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GENE-E specifications

Information


Unique identifier OMICS_15859
Name GENE-E
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Mac OS, Windows
Programming languages Java, R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.6.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Joshua Gould

GENE-E citations

 (107)
library_books

MYR1 Dependent Effectors Are the Major Drivers of a Host Cell’s Early Response to Toxoplasma, Including Counteracting MYR1 Independent Effects

2018
MBio
PMCID: 5885026
PMID: 29615509
DOI: 10.1128/mBio.02401-17

[…] value at a 10% false-discovery rate (FDR) with a q value of <0.05. Among these genes, only those with average RPKM ratios of ≥1.5 were counted as changed in expression.Heat maps were generated using Gene E (https://software.broadinstitute.org/GENE-E/index.html). Venn diagrams were created using BioVenn (). […]

library_books

Defining the Transcriptional Landscape during Cytomegalovirus Latency with Single Cell RNA Sequencing

2018
MBio
PMCID: 5850328
PMID: 29535194
DOI: 10.1128/mBio.00013-18

[…] s done with HTSeq-count (). Annotation of gff files is based on NCBI data, with some adjustment taking into account correction for the nonstranded library. The clustering for and was generated with GENE-E (). The analysis of the CD34+ GEO samples was carried out in the same way. The list of data sets that were used is presented in . […]

library_books

Nc886 is epigenetically repressed in prostate cancer and acts as a tumor suppressor through the inhibition of cell growth

2018
BMC Cancer
PMCID: 5797390
PMID: 29394925
DOI: 10.1186/s12885-018-4049-7

[…] c886 TSS200 promoter (cg18678645, cg06536614, cg26328633, cg25340688, cg26896946, cg00124993) were calculated. Hierarchical clusterization obtained through Euclidean algorithm was performed using the Gene-E (http://www.broadinstitute.org/cancer/software/GENE-E/) for the methylation beta-values and Morpheus (https://software.broadinstitute.org/morpheus/) for gene expression values. […]

library_books

Molecular profiling and combinatorial activity of CCT068127: a potent CDK2 and CDK9 inhibitor

2018
Mol Oncol
PMCID: 5830651
PMID: 29063678
DOI: 10.1002/1878-0261.12148

[…] in GeneSpring (Silicon Genetics, Redwood City, CA, USA). Gene expression data were analyzed relative to the DMSO controls by comparative marker selection using a t‐test to rank expression changes in Gene‐E (http://www.broadinstitute.org/cancer/software/GENE-E/). A ≥ twofold change in expression was used to refine the selection criteria. Gene expression profiles were analyzed using Connectivity Ma […]

library_books

High resolution spatiotemporal transcriptome mapping of tomato fruit development and ripening

2018
Nat Commun
PMCID: 5785480
PMID: 29371663
DOI: 10.1038/s41467-017-02782-9

[…] he log2-transformed RPM values of the expressed gene profiles among cell/tissue-type and stages using the prcomp function in R. Hierarchical clustering of ARF and IAA sequences were carried out using GENE-E (https://software.broadinstitute.org/GENE-E/) with one minus Pearson correlation as the distance metric. Pairwise PCC values between the expression patterns of ARF and Aux/IAA genes were calcul […]

library_books

The signature of liver cancer in immune cells DNA methylation

2018
Clin Epigenetics
PMCID: 5774119
PMID: 29375724
DOI: 10.1186/s13148-017-0436-1

[…] r 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/). […]

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