GenePattern statistics

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Protocols

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

 (333)
library_books

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

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

[…] mended 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 based […]

call_split

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

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

[…] thways 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 with the acc […]

library_books

Identification of transcriptome signature for predicting clinical response to bevacizumab in recurrent glioblastoma

2018
PMCID: 5943425
PMID: 29573206
DOI: 10.1002/cam4.1439

[…] s were divided into two groups according to clinical response to bevacizumab.ssGSEA: Single‐sample gene set enrichment analysis (ssGSEA) was used to estimate the enrichment score of each sample using GenePattern software of Broad Institute (http://software.broadinstitute.org/cancer/software/genepattern). Gene expression data were normalized using a “rank” method . The subtype of each sample was as […]

library_books

Functional genomics identifies specific vulnerabilities in PTEN deficient breast cancer

2018
PMCID: 5863852
PMID: 29566768
DOI: 10.1186/s13058-018-0949-3

[…] then uses the shRNAs with consistent profiles to calculate the gene-level viability score for each gene in each cell line (Additional file : Table S9). We ran the ATARiS version 2 algorithm using the GenePattern public server []. ATARiS sometimes generates > 1 solution per gene depending on the number of shRNA clusters showing the same activity profile across cell lines. We used all gene solutions […]

library_books

Expanding the Utilization of Formalin Fixed, Paraffin Embedded Archives: Feasibility of miR Seq for Disease Exploration and Biomarker Development from Biopsies with Clear Cell Renal Cell Carcinoma

2018
Int J Mol Sci
PMCID: 5877664
PMID: 29534467
DOI: 10.3390/ijms19030803

[…] dge Base was used as a reference dataset.Canonical pathways were sorted by their smallest Benjamini-Hochberg-adjusted p-value.Classifier analysis was then performed with the KNN Validation package in GenePattern (Available online: http://www.broadinstitute.org/cancer/software/genepattern). Euclidean distance was used as distance measure, where three neighbours were considered. Additional analyses […]

library_books

Differential effects of α catenin on the invasion and radiochemosensitivity of human colorectal cancer cells

2018
PMCID: 5843400
PMID: 29484367
DOI: 10.3892/ijo.2018.4279

[…] ons using the manufacturer's dedicated Reagent kits. Affymetrix Gene Expression Console (v.1.1) software was used for data processing using standard settings (quantile normalization, RMA correction). GenePattern software (Broad Institute, Cambridge, MA, USA) was used to reduce (collapse) multiple gene occurrences on the arrays via gene symbol to one signal per gene and sample. Microarray data are […]

Citations

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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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