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iGA specifications

Information


Unique identifier OMICS_18766
Name iGA
Alternative name Iterative Group Analysis
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained No

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Publication for Iterative Group Analysis

iGA citations

 (4)
library_books

RNA sequencing provides insights into the evolution of lettuce and the regulation of flavonoid biosynthesis

2017
Nat Commun
PMCID: 5741661
PMID: 29273740
DOI: 10.1038/s41467-017-02445-9

[…] everal eQTLs for different flavonoid-related genes were located in the same region. These data are consistent with the same regulators controlling the expression of these flavonoid-related genes. The iterative group analysis (iGA) approach was used to test this possibility to identify significant regulatory groups (Supplementary Table ) and then to construct the genetic regulatory network (Fig. ). […]

library_books

Comparative transcriptomics of drought responses in Populus: a meta analysis of genome wide expression profiling in mature leaves and root apices across two genotypes

2010
BMC Genomics
PMCID: 3091765
PMID: 21073700
DOI: 10.1186/1471-2164-11-630

[…] querying the annotation tool at The Arabidopsis Information Resource (TAIR) http://www.arabidopsis.org  [,]. Annotations from all origins were compiled to determine functional class enrichments using Iterative Group Analysis (iGA) []. The iGA procedure, which is based on hypergeometric statistic calculations, detects concerted changes in functional classes and assigns a probability of change (PC-v […]

library_books

Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function

2009
BMC Bioinformatics
PMCID: 2761411
PMID: 19775443
DOI: 10.1186/1471-2105-10-307

[…] istribution function; GO: Gene Ontology; GEVD: Generalized Extreme Value Distribution function; GSA: Gene Set Analysis; GSEA: Gene Set Enrichment Analysis; IBMT: Intensity Based Modified T-test; iGA: iterative Group Analysis; KS: Kolmogorov-Smirnov test; LR: Likelihood Ratio; ML: Maximum Likelihood; modKS: modified Kolmogorov-Smirnov; OGL: Ordered Gene List; RMA: Robust Multi-array Average; SP: Si […]

call_split

Genes of cell cell interactions, chemotherapy detoxification and apoptosis are induced during chemotherapy of acute myeloid leukemia

2009
BMC Cancer
PMCID: 2673224
PMID: 19265549
DOI: 10.1186/1471-2407-9-77
call_split See protocol

[…] les were compared to the untreated ones. The Rank product method [] was used to identify genes consistently up- or down-regulated. Gene ontology (GO) analysis was applied for functional studies using iterative group analysis (iGA) [] utilizing the Source database http://source.stanford.edu[]. False discovery rates for GO-terms were estimated by performing 100 permutations.In the ex vivo experiment […]

Citations

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iGA institution(s)
Plant Science Group, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, UK; Bioinformatics Research Centre, Department of Computing Science, University of Glasgow, Glasgow, UK; Sir Henry Wellcome Functional Genomics Facility, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, UK
iGA funding source(s)
Supported by BBSRC grants 17/GG17989 and 17/P17237.

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