Post on 30-Dec-2015
description
Babelomics
Functional interpretation of genome-scale experiments
Barcelona, 28 November de 2007
Ignacio Medinaimedina@cipf.esDavid Montaner
dmontaner@cipf.eshttp://bioinfo.cipf.es
Bioinformatics DepartmentCENTRO DE INVESTIGACION PRINCIPE FELIPE
(VALENCIA)
Babelomics: A systems biology web resource for the functional interpretation of
genome-scale experiments.
http://babelomics.bioinfo.cipf.es
Genome-scale experiment output
1007_s_at1053_at117_at121_at
1255_g_at1294_at1316_at
.
.1320_at
1405_i_at1431_at1438_at1487_at
1494_f_at1598_g_at160020_at
1729_at1773_at177_at
.
.
1007_s_at 12.4
1053_at 11.5
117_at 10.3
121_at 10.2
1255_g_at 9.9
1294_at 9.3
1316_at 8.2
1320_at 8.1
1405_i_at 7.7
1431_at 7.4
1438_at 6.5
1487_at 6.2
1494_f_at 5.9
1598_g_at 5.8
160020_at 4.8
1729_at 4.7
. .
. .
Functional
Interpretation
ENSEMBLwww.ensembl.org
Ensembl ID
HGNC symbol
EMBL acc
UniProt/Swiss-Prot
UniProtKB/TrEMBL
Ensembl IDs
RefSeq
EntrezGene
Affymetrix
Agilent
PDB
Protein Id
IPI….
Arabidopsis thaliana
Homo sapiens
Mus musculus
Rattus norvegicus
Drosophila melanogaster
Caenorhabditis elegans
Saccharmoyces cerevisae
GO
KEGG
Interpro
Transcription
Factors
Gene expressio
n
Cisred
Bioentities
Literature
Gallus gallus
Babelomics imported databases
Babelomics toolsFatiGO: Finds differential distributions of Gene Ontology terms between two
groups of genes.
FatiGOplus: an extension of FatiGO for InterPro motifs, pathways and
SwissProt KW , transcription factors (TF), gene expression in tissues,
bioentities from scientific literature, cis-regulatory elements CisRed.
Tissues Mining Tool: compares reference values of gene expression in
tissues to your results.
MARMITE Finds differential distributions of bioentities extracted from PubMed
between two groups of genes.
FatiScan: detect significant functions with Gene Ontology, InterPro motifs,
Swissprot KW and KEGG pathways in lists of genes ordered according to
differents characteristics.
MarmiteScan: Use chemical and disease-related information to detect related
blocks of genes in a gene list with associated values.
GSEA: Detects blocks of functionally related genes with significant coordinate
over- or under-expression using the Gene Set Enrichment Analysis.
1007_s_at
1053_at117_at121_at
1255_g_at1294_at1316_at
.
.
1320_at1405_i_at1431_at1438_at1487_at
1494_f_at1598_g_at160020_at
1729_at1773_at177_at
.
.
1007_s_at 12.4
1053_at 11.5
117_at 10.3
121_at 10.2
1255_g_at 9.9
1294_at 9.3
1316_at 8.2
1320_at 8.1
1405_i_at 7.7
Gene List1
Gene List2
Organism
Biological process Molecular functionCellular component
KEGG pathwaysBiocarta Pathways (new)
Interpro motifsSwissprot keywords
Bioentities from literature (Marmite)Gene Expression (TMT)
Transcription Factor binding sitesCis-regulatory elements (CisReD)
miRNAs (new)
FatiGO
Text files with a column of identifiers
emailme@cipf.esyour project name
Testing the distribution of functional terms among two groups of genes
(remember, we have to test hundreds of GOs)
Biosynthesis 60% Biosynthesis 20%
Sporulation 20% Sporulation 20%
Group A Group B
Genes in group A have significantly to do with biosynthesis, but not with sporulation.
Are this two groups of genes
carrying out different
biological roles?
84No biosynthesis
26Biosynthesis
BA
FatiGO ResultsGene group1 is enriched in this functional block
Gene group2 is enriched in this functional block
percentages
p-values
corrected p-values
Organism
Gene Listordered
according the
experimentalvalue
FatiScan
Gene1 12.4
Gene2 11.5
Gene3 10.3
Gene4 10.2
Gene5 9.9
Gene6 9.3
Gene7 8.2
Gne8 8.1
Gene10 7.7
gene11 7.4
. .
Biological process Molecular functionCellular component
KEGG pathwaysInterpro motifs
Keywords SwissprotTranscription Factor
Cis-regulatory elements
•Index ranking genes according to some biological aspect under study.
•Database that stores gene class membership information.
•FatiScan searches over the whole ordered list, trying to find runs of functionally related genes.
List of genes
+
-
Annotation label A
Annotation label B
Annotation label CBA C
Testing along the ordered list
Block of genes enriched in the annotation A
Annotation C is homogeneously
distributed along the list
Block of genes enriched in the annotation B
% Genes with the specific GO annotation for each partition
Fatiscan results
List of genes
+
-
BA C
% Genes with the specific GO annotation for each partition
GO over-represented
among genes over-expressed in
A
GO over-represented among
genes over-expressed in B
A B
Expression
level
-
+
Functional interpretation
FatiScan ExampleTumor Control
+ t
- t
t ~ Tumor mean expression – Control mean expression
All
gene
s in
the
arr
ay
Proliferation
Is more associated with the genes on the top of the list
Is more associated with the genes that show higher expression in Tumors