Functional Annotation of the Human Chromosome 7 “Missing” Proteins: A Bioinformatics Approach

The chromosome-centric human proteome project aims to
systematically
map all human proteins, chromosome by chromosome, in a gene-centric
manner through dedicated efforts from national and international teams.
This mapping will lead to a knowledge-based resource defining the
full set of proteins encoded in each chromosome and laying the foundation
for the development of a standardized approach to analyze the massive
proteomic data sets currently being generated. The neXtProt database
lists 946 proteins as the human proteome of chromosome 7. However,
170 (18%) proteins of human chromosome 7 have no evidence at the proteomic,
antibody, or structural levels and are considered “missing”
in this study as they lack experimental support. We have developed
a protocol for the functional annotation of these “missing”
proteins by integrating several bioinformatics analysis and annotation
tools, sequential BLAST homology searches, protein domain/motif and
gene ontology (GO) mapping, and Kyoto Encyclopedia of Genes and Genomes
(KEGG) pathway analysis. Using the BLAST search strategy, homologues
for reviewed non-human mammalian proteins with protein evidence were
identified for 90 “missing” proteins while another 38
had reviewed non-human mammalian homologues. Putative functional annotations
were assigned to 27 of the remaining 43 novel proteins. Proteotypic
peptides have been computationally generated to facilitate rapid identification
of these proteins. Four of the “missing” chromosome
7 proteins have been substantiated by the ENCODE proteogenomic peptide
data.