title: A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17.
abstract: We report progress assembling the parts list for chromosome 17 and illustrate the various processes that we have developed to integrate available data from diverse genomic and proteomic knowledge bases. As primary resources, we have used GPMDB, neXtProt, PeptideAtlas, Human Protein Atlas (HPA), and GeneCards. All sites share the common resource of Ensembl for the genome modeling information. We have defined the chromosome 17 parts list with the following information: 1169 protein-coding genes, the numbers of proteins confidently identified by various experimental approaches as documented in GPMDB, neXtProt, PeptideAtlas, and HPA, examples of typical data sets obtained by RNASeq and proteomic studies of epithelial derived tumor cell lines (disease proteome) and a normal proteome (peripheral mononuclear cells), reported evidence of post-translational modifications, and examples of alternative splice variants (ASVs). We have constructed a list of the 59 "missing" proteins as well as 201 proteins that have inconclusive mass spectrometric (MS) identifications. In this report we have defined a process to establish a baseline for the incorporation of new evidence on protein identification and characterization as well as related information from transcriptome analyses. This initial list of "missing" proteins that will guide the selection of appropriate samples for discovery studies as well as antibody reagents. Also we have illustrated the significant diversity of protein variants (including post-translational modifications, PTMs) using regions on chromosome 17 that contain important oncogenes. We emphasize the need for mandated deposition of proteomics data in public databases, the further development of improved PTM, ASV, and single nucleotide variant (SNV) databases, and the construction of Web sites that can integrate and regularly update such information. In addition, we describe the distribution of both clustered and scattered sets of protein families on the chromosome. Since chromosome 17 is rich in cancer-associated genes, we have focused the clustering of cancer-associated genes in such genomic regions and have used the ERBB2 amplicon as an example of the value of a proteogenomic approach in which one integrates transcriptomic with proteomic information and captures evidence of coexpression through coordinated regulation.
authors.affiliation: Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States.
authors.forename: Suli
authors.initials: S
authors.lastname: Liu
authors.forename: Hogune
authors.initials: H
authors.lastname: Im
authors.forename: Amos
authors.initials: A
authors.lastname: Bairoch
authors.forename: Massimo
authors.initials: M
authors.lastname: Cristofanilli
authors.forename: Rui
authors.initials: R
authors.lastname: Chen
authors.forename: Eric W
authors.initials: EW
authors.lastname: Deutsch
authors.forename: Stephen
authors.initials: S
authors.lastname: Dalton
authors.forename: David
authors.initials: D
authors.lastname: Fenyo
authors.forename: Susan
authors.initials: S
authors.lastname: Fanayan
authors.forename: Chris
authors.initials: C
authors.lastname: Gates
authors.forename: Pascale
authors.initials: P
authors.lastname: Gaudet
authors.forename: Marina
authors.initials: M
authors.lastname: Hincapie
authors.forename: Samir
authors.initials: S
authors.lastname: Hanash
authors.forename: Hoguen
authors.initials: H
authors.lastname: Kim
authors.forename: Seul-Ki
authors.initials: SK
authors.lastname: Jeong
authors.forename: Emma
authors.initials: E
authors.lastname: Lundberg
authors.forename: George
authors.initials: G
authors.lastname: Mias
authors.forename: Rajasree
authors.initials: R
authors.lastname: Menon
authors.forename: Zhaomei
authors.initials: Z
authors.lastname: Mu
authors.forename: Edouard
authors.initials: E
authors.lastname: Nice
authors.forename: Young-Ki
authors.initials: YK
authors.lastname: Paik
authors.forename: Mathias
authors.initials: M
authors.lastname: Uhlen
authors.forename: Lance
authors.initials: L
authors.lastname: Wells
authors.forename: Shiaw-Lin
authors.initials: SL
authors.lastname: Wu
authors.forename: Fangfei
authors.initials: F
authors.lastname: Yan
authors.forename: Fan
authors.initials: F
authors.lastname: Zhang
authors.forename: Yue
authors.initials: Y
authors.lastname: Zhang
authors.forename: Michael
authors.initials: M
authors.lastname: Snyder
authors.forename: Gilbert S
authors.initials: GS
authors.lastname: Omenn
authors.forename: Ronald C
authors.initials: RC
authors.lastname: Beavis
authors.forename: William S
authors.initials: WS
authors.lastname: Hancock
mesh_terms: D000595:Amino Acid Sequence; D002886:Chromosomes, Human, Pair 17 / Q000235:genetics / Q000378:metabolism; D030562:Databases, Protein; D015870:Gene Expression; D015894:Genome, Human; D016045:Human Genome Project; D006801:Humans; D011506:Proteins / Q000145:classification / Q000235:genetics / Q000378:metabolism; D040901:Proteomics
chemical_list: D011506:Proteins