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 language | English |
|---|---|
| Pages (from-to) | 33-44 |
| Number of pages | 12 |
| Journal | Journal of Proteome Research |
| Volume | 12 |
| Issue number | 1 |
| DOIs | |
| Publication status | Published - 2013 Jan 4 |
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All Science Journal Classification (ASJC) codes
- Biochemistry
- Chemistry(all)
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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 journal › Review 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
EP - 44
JO - Journal of Proteome Research
JF - Journal of Proteome Research
SN - 1535-3893
IS - 1
ER -