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GeneCluster specifications


Unique identifier OMICS_23791
Name GeneCluster
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Input data A file containing the gene intensity values for each sample scanned along with the associated annotations.
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 2.0
Maintained No


No version available

Publication for GeneCluster

GeneCluster citations


Alterations in the p53 SOCS2 axis contribute to tumor growth in colon cancer

PMCID: 5940812
PMID: 29622769
DOI: 10.1038/s12276-017-0001-1
call_split See protocol

[…] all samples in at least 10% of samples were selected for cluster analysis. Average linkage hierarchical cluster analysis was carried out using Pearson correlation as the similarity metric, using the GeneCluster/TreeView program ( We used t test P = 0.01. To ascertain biological relevance, a fold-change cutoff value of 1.5 from the mean was chosen. […]


Identification of nuclear genes controlling chlorophyll synthesis in barley by RNA seq

BMC Plant Biol
PMCID: 5123340
PMID: 28105957
DOI: 10.1186/s12870-016-0926-x

[…] produced by Cufflinks pipeline was used as a reference genome annotation in order to assess table of counts from STAR mappings. These estimates of the mRNA fragments expression were used as input to GeneCluster3.0 [] software to cluster six libraries by UPGMA method using average clustering method. Reconstructed tree describing similarity of mRNA expression estimates in all six libraries was visu […]


A dataset for assessing temporal changes in gene expression during the aging process of adult Drosophila melanogaster

PMCID: 4874455
PMID: 27252981
DOI: 10.1016/j.dib.2016.04.072

[…] ed with Linear Models for Microarray Analysis (LIMMA) package in Bioconductor , , . The genes identified as differentially expressed across all the time points were subjected to cluster analyses. The GeneCluster 2 package, a self-organizing map (SOM) clustering algorithm , was applied to the significantly differentially expressed genes. From this, self-organizing map (SOM) and hierarchical cluster […]


Establishment of a prediction model of changing trends in cardiac hypertrophy disease based on microarray data screening

PMCID: 4840528
PMID: 27168795
DOI: 10.3892/etm.2016.3105

[…] B metabolic genes in human pulmonary type II cells () and nuclear factor-kappaB pathway in a mouse model of genitourinary inflammation (), have been identified via mathematical cluster analysis using GENECLUSTER, which is a publicly available computer package that contributed to the establishment of an effective treatment for acute promyelocytic leukemia (). According to a previous study conducted […]


The potential role of Alu Y in the development of resistance to SN38 (Irinotecan) or oxaliplatin in colorectal cancer

BMC Genomics
PMCID: 4440512
PMID: 25997618
DOI: 10.1186/s12864-015-1552-y

[…] thylation states for a given locus across samples []. We applied WebLogo 3.3 [] to extract the flanking sequence (up- and down- stream 20 bp) motifs for the investigated genomic sequences. We applied GeneCluster 2.0 [] to perform the supervised cluster analysis and prediction analysis. […]


Genome Wide Gene Expression in relation to Age in Large Laboratory Cohorts of Drosophila melanogaster

PMCID: 4454753
PMID: 26090231
DOI: 10.1155/2015/835624

[…] nalysis. The profile for each gene was standardized so that each profile had a mean = 0 and a standard deviation = 1. Data matrices were constructed with genes in rows and time points in columns. The GeneCluster 2 package was used []. The number of iterations in SOM clustering was set to 500,000. From this, self-organizing map (SOM) and hierarchical clustering heat map (correlation-based distance, […]


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GeneCluster institution(s)
The Eli and Edythe L. Broad Institute, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard University, Cambridge, MA, USA

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