Micro-RNA web tools UBio Training Courses Gonzalo Gómez//ggomez@cnio.es Introduction mirnas, target prediction, biology Experimental data Network Filtering Pathway interpretation mirs-pathways network Microarray expression data inferred network i.e. DOWNREGULATED mirs (FDR<0.05) UPREGULATED genes (FDR<0.05) mirs-predicted targets network i.e. Target Scan v5.1 >1.240.300 target predictions in human i.e. DOWNREGULATED mirs (SAM, FDR<0.05; Fisher, FDR<0.05) ENRICHED pathways (GSEA, FDR<0.25)
Introduction Tools 1. MMIA (http://156.56.93.156/~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. Circuits DB (http://biocluster.di.unito.it/circuits/index.php) mirnas-targets-tfs networks. 4. Whichgenes (www.whichgenes.org) Updated mirnas targets for Gene Set Enrichment Analysis (mirbase, TargetScan) 5. FatiScan (www.babelomics.org) mirnas gene set analysis in FatiScan 6. Ingenuity IPA (http://www.ingenuity.com/) mirnas-targets networks, see Functional Analysis Course 1. MMIA http://156.56.93.156/~mmia/index.html Microarray and mrna integrated analysis. MMIA workflow
1. MMIA Workflow Details 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
1. MMIA Analysis: Step 1 1. MMIA Analysis: Step 2 If Skipped! option 2 selected
1. MMIA Analysis: Step 3 Download example file and Load to run the analysis 1. MMIA Analysis: Step 4 Pathways GSEA gene sets Gene2Disease http://www.ogic.ca/projects/g2d_2/ Run
1. MMIA Analysis: Step 5 1. MMIA Results
1. MMIA Results Help 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.
2. DIANA mirpath Single mirna-kegg analysis. Multiple mirna-kegg analysis. 2. DIANA Single Analysis 1. Select specie. 4. Results output. 2. Select target prediction software. 3. Select mirna.
2. DIANA Multiple mirna Analysis 5. Wait results email 6. Results output 1. Job name. 2. Email address. 3. Select mirnas. 4. Run analysis. 2. DIANA Multiple mirna Analysis Union of mirnas targets -ln(p-value). The higher the more significant Intersection of mirnas targets KEGG pathways
3. CircuitsDB http://biocluster.di.unito.it/circuits/index.php Friard et al., BMC Bioinformatics. 2010 - PMID: 20731828 4. WhichGenes http://www.whichgenes.org - Retrieve mirnas targets for Gene Set Enrichment Analysis (mirbase, TargetScan) - Always updated! Enter if you simply want to download gene sets. Login whether you want to download and store your gene sets
4. WhichGenes Create Sets 1. Choose oraanism. -Human - Mouse Looking for examples? 2. Select source: - mirbase, TScan - Other sources 3. Copy and paste mirnas identifiers. Create set per items. Retrieving targets 4. Job name. 4. 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!!!
5. FatiScan http://babelomics.bioinfo.cipf.es/ - Gene Set Enrichment Analysis using predicted mirnas targets - Custom annotations accepted (keep in mind whichgenes here ) Choose mirnas for gene set analysis. http://bioinfo.cnio.es/ VISIT UBIO WEB! Thanks!