1. UBio Training Courses Micro-RNA web tools Gonzalo Gómez//ggomez@cnio.es

2. Microarray expression data inferred network i.e. DOWNREGULATED miRs (FDR<0.05) UPREGULATED genes (FDR<0.05) Network Filtering miRs-predicted targets network i.e. Target Scan v5.1 >1.240.300 target predictions in human Pathway interpretation miRs-pathways network i.e. DOWNREGULATED miRs (SAM, FDR<0.05; Fisher, FDR<0.05) ENRICHED pathways (GSEA, FDR<0.25) Experimental data Introduction miRNAs, target prediction, biology…

3. 1. MMIA (http://129.79.233.81/~MMIA/index.html) Microarray and mRNA integrated analysis. 2. Diana (http://diana.cslab.ece.ntua.gr/?sec=home) MicroT  target prediction mirExTra  miRNA-gene expression mirPath  miRNA-pathway relationships 3. Whichgenes (www.whichgenes.org) Updated miRNAs targets for Gene Set Enrichment Analysis (miRBase, TargetScan) 4. FatiScan (www.babelomics.org) miRNAs in FatiScan 5. Ingenuity IPA (http://www.ingenuity.com/) miRNAs-targets networks, Functional Analysis Introduction Tools

4. 1. MMIA http://129.79.233.81/~MMIA/index.html MMIA workflow Microarray and mRNA integrated analysis.

5. 1. MMIA Workflow Details

6. 1. MMIA Input File Format.SIP format ~ GEPAS format.txt file Tab delimited No spaces in sample names Log 2 not accepted IDs accepted Swiss-Prot Ensembl RefSeq Entrez Gene NCBI prot Gene Symbol Affy probe set

7. 1. MMIA Analysis: Step 1

8. 1. MMIA Analysis: Step 2 If “Skipped”  option 2 selected

9. 1. MMIA Analysis: Step 3 Download example file and Load to run the analysis

10. 1. MMIA Analysis: Step 4 Pathways GSEA gene sets http://www.ogic.ca/projects/g2d_2/ Gene2Disease Run

11. Analysis: Step 5 1. MMIA

12. Results

13. 1. MMIA Results Help

14. 2. DIANA http://diana.cslab.ece.ntua.gr/?sec=home Diana microT is an algorithm for the prediction of miRNA target genes. The DIANA microT v3.0 application may be used to search for target genes of annotated or user defined miRNA sequences. The mirExTra application, helps users identify miRNAs that may be involved in a process of interest. It is usually used with differential gene expression data (microarray data). The mirExTra algorithm identifies overrepresented six nucleotide long motifs (hexamers) on the 3'UTR sequences of deregulated genes. The Diana mirPath Software was designed in order to cover the need of a quick and easy interpretation of the involvement of a series of genes in biological processes.

15. 2. DIANA mirPath Single miRNA-KEGG analysis. Multiple miRNA-KEGG analysis.

16. 2. DIANA Single Analysis 1. Select specie. 2. Select target prediction software. 3. Select miRNA. 4. Results output.

17. 2. DIANA Multiple miRNA Analysis 1. Job name. 2. Email address. 3. Select miRNAs. 4. Run analysis. 5. Wait results email6. Results output

18. 2. DIANA Multiple miRNA Analysis -ln(p-value). The higher the more significant KEGG pathways Union of miRNAs targets Intersection of miRNAs targets

19. 3. WhichGenes http://www.whichgenes.org - Retrieve miRNAs targets for Gene Set Enrichment Analysis (miRBase, TargetScan) - Always updated ! Login whether you want to download and store your gene sets Enter if you simply want to download gene sets.

20. 3. WhichGenes 1. Choose oraanism. -Human - Mouse 2. Select source: - miRBase, TScan - Other sources 3. Copy and paste miRNAs identifiers. Create set per items. 4. Job name. Create Sets Looking for examples ? Try a preloaded example!!! Retrieving targets

21. 3. WhichGenes Gene Sets Cart 1. Choose gene sets for downloading. 2. Select output format. e.g..CSV,.TSV,.gmt,.gmx 3. Select identifier. e.g. Agilent, Affy, Mgi… 4. DOWNLOAD GENE SETS !!!

22. 4. FatiScan http://babelomics.bioinfo.cipf.es/ Choose miRNAs for gene set analysis. - Gene Set Enrichment Analysis using predicted miRNAs targets - Custom annotations accepted (keep in mind whichgenes here…)

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