ubio training courses micro-rna web tools gonzalo gómez//[email protected]
TRANSCRIPT
Microarray expression data inferred networki.e.DOWNREGULATED miRs (FDR<0.05)UPREGULATED genes (FDR<0.05)
Network Filtering
miRs-predicted targets networki.e. Target Scan v5.1 >1.240.300 target predictions in human
Pathway interpretation
miRs-pathways networki.e.DOWNREGULATED miRs(SAM, FDR<0.05; Fisher, FDR<0.05)ENRICHED pathways (GSEA, FDR<0.25)
Experimental data
Introduction
miRNAs, target prediction, biology…
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 predictionmirExTra miRNA-gene expressionmirPath 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
1. MMIA
http://129.79.233.81/~MMIA/index.html
MMIA workflow
Microarray and mRNA integrated analysis.
1. MMIA
Workflow Details
1. MMIA
Input File Format
.SIP format ~ GEPAS format
.txt file Tab delimitedNo spaces in sample namesLog 2 not accepted
IDs acceptedSwiss-ProtEnsemblRefSeqEntrez GeneNCBI protGene SymbolAffy 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 andLoad to run the analysis
1. MMIA
Analysis: Step 4
PathwaysGSEA gene sets
http://www.ogic.ca/projects/g2d_2/
Gene2Disease
Run
Analysis: Step 5
1. MMIA
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.
2. Select target prediction software.
3. Select miRNA.
4. Results output.
2. DIANA
Multiple miRNA Analysis
1. Job name.
2. Email address.
3. Select miRNAs.
4. Run analysis.
5. Wait results email 6. Results output
2. DIANA
Multiple miRNA Analysis
-ln(p-value).The higher the more significant
KEGG pathways
Union of miRNAstargets
Intersection of miRNAs targets
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.
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
3. WhichGenes
Gene Sets Cart
1. Choose gene sets for downloading.
2. Select output format. e.g. .CSV, .TSV, .gmt, .gmx3. Select identifier.e.g. Agilent, Affy, Mgi…
4. DOWNLOAD GENE SETS !!!
4. FatiScan
http://babelomics.bioinfo.cipf.es/
Choose miRNAsfor gene set
analysis.
- Gene Set Enrichment Analysis using predicted miRNAs targets- Custom annotations accepted (keep in mind whichgenes here…)
VISIT UBIO WEB !
Thanks !
http://bioinfo.cnio.es/