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chevron_left Quality control File format conversion Differential expression detection Gene expression data mining CNV detection Workflow management systems Differential protein expression Manual gating Peak detection Automated gating Peak alignment Variant detection Data preprocessing chevron_right
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GenePattern specifications

Information


Unique identifier OMICS_01855
Name GenePattern
Software type Framework/Library
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Computer skills Medium
Version 3.9.10
Stability Stable
Maintained Yes

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Versioning


No version available

Documentation


Maintainers


  • person_outline Jill Mesirov <>
  • person_outline Ryan R. Brinkman <>
  • person_outline Michael Reich <>

Additional information


http://software.broadinstitute.org/cancer/software/genepattern/user-guide#user-guide http://software.broadinstitute.org/cancer/software/genepattern/FAQ

Information


Unique identifier OMICS_01855
Name GenePattern
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
High performance computing Yes
Registration required Yes
Maintained Yes

Documentation


Maintainers


  • person_outline Jill Mesirov <>
  • person_outline Ryan R. Brinkman <>
  • person_outline Michael Reich <>

Additional information


http://software.broadinstitute.org/cancer/software/genepattern/user-guide#user-guide http://software.broadinstitute.org/cancer/software/genepattern/FAQ

Publications for GenePattern

GenePattern citations

 (596)
library_books

Analysis of the microRNA signature in left atrium from patients with valvular heart disease reveals their implications in atrial fibrillation

2018
PMCID: 5933750
PMID: 29723239
DOI: 10.1371/journal.pone.0196666

[…] were calculated to test the difference of specific mirna based on threshold cycle (ct) values., hierarchical clustering was calculated by using pairwise average-linkage clustering and drawn by using genepattern (v3.2.3, http://pwbc.garvan.unsw.edu.au/gp, [, ])., mirna target gene predictions are from targetscan 7.0 (http://www.targetscan.org/vert_70/) [] which predicts biological targets […]

library_books

Multi omics profiling of younger Asian breast cancers reveals distinctive molecular signatures

2018
PMCID: 5928087
PMID: 29713003
DOI: 10.1038/s41467-018-04129-4

[…] by varscan2. all germline and somatic mutations were annotated using the ensembl variant effect predictor. significantly mutated gene analysis was performed using mutsigcv v1.2 from the online genepattern tools. we used gatk to estimate depth of coverage from the bam files of 186 smc tumor/normal samples using hg19 as genome reference. cnv segmentation was then called by exomecnv v1.4 […]

library_books

Snail promotes ovarian cancer progression by recruiting myeloid derived suppressor cells via CXCR2 ligand upregulation

2018
PMCID: 5923228
PMID: 29703902
DOI: 10.1038/s41467-018-03966-7

[…] the tcga hg-u133a dataset from the tcga data portal (http://cancergenome.nih.gov) was analyzed by single-sample gene set enrichment analysis (ssgsea) at the gene level, as previously described (genepattern version 3.5.1; http://www.broadinstitute.org/cancer/software/genepattern). generic emt scoring was used as previously described in ref. . for data analyses, the ssgsea scores […]

library_books

A systematic and prospectively validated approach for identifying synergistic drug combinations against malaria

2018
PMCID: 5896032
PMID: 29642892
DOI: 10.1186/s12936-018-2294-5

[…] approach developed earlier [] was used to predict single compounds with activity against malaria. for this purpose geo dataset [] gds4259 was downloaded using the geoimporter [] tool of genepattern []. this dataset contains data derived from peripheral blood samples from five malawian children with severe p. falciparum malaria, compared to the same children who presented with a mild […]

library_books

Classical NF κB Metabolically Reprograms Sarcoma Cells Through Regulation of Hexokinase 2

2018
PMCID: 5904193
PMID: 29696133
DOI: 10.3389/fonc.2018.00104

[…] gene set collection. statistical significance was determined using 1,000 random permutations of each gene set to obtain a nominal p-value and false discovery rate. heat map was generated using genepattern (). heatmapviewer (v11) was used to display values in heat map format for the genes identified from gsea analysis., the microarray data have been deposited into the geo database […]

library_books

The Factor Inhibiting HIF Asparaginyl Hydroxylase Regulates Oxidative Metabolism and Accelerates Metabolic Adaptation to Hypoxia

2018
PMCID: 5887987
PMID: 29617647
DOI: 10.1016/j.cmet.2018.02.020

[…] relevant to fih ko, vhl ko and vhl/fih dko mouse embryonic fibroblasts was downloaded from ncbi geo (geo: gds3769). a principal component analysis was first performed using the relevant function on genepattern (broad institute, usa) server, to visualize differences. the dataset was filtered through a preprocessdataset function on genepattern, applying lower and upper limits of 0 and 20 000 […]


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GenePattern institution(s)
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada; Computational Biology and Bioinformatics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Vaccine and Gene Therapy Institute of Florida, Port Saint Lucie, FL, USA; J. Craig Venter Institute, San Diego, CA, USA; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
GenePattern funding source(s)
Supported by Genome BC, Genome Quebec, Genome Canada, the Terry Fox Research Institute and the Terry Fox Foundation, and by a Scholar Award from the Michael Smith Foundation for Health Research.

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