Proteogenomic analysis of human chromosome 9-encoded genes from human samples and lung cancer tissues

Jung Mo Ahn, Min Sik Kim, Yong In Kim, Seul Ki Jeong, Hyoung Joo Lee, Sun Hee Lee, Young-Ki Paik, Akhilesh Pandey, Je Yoel Cho

Research output: Contribution to journalArticle

14 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)137-146
Number of pages10
JournalJournal of Proteome Research
Volume13
Issue number1
DOIs
Publication statusPublished - 2014 Jan 3

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Chromosomes, Human, Pair 9
Human Chromosomes
Chromosomes
Lung Neoplasms
Genes
Tissue
Proteome
Proteomics
Mutation
Single Nucleotide Polymorphism
Cells
Proteins
Cell Line
Human Genome
Proteogenomics
Computational Biology
Mass Spectrometry
Bioinformatics
Polymorphism
Databases

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Chemistry(all)

Cite this

Ahn, J. M., Kim, M. S., Kim, Y. I., Jeong, S. K., Lee, H. J., Lee, S. H., ... Cho, J. Y. (2014). Proteogenomic analysis of human chromosome 9-encoded genes from human samples and lung cancer tissues. Journal of Proteome Research, 13(1), 137-146. https://doi.org/10.1021/pr400792p
Ahn, Jung Mo ; Kim, Min Sik ; Kim, Yong In ; Jeong, Seul Ki ; Lee, Hyoung Joo ; Lee, Sun Hee ; Paik, Young-Ki ; Pandey, Akhilesh ; Cho, Je Yoel. / Proteogenomic analysis of human chromosome 9-encoded genes from human samples and lung cancer tissues. In: Journal of Proteome Research. 2014 ; Vol. 13, No. 1. pp. 137-146.
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Ahn, JM, Kim, MS, Kim, YI, Jeong, SK, Lee, HJ, Lee, SH, Paik, Y-K, Pandey, A & Cho, JY 2014, 'Proteogenomic analysis of human chromosome 9-encoded genes from human samples and lung cancer tissues', Journal of Proteome Research, vol. 13, no. 1, pp. 137-146. https://doi.org/10.1021/pr400792p

Proteogenomic analysis of human chromosome 9-encoded genes from human samples and lung cancer tissues. / Ahn, Jung Mo; Kim, Min Sik; Kim, Yong In; Jeong, Seul Ki; Lee, Hyoung Joo; Lee, Sun Hee; Paik, Young-Ki; Pandey, Akhilesh; Cho, Je Yoel.

In: Journal of Proteome Research, Vol. 13, No. 1, 03.01.2014, p. 137-146.

Research output: Contribution to journalArticle

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