Decoding the disease-associated proteins encoded in the human chromosome 4

Lien Chin Chen, Mei Ying Liu, Yung Chin Hsiao, Wai Kok Choong, Hsin Yi Wu, Wen Lian Hsu, Pao-Chi Liao, Ting Yi Sung, Shih Feng Tsai, Jau Song Yu, Yu Ju Chen

Research output: Contribution to journalReview article

4 Citations (Scopus)

Abstract

Chromosome 4 is the fourth largest chromosome, containing approximately 191 megabases (∼6.4% of the human genome) with 757 protein-coding genes. A number of marker genes for many diseases have been found in this chromosome, including genetic diseases (e.g., hepatocellular carcinoma) and biomedical research (cardiac system, aging, metabolic disorders, immune system, cancer and stem cell) related genes (e.g., oncogenes, growth factors). As a pilot study for the chromosome 4-centric human proteome project (Chr 4-HPP), we present here a systematic analysis of the disease association, protein isoforms, coding single nucleotide polymorphisms of these 757 protein-coding genes and their experimental evidence at the protein level. We also describe how the findings from the chromosome 4 project might be used to drive the biomarker discovery and validation study in disease-oriented projects, using the examples of secretomic and membrane proteomic approaches in cancer research. By integrating with cancer cell secretomes and several other existing databases in the public domain, we identified 141 chromosome 4-encoded proteins as cancer cell-secretable/shedable proteins. Additionally, we also identified 54 chromosome 4-encoded proteins that have been classified as cancer-associated proteins with successful selected or multiple reaction monitoring (SRM/MRM) assays developed. From literature annotation and topology analysis, 271 proteins were recognized as membrane proteins while 27.9% of the 757 proteins do not have any experimental evidence at the protein-level. In summary, the analysis revealed that the chromosome 4 is a rich resource for cancer-associated proteins for biomarker verification projects and for drug target discovery projects.

Original languageEnglish
Pages (from-to)33-44
Number of pages12
JournalJournal of Proteome Research
Volume12
Issue number1
DOIs
Publication statusPublished - 2013 Jan 4

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Chromosomes, Human, Pair 4
Human Chromosomes
Chromosomes
Decoding
Proteins
Genes
Biomarkers
Neoplasms
Cells
Inborn Genetic Diseases
Neoplastic Stem Cells
Validation Studies
Public Sector
Immune system
Human Genome
Drug Discovery
Proteome
Stem cells
Polymorphism
Oncogenes

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Chemistry(all)

Cite this

Chen, L. C., Liu, M. Y., Hsiao, Y. C., Choong, W. K., Wu, H. Y., Hsu, W. L., ... Chen, Y. J. (2013). Decoding the disease-associated proteins encoded in the human chromosome 4. Journal of Proteome Research, 12(1), 33-44. https://doi.org/10.1021/pr300829r
Chen, Lien Chin ; Liu, Mei Ying ; Hsiao, Yung Chin ; Choong, Wai Kok ; Wu, Hsin Yi ; Hsu, Wen Lian ; Liao, Pao-Chi ; Sung, Ting Yi ; Tsai, Shih Feng ; Yu, Jau Song ; Chen, Yu Ju. / Decoding the disease-associated proteins encoded in the human chromosome 4. In: Journal of Proteome Research. 2013 ; Vol. 12, No. 1. pp. 33-44.
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title = "Decoding the disease-associated proteins encoded in the human chromosome 4",
abstract = "Chromosome 4 is the fourth largest chromosome, containing approximately 191 megabases (∼6.4{\%} of the human genome) with 757 protein-coding genes. A number of marker genes for many diseases have been found in this chromosome, including genetic diseases (e.g., hepatocellular carcinoma) and biomedical research (cardiac system, aging, metabolic disorders, immune system, cancer and stem cell) related genes (e.g., oncogenes, growth factors). As a pilot study for the chromosome 4-centric human proteome project (Chr 4-HPP), we present here a systematic analysis of the disease association, protein isoforms, coding single nucleotide polymorphisms of these 757 protein-coding genes and their experimental evidence at the protein level. We also describe how the findings from the chromosome 4 project might be used to drive the biomarker discovery and validation study in disease-oriented projects, using the examples of secretomic and membrane proteomic approaches in cancer research. By integrating with cancer cell secretomes and several other existing databases in the public domain, we identified 141 chromosome 4-encoded proteins as cancer cell-secretable/shedable proteins. Additionally, we also identified 54 chromosome 4-encoded proteins that have been classified as cancer-associated proteins with successful selected or multiple reaction monitoring (SRM/MRM) assays developed. From literature annotation and topology analysis, 271 proteins were recognized as membrane proteins while 27.9{\%} of the 757 proteins do not have any experimental evidence at the protein-level. In summary, the analysis revealed that the chromosome 4 is a rich resource for cancer-associated proteins for biomarker verification projects and for drug target discovery projects.",
author = "Chen, {Lien Chin} and Liu, {Mei Ying} and Hsiao, {Yung Chin} and Choong, {Wai Kok} and Wu, {Hsin Yi} and Hsu, {Wen Lian} and Pao-Chi Liao and Sung, {Ting Yi} and Tsai, {Shih Feng} and Yu, {Jau Song} and Chen, {Yu Ju}",
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Chen, LC, Liu, MY, Hsiao, YC, Choong, WK, Wu, HY, Hsu, WL, Liao, P-C, Sung, TY, Tsai, SF, Yu, JS & Chen, YJ 2013, 'Decoding the disease-associated proteins encoded in the human chromosome 4', Journal of Proteome Research, vol. 12, no. 1, pp. 33-44. https://doi.org/10.1021/pr300829r

Decoding the disease-associated proteins encoded in the human chromosome 4. / Chen, Lien Chin; Liu, Mei Ying; Hsiao, Yung Chin; Choong, Wai Kok; Wu, Hsin Yi; Hsu, Wen Lian; Liao, Pao-Chi; Sung, Ting Yi; Tsai, Shih Feng; Yu, Jau Song; Chen, Yu Ju.

In: Journal of Proteome Research, Vol. 12, No. 1, 04.01.2013, p. 33-44.

Research output: Contribution to journalReview article

TY - JOUR

T1 - Decoding the disease-associated proteins encoded in the human chromosome 4

AU - Chen, Lien Chin

AU - Liu, Mei Ying

AU - Hsiao, Yung Chin

AU - Choong, Wai Kok

AU - Wu, Hsin Yi

AU - Hsu, Wen Lian

AU - Liao, Pao-Chi

AU - Sung, Ting Yi

AU - Tsai, Shih Feng

AU - Yu, Jau Song

AU - Chen, Yu Ju

PY - 2013/1/4

Y1 - 2013/1/4

N2 - Chromosome 4 is the fourth largest chromosome, containing approximately 191 megabases (∼6.4% of the human genome) with 757 protein-coding genes. A number of marker genes for many diseases have been found in this chromosome, including genetic diseases (e.g., hepatocellular carcinoma) and biomedical research (cardiac system, aging, metabolic disorders, immune system, cancer and stem cell) related genes (e.g., oncogenes, growth factors). As a pilot study for the chromosome 4-centric human proteome project (Chr 4-HPP), we present here a systematic analysis of the disease association, protein isoforms, coding single nucleotide polymorphisms of these 757 protein-coding genes and their experimental evidence at the protein level. We also describe how the findings from the chromosome 4 project might be used to drive the biomarker discovery and validation study in disease-oriented projects, using the examples of secretomic and membrane proteomic approaches in cancer research. By integrating with cancer cell secretomes and several other existing databases in the public domain, we identified 141 chromosome 4-encoded proteins as cancer cell-secretable/shedable proteins. Additionally, we also identified 54 chromosome 4-encoded proteins that have been classified as cancer-associated proteins with successful selected or multiple reaction monitoring (SRM/MRM) assays developed. From literature annotation and topology analysis, 271 proteins were recognized as membrane proteins while 27.9% of the 757 proteins do not have any experimental evidence at the protein-level. In summary, the analysis revealed that the chromosome 4 is a rich resource for cancer-associated proteins for biomarker verification projects and for drug target discovery projects.

AB - Chromosome 4 is the fourth largest chromosome, containing approximately 191 megabases (∼6.4% of the human genome) with 757 protein-coding genes. A number of marker genes for many diseases have been found in this chromosome, including genetic diseases (e.g., hepatocellular carcinoma) and biomedical research (cardiac system, aging, metabolic disorders, immune system, cancer and stem cell) related genes (e.g., oncogenes, growth factors). As a pilot study for the chromosome 4-centric human proteome project (Chr 4-HPP), we present here a systematic analysis of the disease association, protein isoforms, coding single nucleotide polymorphisms of these 757 protein-coding genes and their experimental evidence at the protein level. We also describe how the findings from the chromosome 4 project might be used to drive the biomarker discovery and validation study in disease-oriented projects, using the examples of secretomic and membrane proteomic approaches in cancer research. By integrating with cancer cell secretomes and several other existing databases in the public domain, we identified 141 chromosome 4-encoded proteins as cancer cell-secretable/shedable proteins. Additionally, we also identified 54 chromosome 4-encoded proteins that have been classified as cancer-associated proteins with successful selected or multiple reaction monitoring (SRM/MRM) assays developed. From literature annotation and topology analysis, 271 proteins were recognized as membrane proteins while 27.9% of the 757 proteins do not have any experimental evidence at the protein-level. In summary, the analysis revealed that the chromosome 4 is a rich resource for cancer-associated proteins for biomarker verification projects and for drug target discovery projects.

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U2 - 10.1021/pr300829r

DO - 10.1021/pr300829r

M3 - Review article

VL - 12

SP - 33

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JF - Journal of Proteome Research

SN - 1535-3893

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ER -