TM4 pipeline

TM4 specifications

Information


Unique identifier OMICS_21567
Name TM4
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Java
License Artistic License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Subtool


  • ExpressConverter

Versioning


Add your version

Maintainer


  • person_outline John Quackenbush <>

Publication for TM4

TM4 citations

 (14)
2017
PMCID: 5501815

[…] screen trait-associated modules, we set a cutoff p-value of 0.05 (fig. 6). to investigate the correlation of different modules, hierarchical clustering for all module eigengenes was conducted using tm4 (v4.9)60. we used in-house perl scripts to find r, prr, tf and lncrna transcripts within modules, and performed go and conserved-domain enrichment analysis for protein-coding transcripts within […]

2017
PMCID: 5331639

[…] made on the website http://bioinfogp.cnb.csic.es/tools/venny/. probe-set expression pattern clustering was performed using the multi experiment viewer software in the java environment (http://mev.tm4.org/). the go analysis was performed on the website http://omicslab.genetics.ac.cn/goeast/php/affymetrix.php?#step1_anchor [33]. all of the expression-differential probes were previously […]

2016
PMCID: 4707443

[…] , http://www.fagaceae.org/ , http://www.arabidopsis.org/ , http://bio-bwa.sourceforge.net , http://bioinfogp.cnb.csic.es/tools/venny/index.html , http://cdbfasta.sourceforge.net/ , http://www.tm4.org/mev.html , http://bioinformatics.ysu.edu/tools/orfpredictor.html , http://www.arabidopsis.org , http://arabidopsis.med.ohio-state.edu/attfdb/ , http://www.corkoakdb.org/ , […]

2015
PMCID: 4613645

[…] each donor treatment. gene expression signature was carried out for fold changes in expression > |1.2|, p < 0.05., differentially expressed genes were hierarchically clustered using the tm4 microarray software suite57 with the euclidian distance metric and average linkage method. clustering and heatmaps involved tm4 software suite. gene expression data with log values < 3 […]

2015
PMCID: 4314081

[…] and fluorescent intensities of hybridization signals were extracted using the agilent feature extraction software. for data analysis, statistics were performed using microsoft excel and mev v4.7 tm4 open-source software [34]. up- and down-regulated genes were defined by producing a five-fold difference in signal intensity in relation to an average of three housekeeping genes (see results […]

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