GO2MSIG specifications

Information


Unique identifier OMICS_04146
Name GO2MSIG
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Information


Unique identifier OMICS_04146
Name GO2MSIG
Interface Web user interface
Restrictions to use None
Programming languages Perl
Computer skills Basic
Stability Stable
Maintained Yes

Publication for GO2MSIG

GO2MSIG in publications

 (5)
PMCID: 5811979
PMID: 29439658
DOI: 10.1186/s12864-018-4512-5

[…] each of the 8 clusters, using the gsea software (3.0, gseapreranked tool). go annotations (mus muculus, biological process) was used as the gene set database and were converted to .gmt format using go2msig []. for each timepoint, all genes with at least 1 mapped read were divided into those that are 1) up-regulated or 2) down-regulated in fresh cells relative to preserved cells based […]

PMCID: 5724891
PMID: 29228019
DOI: 10.1371/journal.pone.0188997

[…] panther. gene sets from go consisted of 324 cellular compartment, 447 molecular function, and 2376 biological processes specific to bos taurus from level 5 of the hierarchical tree obtained from the go2msig database []. in addition to the go gene sets, 674 gene sets were included from reactome [], 186 gene sets were included from kegg [], 217 gene sets were included from biocarta [], and 165 […]

PMCID: 5703887
PMID: 29180639
DOI: 10.1038/s41467-017-01903-8

[…] p-value <0.05 and an absolute log fold change of 2 were considered differentially expressed. gsea was performed using the clusterprofiler package. go genesets in gmt format were obtained from go2msig (release of april 2015). we added some custom genesets to the biological process terms list (supplementary table ). for each treatment, all expressed genes were ordered by decreasing fold […]

PMCID: 4939893
PMID: 27499907
DOI: 10.1002/cjp2.25

[…] fold changes (fc) between highly mutated tumours (22 or more mutations) and lowly mutated tumours (21 or less mutations) were calculated. gene ontology (go) categories were obtained from go2msig ., univariate and multivariate survival analysis was executed using the function coxph from the r package survival. p‐values < 0.05 were considered significant. prognostic evaluation […]

PMCID: 4455778
PMID: 24847916
DOI: 10.1534/g3.114.011841

[…] (gsea), the lists of genes ranked by log2(control/treatment) ratios were analyzed using the preranked tool of gsea v2.0.13 (). the go-derived msigdb format gene sets were downloaded from the go2msig website (http://www.go2msig.org/cgi-bin/prebuilt.cgi). the high-quality annotations-only gene sets of september 2013 were used., strains of the h90 mating type were spotted on spas plates […]


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GO2MSIG institution(s)
Takeda Cambridge Ltd, Cambridge, UK

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