Bioinformatics Annotation of Human Y Chromosome-Encoded Protein Pathways and Interactions

J Proteome Res. 2015 Sep 4;14(9):3503-18. doi: 10.1021/acs.jproteome.5b00491. Epub 2015 Aug 21.


We performed a comprehensive analysis of human Y chromosome-encoded proteins, their pathways, and their interactions using bioinformatics tools. From the NCBI annotation release 107 of human genome, we retrieved a total of 66 proteins encoded on Y chromosome. Most of the retrieved proteins were also matched with the proteins listed in the core databases of the Human Proteome Project including neXtProt, PeptideAtlas, and the Human Protein Atlas. When we examined the pathways of human Y-encoded proteins through KEGG database and Pathway Studio software, many of proteins fall into the categories related to cell signaling pathways. Using the STRING program, we found a total of 49 human Y-encoded proteins showing strong/medium interaction with each other. While using the Pathway studio software, we found that a total of 16 proteins interact with other chromosome-encoded proteins. In particular, the SRY protein interacted with 17 proteins encoded on other chromosomes. Additionally, we aligned the sequences of human Y-encoded proteins with the sequences of chimpanzee and mouse Y-encoded proteins using the NCBI BLAST program. This analysis resulted in a significant number of orthologous proteins between human, chimpanzee, and mouse. Collectively, our findings provide the scientific community with additional information on the human Y chromosome-encoded proteins.

Keywords: Chromosome-Centric Human Proteome Project (C-HPP); human Y chromosome; protein annotation; protein interactions; protein orthologs; protein pathways.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromosomes, Human, Y*
  • Computational Biology*
  • Humans
  • Mice
  • Pan troglodytes
  • Proteins / genetics*


  • Proteins