein).', 'DMWD (gene/protein) has a direct relationship of ppi with VCP (gene/protein).', 'SPRY2 (gene/protein) has a direct relationship of ppi with CBLC (gene/protein).', 'CTNNB1 (gene/protein) has a direct relationship of ppi with TXN (gene/protein).', 'EXOC5 (gene/protein) has a direct relationship of ppi with DTNBP1 (gene/protein).', 'COPS6 (gene/protein) has a direct relationship of ppi with KLHL10 (gene/protein).', 'COX15 (gene/protein) has a direct relationship of ppi with GANAB (gene/protein).', 'UGT8 (gene/protein) has a direct relationship of ppi with TRDN (gene/protein).', 'GINS1 (gene/protein) has a direct relationship of ppi with TIPIN (gene/protein).', 'KIF5B (gene/protein) has a direct relationship of ppi with SNAP25 (gene/protein).', 'SLU7 (gene/protein) has a direct relationship of ppi with NSD3 (gene/protein).', 'KIFC3 (gene/protein) has a direct relationship of ppi with CEP55 (gene/protein).', 'ERBB2 (gene/protein) has a direct relationship of ppi with SRC (gene/protein).', 'UBE2D1 (gene/protein) has a direct relationship of ppi with TRIM26 (gene/protein).', 'MRPS30 (gene/protein) has a direct relationship of ppi with MRPL39 (gene/protein).', 'EGR1 (gene/protein) has a direct relationship of ppi with UBP1 (gene/protein).', 'YBX1 (gene/protein) has a direct relationship of ppi with PABPC1 (gene/protein).', 'SERF2 (gene/protein) has a direct relationship of ppi with TENT5A (gene/protein).', 'CTBP1 (gene/protein) has a direct relationship of ppi with FANCL (gene/protein).', 'RPL11 (gene/protein) has a direct relationship of ppi with RPS26 (gene/protein).', 'GLYAT (gene/protein) has a direct relationship of ppi with NBPF19 (gene/protein).', 'BAIAP2 (gene/protein) has a direct relationship of ppi with RTN4 (gene/protein).', 'PRPF4B (gene/protein) has a direct relationship of ppi with EFTUD2 (gene/protein).', 'HSPH1 (gene/protein) has a direct relationship of ppi with ANO3 (gene/protein).', 'AQP3 (gene/protein) has a direct relationship of ppi with LEUTX (gene/protein).', 'FARP2 (gene/protein) has a direct relationship of ppi with NCBP3 (gene/protein).', 'SMYD3 (gene/protein) has a direct relationship of ppi with H3-5 (gene/protein).', 'LGALS4 (gene/protein) has a direct relationship of ppi with BANP (gene/protein).', 'CDC20 (gene/protein) has a direct relationship of ppi with FBXO5 (gene/protein).', 'DLG4 (gene/protein) has a direct relationship of ppi with GRIA2 (gene/protein).', 'ZBTB33 (gene/protein) has a direct relationship of ppi with NANP (gene/protein).', 'RFTN1 (gene/protein) has a direct relationship of ppi with SLC25A41 (gene/protein).', 'DCTN1 (gene/protein) has a direct relationship of ppi with DERL1 (gene/protein).', 'PAX5 (gene/protein) has a direct relationship of ppi with LARP4 (gene/protein).', 'IL13RA2 (gene/protein) has a direct relationship of ppi with ALG5 (gene/protein).', 'ATR (gene/protein) has a direct relationship of ppi with AATF (gene/protein).', 'SYNGAP1 (gene/protein) has a direct relationship of ppi with MID2 (gene/protein).', 'COL5A1 (gene/protein) has a direct relationship of ppi with FN1 (gene/protein).', ...]
In [11]:
Copied!
# # For more detailed information, we can include head and tail node information in the enriched edge
# enriched_heads = primekg_edges.join(primekg_nodes.set_index('node_index'), on='head_index')[['enriched_node']].values.flatten().tolist()
# enriched_tails = primekg_edges.join(primekg_nodes.set_index('node_index'), on='tail_index')[['enriched_node']].values.flatten().tolist()
# # Concatenate the enriched head and tail nodes with the enriched edge
# mini_batch_size = 10000
# enriched_edges_final = []
# for i in tqdm(range(0, len(enriched_edges), mini_batch_size)):
# outputs = [f"{head} {edge} {tail}" for head, edge, tail in zip(enriched_heads[i:i+mini_batch_size], enriched_edges[i:i+mini_batch_size], enriched_tails[i:i+mini_batch_size])]
# enriched_edges_final.extend(outputs)
# enriched_edges_final
# # For more detailed information, we can include head and tail node information in the enriched edge
# enriched_heads = primekg_edges.join(primekg_nodes.set_index('node_index'), on='head_index')[['enriched_node']].values.flatten().tolist()
# enriched_tails = primekg_edges.join(primekg_nodes.set_index('node_index'), on='tail_index')[['enriched_node']].values.flatten().tolist()
# # Concatenate the enriched head and tail nodes with the enriched edge
# mini_batch_size = 10000
# enriched_edges_final = []
# for i in tqdm(range(0, len(enriched_edges), mini_batch_size)):
# outputs = [f"{head} {edge} {tail}" for head, edge, tail in zip(enriched_heads[i:i+mini_batch_size], enriched_edges[i:i+mini_batch_size], enriched_tails[i:i+mini_batch_size])]
# enriched_edges_final.extend(outputs)
# enriched_edges_final
In [12]:
Copied!
# Check the enriched edges
# primekg_edges['enriched_edge'] = enriched_edges_final
primekg_edges['enriched_edge'] = enriched_edges
primekg_edges.head()
# Check the enriched edges
# primekg_edges['enriched_edge'] = enriched_edges_final
primekg_edges['enriched_edge'] = enriched_edges
primekg_edges.head()
Out[12]:
| head_index | head_name | head_source | head_id | head_type | tail_index | tail_name | tail_source | tail_id | tail_type | display_relation | relation | enriched_edge | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 0 | PHYHIP | NCBI | 9796 | gene/protein | 8889 | KIF15 | NCBI | 56992 | gene/protein | ppi | protein_protein | PHYHIP (gene/protein) has a direct relationshi... |
| 1 | 1 | GPANK1 | NCBI | 7918 | gene/protein | 2798 | PNMA1 | NCBI | 9240 | gene/protein | ppi | protein_protein | GPANK1 (gene/protein) has a direct relationshi... |
| 2 | 2 | ZRSR2 | NCBI | 8233 | gene/protein | 5646 | TTC33 | NCBI | 23548 | gene/protein | ppi | protein_protein | ZRSR2 (gene/protein) has a direct relationship... |
| 3 | 3 | NRF1 | NCBI | 4899 | gene/protein | 11592 | MAN1B1 | NCBI | 11253 | gene/protein | ppi | protein_protein | NRF1 (gene/protein) has a direct relationship ... |
| 4 | 4 | PI4KA | NCBI | 5297 | gene/protein | 2122 | RGS20 | NCBI | 8601 | gene/protein | ppi | protein_protein | PI4KA (gene/protein) has a direct relationship... |
Textual Embedding over PrimeKG¶
We can perform embedding using the enriched nodes and edges using EmbeddingWithSentenceTransformer class.
Here we will use nomic-ai/nomic-embed-text provided by HuggingFace via sentence_transformer library to embed the enriched nodes and edges.
In short, the model nomic-ai/nomic-embed-text requires us to add pre-fix as follows:
search_document: <text here>for embedding texts as documents, for example as documents for a RAG index.search_query: <text here>for embedding texts as questions that documents from a dataset could resolve, for example as queries to be answered by a RAG application.
For more detailed information on this embedding model, please refer to the documentation:
In [13]:
Copied!
# Using nomic-ai/nomic-embed-text-v1.5 model with half precision for faster embedding
emb_model = EmbeddingWithSentenceTransformer(model_name='nomic-ai/nomic-embed-text-v1.5',
model_cache_dir="../../../../data/nomic-ai/nomic-embed-text-v1.5/",
trust_remote_code=True)
# Using nomic-ai/nomic-embed-text-v1.5 model with half precision for faster embedding
emb_model = EmbeddingWithSentenceTransformer(model_name='nomic-ai/nomic-embed-text-v1.5',
model_cache_dir="../../../../data/nomic-ai/nomic-embed-text-v1.5/",
trust_remote_code=True)
INFO:sentence_transformers.SentenceTransformer:Use pytorch device_name: cuda INFO:sentence_transformers.SentenceTransformer:Load pretrained SentenceTransformer: nomic-ai/nomic-embed-text-v1.5 WARNING:transformers_modules.nomic-ai.nomic-bert-2048.40b98394640e630d5276807046089b233113aa87.modeling_hf_nomic_bert:<All keys matched successfully>
Query Embedding¶
Load the pre-processed embeddings, if available.
In [8]:
Copied!
# # # Load the enriched nodes dataframe from parquet file
# starkqa_df = pd.read_parquet(os.path.join(starkqa_data.local_dir, 'starkqaprimekg_queries_embedded.parquet'), engine='pyarrow')
# # Check the dataframe of query embeddings
# starkqa_df.head()
# # # Load the enriched nodes dataframe from parquet file
# starkqa_df = pd.read_parquet(os.path.join(starkqa_data.local_dir, 'starkqaprimekg_queries_embedded.parquet'), engine='pyarrow')
# # Check the dataframe of query embeddings
# starkqa_df.head()
Out[8]:
| node_index | node_name | node_source | node_id | node_type | enriched_node | |
|---|---|---|---|---|---|---|
| 0 | 0 | PHYHIP | NCBI | 9796 | gene/protein | PHYHIP belongs to gene/protein category. Enabl... |
| 1 | 1 | GPANK1 | NCBI | 7918 | gene/protein | GPANK1 belongs to gene/protein category. This ... |
| 2 | 2 | ZRSR2 | NCBI | 8233 | gene/protein | ZRSR2 belongs to gene/protein category. This g... |
| 3 | 3 | NRF1 | NCBI | 4899 | gene/protein | NRF1 belongs to gene/protein category. This ge... |
| 4 | 4 | PI4KA | NCBI | 5297 | gene/protein | PI4KA belongs to gene/protein category. This g... |
If there is no pre-processed query embeddings, run the following codes to generate embeddings.
Otherwise, skip the following cells and go to Node Embedding.
In [14]:
Copied!
# Prepend prefix to the query
starkqa_df['query_prefixed'] = starkqa_df['query'].apply(lambda x: f"search_query: {x}")
starkqa_df.head()
# Prepend prefix to the query
starkqa_df['query_prefixed'] = starkqa_df['query'].apply(lambda x: f"search_query: {x}")
starkqa_df.head()
Out[14]:
| id | query | answer_ids | query_prefixed | |
|---|---|---|---|---|
| 0 | 0 | Could you identify any skin diseases associate... | [95886] | search_query: Could you identify any skin dise... |
| 1 | 1 | What drugs target the CYP3A4 enzyme and are us... | [15450] | search_query: What drugs target the CYP3A4 enz... |
| 2 | 2 | What is the name of the condition characterize... | [98851, 98853] | search_query: What is the name of the conditio... |
| 3 | 3 | What drugs are used to treat epithelioid sarco... | [15698] | search_query: What drugs are used to treat epi... |
| 4 | 4 | Can you supply a compilation of genes and prot... | [7161, 22045] | search_query: Can you supply a compilation of ... |
In [15]:
Copied!
# Since the records of queries has large amount of data, we will split them into mini-batches
mini_batch_size = 1000
query_embeddings = []
for i in tqdm(range(0, starkqa_df.shape[0], mini_batch_size)):
outputs = emb_model.embed_documents(starkqa_df.query_prefixed.values.tolist()[i:i+mini_batch_size])
query_embeddings.extend(outputs)
query_embeddings
# Since the records of queries has large amount of data, we will split them into mini-batches
mini_batch_size = 1000
query_embeddings = []
for i in tqdm(range(0, starkqa_df.shape[0], mini_batch_size)):
outputs = emb_model.embed_documents(starkqa_df.query_prefixed.values.tolist()[i:i+mini_batch_size])
query_embeddings.extend(outputs)
query_embeddings
100%|██████████| 12/12 [00:06<00:00, 1.91it/s]
Out[15]: