| Utilizing RNA-Seq data for de novo coexpression network inference. | |
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MedLine Citation:
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PMID: 22556371 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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MOTIVATION: RNA-Seq experiments have shown great potential for transcriptome profiling. While sequencing increases the level of biological detail, integrative data analysis is also important. One avenue is the construction of coexpression networks. Because the capacity of RNA-Seq data for network construction has not been previously evaluated, we constructed a coexpression network using striatal samples, derived its network properties and compared it with microarray-based networks. RESULTS: The RNA-Seq coexpression network displayed scale-free, hierarchical network structure. We detected transcripts groups (modules) with correlated profiles; modules overlap distinct ontology categories. Neuroanatomical data from the Allen Brain Atlas reveal several modules with spatial colocalization. The network was compared with microarray-derived networks; correlations from RNA-Seq data were higher, likely because greater sensitivity and dynamic range. Higher correlations result in higher network connectivity, heterogeneity and centrality. For transcripts present across platforms, network structure appeared largely preserved. From this study, we present the first RNA-Seq data de novo network inference. |
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Authors:
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Ovidiu D Iancu; Sunita Kawane; Daniel Bottomly; Robert Searles; Robert Hitzemann; Shannon McWeeney |
Publication Detail:
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Type: Comparative Study; Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S. Date: 2012-05-03 |
Journal Detail:
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Title: Bioinformatics (Oxford, England) Volume: 28 ISSN: 1367-4811 ISO Abbreviation: Bioinformatics Publication Date: 2012 Jun |
Date Detail:
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Created Date: 2012-06-12 Completed Date: 2013-01-31 Revised Date: 2013-05-20 |
Medline Journal Info:
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Nlm Unique ID: 9808944 Medline TA: Bioinformatics Country: England |
Other Details:
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Languages: eng Pagination: 1592-7 Citation Subset: IM |
Affiliation:
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Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239-3098, USA. iancuo@ohsu.edu |
Export Citation:
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APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
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Animals Gene Expression Profiling / methods* Gene Regulatory Networks* Male Mice Mice, Inbred C57BL Mice, Inbred DBA Oligonucleotide Array Sequence Analysis / methods RNA / genetics Sequence Analysis, RNA / methods* |
| Grant Support | |
ID/Acronym/Agency:
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5P30CA069533-13/CA/NCI NIH HHS; 5UL1RR024140/RR/NCRR NIH HHS; AA010760/AA/NIAAA NIH HHS; AA011114/AA/NIAAA NIH HHS; AA013484/AA/NIAAA NIH HHS; DA005228/DA/NIDA NIH HHS; MH051372/MH/NIMH NIH HHS; P30 CA069533/CA/NCI NIH HHS; UL1 TR000128/TR/NCATS NIH HHS |
| Chemical | |
Reg. No./Substance:
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63231-63-0/RNA |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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