title: Proteogenomic analysis of human chromosome 9-encoded genes from human samples and lung cancer tissues.
abstract: The Chromosome-centric Human Proteome Project (C-HPP) was recently initiated as an international collaborative effort. Our team adopted chromosome 9 (Chr 9) and performed a bioinformatics and proteogenomic analysis to catalog Chr 9-encoded proteins from normal tissues, lung cancer cell lines, and lung cancer tissues. Approximately 74.7% of the Chr 9 genes of the human genome were identified, which included approximately 28% of missing proteins (46 of 162) on Chr 9 compared with the list of missing proteins from the neXtProt Master Table (2013-09). In addition, we performed a comparative proteomics analysis between normal lung and lung cancer tissues. On the basis of the data analysis, 15 proteins from Chr 9 were detected only in lung cancer tissues. Finally, we conducted a proteogenomic analysis to discover Chr 9-residing single nucleotide polymorphisms (SNP) and mutations described in the COSMIC cancer mutation database. We identified 21 SNPs and four mutations containing peptides on Chr 9 from normal human cells/tissues and lung cancer cell lines, respectively. In summary, this study provides valuable information of the human proteome for the scientific community as part of C-HPP. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD000603.
authors.affiliation: Department of Biochemistry, College of Veterinary Medicine, Seoul National University , Seoul, Korea.
authors.forename: Jung-Mo
authors.initials: JM
authors.lastname: Ahn
authors.forename: Min-Sik
authors.initials: MS
authors.lastname: Kim
authors.forename: Yong-In
authors.initials: YI
authors.lastname: Kim
authors.forename: Seul-Ki
authors.initials: SK
authors.lastname: Jeong
authors.forename: Hyoung-Joo
authors.initials: HJ
authors.lastname: Lee
authors.forename: Sun Hee
authors.initials: SH
authors.lastname: Lee
authors.forename: Young-Ki
authors.initials: YK
authors.lastname: Paik
authors.forename: Akhilesh
authors.initials: A
authors.lastname: Pandey
authors.forename: Je-Yoel
authors.initials: JY
authors.lastname: Cho
mesh_terms: D002899:Chromosomes, Human, Pair 9; D015894:Genome, Human; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics*; D009154:Mutation; D020641:Polymorphism, Single Nucleotide; D020543:Proteome
chemical_list: D020543:Proteome