Correlation signature of the macroscopic states of the gene regulatory network in cancer
Open accessAbstract
Although cancer types differ substantially, many cancers share common gene expression signatures. Consistent with this observation, we find convergent and representative distributions and correlation vectors that are distinct in cancer and noncancer ensembles. These differences originate in many genes, but comparatively few genes account for the major differences. We identify genes with different combinatorial regulation in cancer and noncancer as indicated by significant differences in their correlation vectors. Among the identified genes are many established oncogenes and apoptotic genes (such as members of the Bcl-2, the MAPK, and the Ras families) and new candidate oncogenes. Our findings expand and complement the tumorigenic role of up and down regulation of these genes by emphasizing cancer-specific changes in their couplings and correlation patterns at genome-wide level that are independent from their mean levels of expression in cancer cells. Given the central role of these genes in defining the cancerous state it may be worth investigating them and the differences in their combinatorial regulation for developing wide-spectrum anticancer drugs.
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Tumor samples have discrete transcriptome profile differences.
“Thus, tumor samples have discrete transcriptome profile differences89,90”
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Self-citation
- Authors
- Slavov, N., & Dawson, K. A.
- Affiliations
- University College Dublin (IE)
- Princeton University (US)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2009-03-17
- Volume
- 106
- Issue
- 11
- Pages
- 4079-4084
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC2657377
- OpenAlex
- W2138017291
- Cited by
- 49
- References
- 15
- Citations by year
- 2025: 1 · 2024: 1 · 2021: 4 · 2019: 3 · 2018: 2 · 2017: 3 · 2016: 1 · 2015: 7 · 2014: 9 · 2013: 6 · 2012: 6
- FWCI
- 1.61
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- gene regulatory networks, cancer, gene expression signatures, combinatorial gene regulation, oncogenes, apoptosis-related genes, Bcl-2 family proteins, MAPK signaling, Ras family, gene co-expression, anticancer drug development
- MeSH terms
- Humans, Neoplasms, Oncogenes, Models, Statistical, Genome, Human, Gene Expression Regulation, Neoplastic, Cluster Analysis, Apoptosis, Computational Biology, Gene Expression Profiling, Genomics, Gene Regulatory Networks
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