GeneE specifications

Information


Unique identifier OMICS_07924
Name GeneE
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No

Maintainer


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Publication for GeneE

GeneE in publications

 (22)
PMCID: 5832790
PMID: 29497042
DOI: 10.1038/s41467-018-03395-6

[…] locus.table 1hrinc hr increase, hrrx hr recovery at x seconds, chr chromosome, ea effect allele, nea non-effect allele, se standard errorn nearest gene or any other gene in 10 kbc coding variant genee eqtl geneh hi-c long-range interaction genemore detailed information can be found in supplementary table  and fig. 2, hrinc hr increase, hrrx hr recovery at x seconds, chr chromosome, ea effect […]

PMCID: 5774119
PMID: 29375724
DOI: 10.1186/s13148-017-0436-1

[…] two groups was determined using hypergeometric fisher exact test in r. hierarchical clustering was performed using one minus pearson correlation, and heatmaps were generated in the broad institute genee application (https://software.broadinstitute.org/gene-e/)., pyrosequencing was performed using the pyro mark q24 (qiagen) machine, and results were analyzed with pyro mark q24 software 2.0 […]

PMCID: 5762365
PMID: 29340097
DOI: 10.18632/oncotarget.22942

[…] (ipa) program (http://www.ingenuity.com/index.html) was used to compute enriched gene networks, functional categories, canonical pathways and upstream regulators. heatmaps were created using genee (http://www.broadinstitute.org/cancer/software/gene-e/doc.html). gsea was used to examine gene-set enrichment of differentially methylated genes in response to sam and their expression profile […]

PMCID: 5589240
PMID: 28880937
DOI: 10.1371/journal.pone.0184317

[…] for the generation of heat maps, human and murine datasets were separately z-scored (setting the data to a mean = 0 and a variance = 1), and heat maps were generated using freely availably genee program (http://www.broadinstitute.org/)., human blood peripheral blood mononuclear cells (pbmcs) were isolated from buffy coats by ficoll density centrifugation (lucron bioproducts). buffy […]

PMCID: 5589094
PMID: 28880903
DOI: 10.1371/journal.pone.0181538

[…] gene set size minimum, 1000 permutations) was performed using c2cp gene sets and custom gene sets curated from the literature. data were further analyzed using david for functional classification. genee data visualization tool (http://www.broadinstitute.org/cancer/software/gene-e/index.html) was used to create heatmaps of selected genes., enrichment maps of gsea data were created using […]


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GeneE institution(s)
Department of Medical Informatics, Erasmus University Medical Center Rotterdam, CA, Rotterdam, Netherlands

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