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HeatMapViewer specifications

Information


Unique identifier OMICS_04852
Name HeatMapViewer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Javascript
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Guy Yachdav

Publication for HeatMapViewer

HeatMapViewer citations

 (24)
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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

[…] 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 accession number GS […]

library_books

The impact on high‐grade serous ovarian cancer of obesity and lipid metabolism‐related gene expression patterns: the underestimated driving force affecting prognosis

2017
J Cell Mol Med
PMCID: 5824367
PMID: 29266765
DOI: 10.1111/jcmm.13463

[…] genepattern) to calculate the significant differences in gene expression between classes. Array‐based data, either for mRNA or protein expression levels, were displayed in a heat map format using the HeatMapViewer v14 module (genepattern) to facilitate pattern identification.The most robust NMF consensus clustering of copy number variations (579 samples, 73 copy number focal peak regions, https:// […]

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Isolation and detection of circulating tumour cells from metastatic melanoma patients using a slanted spiral microfluidic device

2017
Oncotarget
PMCID: 5620178
PMID: 28978038
DOI: 10.18632/oncotarget.18641
call_split See protocol

[…] were carried out in a ViiA™ 7 Real-Time PCR system (Thermo Fisher Scientific) []. Expression values were represented as the reciprocal Ct value for each target gene and plotted in a heatmap using the HeatMapViewer module (version 13.9; Broad Institute) at the GenePattern platform []. RNA isolated from cells in the CTC outlet after processing the blood of healthy individuals and from a sample spike […]

library_books

Bone morphogenetic protein 2 mediated pain and inflammation in a rat model of posterolateral arthrodesis

2016
BMC Neurosci
PMCID: 5134101
PMID: 27905881
DOI: 10.1186/s12868-016-0314-3

[…] Differentially expressed BeadArray features corresponding to transcripts were queried for relationships using GO, GATHER, and GSEA [, ]. Heatmaps of enriched transcript subsets were visualized using HeatMapViewer within GenePattern 3.8.0. […]

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Underexpression of HOXA11 Is Associated with Treatment Resistance and Poor Prognosis in Glioblastoma

2016
PMCID: 5398402
PMID: 27456940
DOI: 10.4143/crt.2016.106
call_split See protocol

[…] ates (FDRs) were calculated using three GenePattern software modules (http://www.broadinstitute.org/cancer/software/genepattern; ComparativeMarkerSelection ver. 10, HierarchicalClustering ver. 6, and HeatMapViewer ver. 13) []. The cutoff value for FDR significance was < 0.05. The significantly regulated genes were subjected to functional gene classification using the DAVID Bioinformatics Resources […]

library_books

Transcriptional profiling reveals intrinsic mRNA alterations in multipotent mesenchymal stromal cells isolated from bone marrow of newly diagnosed type 1 diabetes patients

2016
PMCID: 4942931
PMID: 27406064
DOI: 10.1186/s13287-016-0351-y

[…] y analyses were performed using algorithms available in the R platform (R Foundation, Vienna, Austria) through the Linear Models for Microarray Data (LIMMA) package []. Heatmaps were generated by the HeatMapViewer module of GenePattern 2.0 software []. Genes with p < 0.05 and fold change (FC) > 2.0 were considered differentially expressed. Microarray data were deposited in the public database Arra […]

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HeatMapViewer institution(s)
TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/ Munich, Germany; TUM Graduate School of Information Science in Health (GSISH), Garching/Munich, Germany; Biosof LLC, New York, NY, USA; Bioinformatics Unit, G.S.W. Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel

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