Transcript miRNAs_practica

Micro-RNA web tools
UBio Training Courses
Gonzalo Gómez//[email protected]
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://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
1. MMIA
http://129.79.233.81/~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
4. Results output.
1. Select specie.
2. Select target
prediction software.
3. Select miRNA.
2. DIANA
Multiple miRNA Analysis
5. Wait results email
1. Job name.
2. Email address.
3. Select miRNAs.
4. Run analysis.
6. Results output
2. DIANA
Multiple miRNA Analysis
Union of miRNAs
targets
-ln(p-value).
The higher the more
significant
KEGG pathways
Intersection of
miRNAs targets
3. 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
3. 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.
4. Job name.
Retrieving targets
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 !!!
4. 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 !