MMIA- MicroRNA and mRNA integrated analysis Tool name | MMIA- MicroRNA and mRNA integrated analysis |
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URL | 1. http://129.79.244.122/~MMIA/mmia_main.html 2. http://cancer.informatics.indiana.edu/mmia |
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Important features | Computational tool for analyzing biological functions of microRNA expression by combining microRNA and mRNA expression data with computationally identified microRNA target information from TargetScan, PITA and PicTar. |
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Citations | Nam S, Li M, Choi K, Balch C, Kim S, Nephew KP. MicroRNA and mRNA integrated
analysis (MMIA): a web tool for examining biological functions of microRNA
expression. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W356-62. Epub 2009
May 6. PubMed PMID: 19420067; PubMed Central PMCID: PMC2703907.
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Year of publication | 2009 |
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Rank by usage frequency | 100 |
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Comments | |
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Function | FUNCTIONAL ANALYSIS: pathways, DISEASE/ TISSUE SPECIFIC, 1. http://129.79.244.122/~MMIA/mmia_main.html 2. http://cancer.informatics.indiana.edu/mmia, Computational tool for analyzing biological functions of microRNA expression by combining microRNA and mRNA expression data with computationally identified microRNA target information from TargetScan- PITA and PicTar., Nam S- Li M- Choi K- Balch C- Kim S- Nephew KP. MicroRNA and mRNA integrated
analysis (MMIA): a web tool for examining biological functions of microRNA
expression. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W356-62. Epub 2009
May 6. PubMed PMID: 19420067; PubMed Central PMCID: PMC2703907.
, 2009, 100, Online, I. SPECIES SUPPORTED INCLUDE: human II. QUERY OR INPUT DATA: 1. Select organism 2. microRNA data analysis: A. Data section-a. Regulated microRNA list b. microRNA expression data B. Option section-a. Down-regulated or up-regulated b. Pre- processing options-default values- 3. microRNA target algorithms: 1. select one (TargetScan5.1- PicTar4way- PicTar5way-PITA-sites-3-15-ALL) or common target genes by intersection. 4. mRNA data analysis: Upload mRNA expression data- select chip platform- option section5. miRNA and mRNA combined analysis: KEGG- MIT MSigDB v2.5- Disease-candidate genes to inherited disease 6. Optional analysis: miRNA gene set analysis: TF binding sites enriched in promoter regions of miRNAs OR down/up/none regulated gene set using miR2Disease database- miRNA and mRNA combined analysis by MIT GSEA software III. OUTPUT DATA: details of groups of microRNA which are up regulated or down regulated- significantly downregulated or upregulated genes- microRNA gene set analysis- predicted mRNA targets by the down regulated miRNAs- KEGG pathways etc. |
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