Can we identify cellular pathways implicated in cancer using gene expression data?

N. Shah; J. Lepre; Y. Tu; G. Stolovitzky

doi:10.1109/CSB.2003.1227308

Can we identify cellular pathways implicated in cancer using gene expression data?

N. Shah, J. Lepre, Y. Tu, G. Stolovitzky

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

3 Scopus citations

Abstract

The cancer state of a cell is characterized by alterations of important cellular processes such as cell proliferation, apoptosis, DNA-damage repair, etc. The expression of genes associated with cancer related pathways, therefore, may exhibit differences between the normal and the cancerous states. We explore various means to find these differences. We analyze 6 different pathways (p53, Ras, Brca, DNA damage repair, NFκb and β-catenin) and 4 different types of cancer: colon, pancreas, prostate and kidney. Our results are found to be mostly consistent with existing knowledge of the involvement of these pathways in different cancers. Our analysis constitutes proof of principle that it may be possible to predict the involvement of a particular pathway in cancer or other diseases by using gene expression data. Such method would be particularly useful for the types of diseases where biology is poorly understood.

Original language	English
Title of host publication	Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	94-103
Number of pages	10
ISBN (Electronic)	0769520006, 9780769520001
DOIs	https://doi.org/10.1109/CSB.2003.1227308
State	Published - 2003
Externally published	Yes
Event	2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003 - Stanford, United States Duration: 11 Aug 2003 → 14 Aug 2003

Publication series

Name	Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003

Conference

Conference	2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003
Country/Territory	United States
City	Stanford
Period	11/08/03 → 14/08/03

Access to Document

10.1109/CSB.2003.1227308

Cite this

Shah, N., Lepre, J., Tu, Y., & Stolovitzky, G. (2003). Can we identify cellular pathways implicated in cancer using gene expression data? In Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003 (pp. 94-103). Article 1227308 (Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/CSB.2003.1227308

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title = "Can we identify cellular pathways implicated in cancer using gene expression data?",

abstract = "The cancer state of a cell is characterized by alterations of important cellular processes such as cell proliferation, apoptosis, DNA-damage repair, etc. The expression of genes associated with cancer related pathways, therefore, may exhibit differences between the normal and the cancerous states. We explore various means to find these differences. We analyze 6 different pathways (p53, Ras, Brca, DNA damage repair, NFκb and β-catenin) and 4 different types of cancer: colon, pancreas, prostate and kidney. Our results are found to be mostly consistent with existing knowledge of the involvement of these pathways in different cancers. Our analysis constitutes proof of principle that it may be possible to predict the involvement of a particular pathway in cancer or other diseases by using gene expression data. Such method would be particularly useful for the types of diseases where biology is poorly understood.",

author = "N. Shah and J. Lepre and Y. Tu and G. Stolovitzky",

note = "Publisher Copyright: {\textcopyright} 2003 IEEE.; 2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003 ; Conference date: 11-08-2003 Through 14-08-2003",

year = "2003",

doi = "10.1109/CSB.2003.1227308",

language = "English",

series = "Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003",

publisher = "Institute of Electrical and Electronics Engineers Inc.",

pages = "94--103",

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Shah, N, Lepre, J, Tu, Y & Stolovitzky, G 2003, Can we identify cellular pathways implicated in cancer using gene expression data? in Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003., 1227308, Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003, Institute of Electrical and Electronics Engineers Inc., pp. 94-103, 2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003, Stanford, United States, 11/08/03. https://doi.org/10.1109/CSB.2003.1227308

Can we identify cellular pathways implicated in cancer using gene expression data? / Shah, N.; Lepre, J.; Tu, Y. et al.
Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003. Institute of Electrical and Electronics Engineers Inc., 2003. p. 94-103 1227308 (Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review