title: Functional annotation of proteome encoded by human chromosome 22.
abstract: As part of the chromosome-centric human proteome project (C-HPP) initiative, we report our progress on the annotation of chromosome 22. Chromosome 22, spanning 51 million base pairs, was the first chromosome to be sequenced. Gene dosage alterations on this chromosome have been shown to be associated with a number of congenital anomalies. In addition, several rare but aggressive tumors have been associated with this chromosome. A number of important gene families including immunoglobulin lambda locus, Crystallin beta family, and APOBEC gene family are located on this chromosome. On the basis of proteomic profiling of 30 histologically normal tissues and cells using high-resolution mass spectrometry, we show protein evidence of 367 genes on chromosome 22. Importantly, this includes 47 proteins, which are currently annotated as "missing" proteins. We also confirmed the translation start sites of 120 chromosome 22-encoded proteins. Employing a comprehensive proteogenomics analysis pipeline, we provide evidence of novel coding regions on this chromosome which include upstream ORFs and novel exons in addition to correcting existing gene structures. We describe tissue-wise expression of the proteins and the distribution of gene families on this chromosome. These data have been deposited to ProteomeXchange with the identifier PXD000561.
authors.affiliation: Institute of Bioinformatics, International Tech Park , Bangalore, Karnataka 560066, India.
authors.forename: Sneha M
authors.initials: SM
authors.lastname: Pinto
authors.forename: Srikanth S
authors.initials: SS
authors.lastname: Manda
authors.forename: Min-Sik
authors.initials: MS
authors.lastname: Kim
authors.forename: KyOnese
authors.initials: K
authors.lastname: Taylor
authors.forename: Lakshmi Dhevi Nagarajha
authors.initials: LD
authors.lastname: Selvan
authors.forename: Lavanya
authors.initials: L
authors.lastname: Balakrishnan
authors.forename: Tejaswini
authors.initials: T
authors.lastname: Subbannayya
authors.forename: Fangfei
authors.initials: F
authors.lastname: Yan
authors.forename: T S Keshava
authors.initials: TS
authors.lastname: Prasad
authors.forename: Harsha
authors.initials: H
authors.lastname: Gowda
authors.forename: Charles
authors.initials: C
authors.lastname: Lee
authors.forename: William S
authors.initials: WS
authors.lastname: Hancock
authors.forename: Akhilesh
authors.initials: A
authors.lastname: Pandey
mesh_terms: D000595:Amino Acid Sequence; D002892:Chromosomes, Human, Pair 22 / Q000235:genetics*; D052138:Genes, Neoplasm; D006801:Humans; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010449:Peptide Mapping; D020543:Proteome / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D040901:Proteomics
chemical_list: D020543:Proteome