PPIs Stats

Organisms	Binary Interactions*	Complexes**
Homo sapiens	439,714	15,252
Saccharomyces cerevisiae	128,319	6,302
Caenorhabditis elegans	22,305	105
Drosophila melanogaster	57,578	810
Mus musculus	57,669	1,304
Rattus norvegicus	5,796	307
Arabidopsis thaliana	56,282	431

* Number of interactions: The number is the sum of self-interaction and binary interaction that all participating proteins have UniProt Accession Number.
** Number of complexes: The number is the sum of complexes that all participating proteins have UniProt Accession Number.

  Data Sources

Original Database	Version
IntAct	version 4.2.15
BioGRID	version 3.5.185
MINT	May 21, 2020
DIP	version 20170205
HPRD	release 9

We identified the same interaction records in the different databases to build a non-redundant dataset.
We also utilized BioMart and UniProt to annotate each protein with the same high-quality information because some of the original records have limited annotation.

Previous releases

  Data Sources & Preprocessing

• Tumor type-specific cancer driver genes were from a recent TCGA Pan-cancer analysis of 9,423 tumor exomes.
• Targets of therapeutic compounds were downloaded from the Genomics of Drug Sensitivity in Cancer (GDSC).
• Cancer transcriptome profiles were downloaded from the Genomic Data Commons (GDC) portal of TCGA (version 20190101). The batch-corrected and upper quartile normalized RSEM measurements were log2 transformed for mRNA expression analysis.
• Cancer proteome data were downloaded from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) data portal (version 20200511). The relative abundance of proteins generated by the Common Data Analysis Pipeline (CDAP) was subjected to quantile normalization using the normalizeQuantiles function implemented in R package limma v3.36.1.
• Both mRNA and protein expression datasets were further filtered by removing genes with zero or NA values in more than 80% of samples.
• Clinical data (survival time, tumor site, age, ethnicity, and grade) were downloaded from both GDC and CPTAC for corresponding samples with molecular data.

  Data Policy

We adhere all aspects of data access and usage policies of the original studies. PINA users should strictly adhere to the policies of the NIH Genomic Data Sharing (GDS) Policy for utilizing RNA-seq/clinical data integrated into PINA, and the CPTAC Data Use Agreement for utilizing proteomic data integrated into PINA.

  Data Stats

mRNA expression datasets:

Dataset name	Cancer name	No. of patients*	No. of genes
TCGA-ACC	Adrenocortical carcinoma	79	18,136
TCGA-BLCA	Bladder Urothelial Carcinoma	408	18,558
TCGA-BRCA	Breast invasive carcinoma	1,095	18,563
TCGA-CESC	Cervical squamous cell carcinoma and endocervical adenocarcinoma	304	18,491
TCGA-CHOL	Cholangiocarcinoma	36	18,377
TCGA-COAD	Colon adenocarcinoma	451	18,039
TCGA-DLBC	Lymphoid Neoplasm Diffuse Large B-cell Lymphoma	48	18,158
TCGA-ESCA	Esophageal carcinoma	184	18,963
TCGA-GBM	Glioblastoma multiforme	154	18,473
TCGA-HNSC	Head and Neck squamous cell carcinoma	520	18,671
TCGA-KICH	Kidney Chromophobe	66	18,152
TCGA-KIRC	Kidney renal clear cell carcinoma	533	18,588
TCGA-KIRP	Kidney renal papillary cell carcinoma	290	18,331
TCGA-LAML	Acute Myeloid Leukemia	173	16,731
TCGA-LIHC	Liver hepatocellular carcinoma	371	18,419
TCGA-LUAD	Lung adenocarcinoma	515	18,620
TCGA-LGG	Brain Lower Grade Glioma	516	18,586
TCGA-LUSC	Lung squamous cell carcinoma	501	18,777
TCGA-MESO	Mesothelioma	87	18,488
TCGA-OV	Ovarian serous cystadenocarcinoma	304	18,950
TCGA-PAAD	Pancreatic adenocarcinoma	178	18,709
TCGA-PCPG	Pheochromocytoma and Paraganglioma	179	18,318
TCGA-PRAD	Prostate adenocarcinoma	497	18,710
TCGA-READ	Rectum adenocarcinoma	160	18,040
TCGA-SARC	Sarcoma	259	18,582
TCGA-SKCM	Skin Cutaneous Melanoma	103	18,422
TCGA-STAD	Stomach adenocarcinoma	415	18,972
TCGA-TGCT	Testicular Germ Cell Tumors	150	19,270
TCGA-THCA	Thyroid carcinoma	505	18,307
TCGA-THYM	Thymoma	120	18,561
TCGA-UCEC	Uterine Corpus Endometrial Carcinoma	532	17,629
TCGA-UCS	Uterine Carcinosarcoma	57	18,918
TCGA-UVM	Uveal Melanoma	80	17,679

Protein expression datasets:

Dataset name	Cancer name	No. of patients*	No. of proteins
CPTAC-CCRCC	Clear Cell Renal Cell Carcinoma	110	9,445
CPTAC-COAD	Colon Adenocarcinoma	97	7,057
CPTAC-EC	Endometrial Carcinoma	100	10,418
CPTAC-GC	Gastric Cancer	80	8,732
CPTAC-HCC	Hepatocellular Carcinoma	159	9,682
CPTAC-LUAD	Lung Adenocarcinoma	111	10,546
TCGA-BRCA	Breast Invasive Carcinoma	105	9,747
TCGA-OV	Ovarian Serous Cystadenocarcinoma	174	7,703

* Only primary tumors were included.