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Identification of putative cancer genes through data integration and comparative genomics between plants and humans

Mauricio Alberto Quimbaya Gomez UGent, Klaas Vandepoele UGent, Eric Raspé UGent, Michiel Matthijs UGent, Stijn Dhondt UGent, Gerrit Beemster UGent, Geert Berx UGent and Lieven De Veylder UGent (2012) CELLULAR AND MOLECULAR LIFE SCIENCES. 69(12). p.2041-2055
abstract
Coordination of cell division with growth and development is essential for the survival of organisms. Mistakes made during replication of genetic material can result in cell death, growth defects, or cancer. Because of the essential role of the molecular machinery that controls DNA replication and mitosis during development, its high degree of conservation among organisms is not surprising. Mammalian cell cycle genes have orthologues in plants, and vice versa. However, besides the many known and characterized proliferation genes, still undiscovered regulatory genes are expected to exist with conserved functions in plants and humans. Starting from genome-wide Arabidopsis thaliana microarray data, an integrative strategy based on coexpression, functional enrichment analysis, and cis-regulatory element annotation was combined with a comparative genomics approach between plants and humans to detect conserved cell cycle genes involved in DNA replication and/or DNA repair. With this systemic strategy, a set of 339 genes was identified as potentially conserved proliferation genes. Experimental analysis confirmed that 20 out of 40 selected genes had an impact on plant cell proliferation; likewise, an evolutionarily conserved role in cell division was corroborated for two human orthologues. Moreover, association analysis integrating Homo sapiens gene expression data with clinical information revealed that, for 45 genes, altered transcript levels and relapse risk clearly correlated. Our results illustrate how a systematic exploration of the A. thaliana genome can contribute to the experimental identification of new cell cycle regulators that might represent novel oncogenes or/and tumor suppressors.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
DISCOVERY, EXPRESSION, HUMAN BREAST, DROSOPHILA, ARABIDOPSIS-THALIANA, TRANSCRIPTION FACTOR, COLORECTAL-CANCER, NF-KAPPA-B, WIDE ASSOCIATION, CELL-CYCLE REGULATION, Comparative genomics, Cancer genomics, Cell cycle, MCF7, Arabidopsis thaliana
journal title
CELLULAR AND MOLECULAR LIFE SCIENCES
Cell. Mol. Life Sci.
volume
69
issue
12
pages
2041 - 2055
Web of Science type
Article
Web of Science id
000305128800008
JCR category
BIOCHEMISTRY & MOLECULAR BIOLOGY
JCR impact factor
5.615 (2012)
JCR rank
45/288 (2012)
JCR quartile
1 (2012)
ISSN
1420-682X
DOI
10.1007/s00018-011-0909-x
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
2965224
handle
http://hdl.handle.net/1854/LU-2965224
date created
2012-07-30 13:43:36
date last changed
2013-05-06 11:10:23
@article{2965224,
  abstract     = {Coordination of cell division with growth and development is essential for the survival of organisms. Mistakes made during replication of genetic material can result in cell death, growth defects, or cancer. Because of the essential role of the molecular machinery that controls DNA replication and mitosis during development, its high degree of conservation among organisms is not surprising. Mammalian cell cycle genes have orthologues in plants, and vice versa. However, besides the many known and characterized proliferation genes, still undiscovered regulatory genes are expected to exist with conserved functions in plants and humans. Starting from genome-wide Arabidopsis thaliana microarray data, an integrative strategy based on coexpression, functional enrichment analysis, and cis-regulatory element annotation was combined with a comparative genomics approach between plants and humans to detect conserved cell cycle genes involved in DNA replication and/or DNA repair. With this systemic strategy, a set of 339 genes was identified as potentially conserved proliferation genes. Experimental analysis confirmed that 20 out of 40 selected genes had an impact on plant cell proliferation; likewise, an evolutionarily conserved role in cell division was corroborated for two human orthologues. Moreover, association analysis integrating Homo sapiens gene expression data with clinical information revealed that, for 45 genes, altered transcript levels and relapse risk clearly correlated. Our results illustrate how a systematic exploration of the A. thaliana genome can contribute to the experimental identification of new cell cycle regulators that might represent novel oncogenes or/and tumor suppressors.},
  author       = {Quimbaya Gomez, Mauricio Alberto and Vandepoele, Klaas and Rasp{\'e}, Eric and Matthijs, Michiel and Dhondt, Stijn and Beemster, Gerrit and Berx, Geert and De Veylder, Lieven},
  issn         = {1420-682X},
  journal      = {CELLULAR AND MOLECULAR LIFE SCIENCES},
  keyword      = {DISCOVERY,EXPRESSION,HUMAN BREAST,DROSOPHILA,ARABIDOPSIS-THALIANA,TRANSCRIPTION FACTOR,COLORECTAL-CANCER,NF-KAPPA-B,WIDE ASSOCIATION,CELL-CYCLE REGULATION,Comparative genomics,Cancer genomics,Cell cycle,MCF7,Arabidopsis thaliana},
  language     = {eng},
  number       = {12},
  pages        = {2041--2055},
  title        = {Identification of putative cancer genes through data integration and comparative genomics between plants and humans},
  url          = {http://dx.doi.org/10.1007/s00018-011-0909-x},
  volume       = {69},
  year         = {2012},
}

Chicago
Quimbaya Gomez, Mauricio Alberto, Klaas Vandepoele, Eric Raspé, Michiel Matthijs, Stijn Dhondt, Gerrit Beemster, Geert Berx, and Lieven De Veylder. 2012. “Identification of Putative Cancer Genes Through Data Integration and Comparative Genomics Between Plants and Humans.” Cellular and Molecular Life Sciences 69 (12): 2041–2055.
APA
Quimbaya Gomez, M. A., Vandepoele, K., Raspé, E., Matthijs, M., Dhondt, S., Beemster, G., Berx, G., et al. (2012). Identification of putative cancer genes through data integration and comparative genomics between plants and humans. CELLULAR AND MOLECULAR LIFE SCIENCES, 69(12), 2041–2055.
Vancouver
1.
Quimbaya Gomez MA, Vandepoele K, Raspé E, Matthijs M, Dhondt S, Beemster G, et al. Identification of putative cancer genes through data integration and comparative genomics between plants and humans. CELLULAR AND MOLECULAR LIFE SCIENCES. 2012;69(12):2041–55.
MLA
Quimbaya Gomez, Mauricio Alberto, Klaas Vandepoele, Eric Raspé, et al. “Identification of Putative Cancer Genes Through Data Integration and Comparative Genomics Between Plants and Humans.” CELLULAR AND MOLECULAR LIFE SCIENCES 69.12 (2012): 2041–2055. Print.