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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

[…] 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., […]


Transcriptomic and bioinformatics analysis of the early time course of the response to prostaglandin F2 alpha in the bovine corpus luteum☆☆☆

PMCID: 5596332
PMID: 28932774
DOI: 10.1016/j.dib.2017.08.026

[…] between each of the time points and the saline control were compared using linear models of microarray analysis in the bioconductor suite in r. the self-organizing map (som) clustering algorithm genecluster 2.0 was applied to differentially expressed genes that had a greater than 1.5-fold change in expression and p-value ≤ 0.05 between pgf2α-treated samples and the saline control. the mean […]


A restriction free method for gene reconstitution using two single primer PCRs in parallel to generate compatible cohesive ends

BMC Biotechnol
PMCID: 5356277
PMID: 28302113
DOI: 10.1186/s12896-017-0346-5

[…] s4) containing 21 genes into pet22b between the start codon atg (289), and the sequence caccaccaccaccaccac (157) (additional file : figure s1). gene cluster 3 was amplified using the primer pair genecluster3-1/genecluster3-2, as shown in additional file : table s4, using e. coli genomic dna as template (fig. , lane 4). gene cluster 3 with a sticky end was generated by single-primer pcr, […]


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 […]


SIRT1 promotes metastasis of human osteosarcoma cells

PMCID: 5346743
PMID: 27793039
DOI: 10.18632/oncotarget.12916

[…] a p-value ≤ 0.5, followed by ratio change (≥ 2.0), was used to generate the list of genes with significant change. the microarray data of selected probe sets were subjected to cluster analysis using genecluster software (uc berkeley & lbnl; michael eisen's lab)., values for all samples were averaged, and the standard error or standard deviation of the mean was calculated. differences […]


Genome Wide Identification and Characterization of Carboxypeptidase Genes in Silkworm (Bombyx mori)

Int J Mol Sci
PMCID: 5000601
PMID: 27483237
DOI: 10.3390/ijms17081203

[…] patterns, silkworm from 20 different time points (from day 3 of the fifth instar larval stage to the moth stage) were collected from both genders. gene expression levels were visualized using genecluster 3.0 (university of tokyo, tokyo, japan) []., newly molted fifth instar larvae were divided into three groups, to test whether carboxypeptidases were induced by starvation. larvae […]

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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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