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Protocols

GeneCluster specifications

Information


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

Versioning


No version available

Publication for GeneCluster

GeneCluster citations

 (28)
call_split

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
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 (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

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 was visu […]

library_books

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

2016
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 […]

library_books

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

2016
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 […]

library_books

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

2015
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. […]

library_books

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

2015
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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