MicroRNA

Post-analysis categorization
- Literature search
Post-survey categorization
- Features validated in most cases
- Features not validated
Simple lists
Preliminary lists

Tool name

MMIA- MicroRNA and mRNA integrated analysis

URL

1. http://129.79.244.122/~MMIA/mmia_main.html 2. http://cancer.informatics.indiana.edu/mmia

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.

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.

Year of publication

2009

Rank by usage frequency

100

Comments

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.