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Protocols

GeneCluster specifications

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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

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No version available

Publication for GeneCluster

GeneCluster citations

 (63)
library_books

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

2018
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 (http://rana.lbl.gov/eisensoftware.htm). we used t test p = 0.01. to ascertain biological relevance, a fold-change cutoff value of 1.5 from the mean was chosen., […]

library_books

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

2017
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 […]

library_books

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

2017
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, […]

library_books

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

2016
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 […]

library_books

SIRT1 promotes metastasis of human osteosarcoma cells

2016
Oncotarget
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 […]

library_books

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

2016
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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