miRvestigator Framework: Detect the miRNAs Driving Co-Expression Signatures

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Citation

miRvestigator Framework Citation

Citations for the miRvestigator Framework
miRvestigator Algorithm Characterization - Christopher L. Plaisier, Min Pan, Nitin S. Baliga. A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers. Genome Res. 2012 Jun 28. PubMed PMID: 22745231. Web Server - Christopher L. Plaisier, J. Christopher Bare, and Nitin S. Baliga. miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling. Nucl. Acids Res. (2011) first published online May 20, 2011 doi:10.1093/nar/gkr374

Supporting Citations
DAVID - Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44-57. PubMed PMID: 19131956. miRBase - Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res. 2008 Jan;36(Database issue):D154-8. Epub 2007 Nov 8. PubMed PMID: 17991681; PubMed Central PMCID: PMC2238936. UCSC Genome Browser - Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR, Giardine BM, Harte RA, Hillman-Jackson J, Hsu F, Kirkup V, Kuhn RM, Learned K, Li CH, Meyer LR, Pohl A, Raney BJ, Rosenbloom KR, Smith KE, Haussler D, Kent WJ. The UCSC Genome Browser database: update 2011. Nucleic Acids Res. 2011 Jan;39(Database issue):D876-82. Epub 2010 Oct 18. PubMed PMID: 20959295. WebLogo - Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Res. 2004 Jun;14(6):1188-90. PubMed PMID: 15173120; PubMed Central PMCID: PMC419797. Weeder - Pavesi G, Mereghetti P, Zambelli F, Stefani M, Mauri G, Pesole G. MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W566-70. PubMed PMID: 16845071; PubMed Central PMCID: PMC1538899.

Support Provided By
This work was supported by grants from NIH (P50GM076547 and 1R01GM077398-01A2), DoE (DE- FG02-04ER64685), NSF (DBI-0640950) and we also thank the Luxembourg Centre for Systems Biomedicine and the University of Luxembourg for support.

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Developed at the Institute for Systems Biology in the Baliga Lab.