The human protein-protein interaction (PPI) data were downloaded from the Protein Interaction Network Analysis (PINA) platform (May 21, 2014) [19], which integrated data from six major public PPI databases, namely IntAct, BioGRID, MINT, DIP, HPRD, and MIPS/MPact. Also, we downloaded the related annotation files from NCBI (ftp://ftp.ncbi.nlm.nih.gov/gene/) (May 24, 2014), including the Entrez gene information database of human (Homo_sapiens.gene_info.gz), the dataset specifying relationship between pairs of NCBI and UniProtKB protein accessions (gene_refseq_uniprotkb_collab.dz), and file containing mappings of Entrez Gene records to Entrez RefSeq Nucleotide sequence records (gene2refseq.gz). Then the human PPI data were mapped to NCBI human protein-coding genes and the unmapped proteins were discarded. After removing self-interactions and redundant interacting pairs, a final human PPI network containing 15,093 nodes and 161,419 edges was obtained.
