IBC > Journal Article
Journal Article Synopsis
IBC 2013, vol. 5, article no. 1, pp. 1-8 | doi: 10.4051/ibc.2013.5.1.0001
view 8326 | download 1942 | rating 6.0 | comment 0
Full Report (Systems biology)
Creating Subnetworks From Transcriptomic Data on Central Nervous System Diseases Informed by a Massive Transcriptomic Network.
Yaping Feng1, Judith A. Syrkin-Nikolau2 and Eve S. Wurtele1,*
1
Department of Genetics, Iowa State University, Ames, IA 50011, USA
2
Macalester College, MN 55105, USA
*Corresponding author
received: January 04, 2013 ; accepted: January 14, 2013 ; published : January 21, 2013
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Synopsis

High quality publicly-available transcriptomic data representing relationships in gene expression across a diverse set of biological conditions is used as a context network to explore transcriptomics of the CNS. The context network, 18367Hu-matrix, contains pairwise Pearson correlations for 22,215 human genes across18,637 human tissue samples1. To do this, we compute a network derived from biological samples from CNS cells and tissues, calculate clusters of co-expressed genes from this network, and compare the significance of these to clusters derived from the larger 18367Hu-matrix network. Sorting and visualization uses the publicly available software, MetaOmGraph (http://www.metnetdb.org/MetNet_MetaOmGraph.htm). This identifies genes that characterize particular disease conditions. Specifically, differences in gene expression within and between two designations of glial cancer, astrocytoma and glioblastoma, are evaluated in the context of the broader network. Such gene groups, which we term outlier-networks, tease out abnormally expressed genes and the samples in which this expression occurs. This approach distinguishes 48 subnetworks of outlier genes associated with astrocytoma and glioblastoma. As a case study, we investigate the relationships among the genes of a small astrocytoma-only subnetwork. This astrocytoma-only subnetwork consists of SVEP1, IGF1, CHRNA3, and SPAG6. All of these genes are highly coexpressed in a single sample of anaplastic astrocytoma tumor (grade III) and a sample of juvenile pilocytic astrocytoma. Three of these genes are also associated with nicotine. This data lead us to formulate a testable hypothesis that this astrocytoma outlier-network provides a link between some gliomas/astrocytomas and nicotine.

Keywords : bioinformatics, transcriptomic, glioblastoma, astrocytoma, brain cancer
This article is a part of the special issue: Translational Bioinformatics Conference 2012(TBC 2012)
Post-publication appraisal
Rate this manuscript
        Exceptional Highly recommended Recommended Fair Current rating: 6.0
Open discussion                       
(Open discussion is for 90 days after the initial publication)
:: Comments
Main text PDF(1840 KB)
(Print version)
Send to a friend
References
Reviewed by
Edited by
- Yoshio Tateno
Author's Commentary
Export Citation
Bookmark
  StumbleUpon Facebook Connotea CiteULike twitter
PubMed
- Yaping Feng
- Eve S. Wurtele
Google Scholar
- Yaping Feng
- Eve S. Wurtele
Interdisciplinary Bio Central (IBC) ISSN : 2005-8543 | Contact IBC//
All site content, except where otherwise noted, is licensed under a Creative Commons Attribution License.