Functional annotation of proteome encoded by human chromosome 22

Sneha M. Pinto, Srikanth S. Manda, Min Sik Kim, Kyonese Taylor, Lakshmi Dhevi Nagarajha Selvan, Lavanya Balakrishnan, Tejaswini Subbannayya, Fangfei Yan, T. S Keshava Prasad, Harsha Gowda, Charles Lee, William S. Hancock, Akhilesh Pandey

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)2749-2760
Number of pages12
JournalJournal of Proteome Research
Volume13
Issue number6
DOIs
StatePublished - Jun 6 2014

Fingerprint

Chromosomes, Human, Pair 22
Human Chromosomes
Proteome
Chromosomes
Genes
Proteins
beta-Crystallins
Gene Dosage
Base Pairing
Proteomics
Open Reading Frames
Immunoglobulins
Exons
Mass Spectrometry
Tissue
Mass spectrometry
Tumors
Pipelines
Neoplasms

Keywords

  • "missing" proteins
  • genome annotation
  • human proteome
  • uORF

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)
  • Medicine(all)

Cite this

Pinto, S. M., Manda, S. S., Kim, M. S., Taylor, K., Selvan, L. D. N., Balakrishnan, L., ... Pandey, A. (2014). Functional annotation of proteome encoded by human chromosome 22. Journal of Proteome Research, 13(6), 2749-2760. https://doi.org/10.1021/pr401169d

Functional annotation of proteome encoded by human chromosome 22. / Pinto, Sneha M.; Manda, Srikanth S.; Kim, Min Sik; Taylor, Kyonese; Selvan, Lakshmi Dhevi Nagarajha; Balakrishnan, Lavanya; Subbannayya, Tejaswini; Yan, Fangfei; Prasad, T. S Keshava; Gowda, Harsha; Lee, Charles; Hancock, William S.; Pandey, Akhilesh.

In: Journal of Proteome Research, Vol. 13, No. 6, 06.06.2014, p. 2749-2760.

Research output: Contribution to journalArticle

Pinto, SM, Manda, SS, Kim, MS, Taylor, K, Selvan, LDN, Balakrishnan, L, Subbannayya, T, Yan, F, Prasad, TSK, Gowda, H, Lee, C, Hancock, WS & Pandey, A 2014, 'Functional annotation of proteome encoded by human chromosome 22', Journal of Proteome Research, vol. 13, no. 6, pp. 2749-2760. https://doi.org/10.1021/pr401169d
Pinto SM, Manda SS, Kim MS, Taylor K, Selvan LDN, Balakrishnan L et al. Functional annotation of proteome encoded by human chromosome 22. Journal of Proteome Research. 2014 Jun 6;13(6):2749-2760. https://doi.org/10.1021/pr401169d
Pinto, Sneha M. ; Manda, Srikanth S. ; Kim, Min Sik ; Taylor, Kyonese ; Selvan, Lakshmi Dhevi Nagarajha ; Balakrishnan, Lavanya ; Subbannayya, Tejaswini ; Yan, Fangfei ; Prasad, T. S Keshava ; Gowda, Harsha ; Lee, Charles ; Hancock, William S. ; Pandey, Akhilesh. / Functional annotation of proteome encoded by human chromosome 22. In: Journal of Proteome Research. 2014 ; Vol. 13, No. 6. pp. 2749-2760.
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