TM4 protocols

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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

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Maintainer


  • person_outline John Quackenbush <>

Publication for TM4

TM4 in pipelines

 (89)
2018
PMCID: 5760739
PMID: 29317509
DOI: 10.1128/mBio.01678-17

[…] in the sra: srr5676707, srr5676716, srr5676717, srr5676703, and srr5676704. hierarchical clustering of log2-transformed read-per-kilobase-per-million (rpkm) data was performed using meviewer tm4 software. data were either clustered as is or linearly mean centered using euclidian distance. color scales were adjusted for presentation purposes., for rt-qpcr analyses, rna was isolated […]

2018
PMCID: 5764346
PMID: 29324804
DOI: 10.1371/journal.pone.0191081

[…] were mapped on sacexp using blastn with e-value of 10−10 as threshold. the expression of transcripts was visualized by a hierarchical clustered heat map performed in the mev software (http://www.tm4.org/mev.html)., the same genotype (sp80-3280) was used to study the expression profile of some of the expansins in sugarcane. the plants were planted in december of 2016 and grown in experimental […]

2018
PMCID: 5799827
PMID: 29449851
DOI: 10.3389/fpls.2018.00048

[…] , www.bioconductor.org/packages/release/bioc/html/limma.html , http://bar.utoronto.ca/ntools/cgi-bin/ntools_classification_superviewer.cgi , https://david.ncifcrf.gov , www.tm4.org/ , http://arabidopsis.med.ohio-state.edu , www.tanpaku.org/autophagy/index.html , http://merops.sanger.ac.uk , http://quantprime.mpimp-golm.mpg.de , the supplementary material […]

2018
PMCID: 5827756
PMID: 29483524
DOI: 10.1038/s41598-018-21866-0

[…] values of all the hsp genes were fetched (p-value ≤ 0.05). a heat map was generated to visualize the transcript level of significantly expressed hsp genes using mev v2.0 software (http://mev.tm4.org/#/welcome)., the arabidopsis hsp90 and hsp70 protein sequences were used as a query to perform blastp similarity search (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/latest/) […]

2018
PMCID: 5866023
PMID: 29436647
DOI: 10.3892/mmr.2018.8560

[…] by a volcano plot. finally, hierarchical clustering was performed to determine the differences in the mirna expression profiles among the samples using webmev software (version 4.6; http://mev.tm4.org/) ()., to further investigate the functional roles of mirna, the putative targets of mir-449a-5p, mir-34b/c-5p and mir-21-5p were predicted by targetscan (http://www.targetscan.org/), […]


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TM4 in publications

 (1961)
PMCID: 5955887
PMID: 29769636
DOI: 10.1038/s41598-018-26070-8

[…] populated regions, clustered around α1, α2 ≈ 0° and α1, α2 ≈ π and below distances of 4.5 nm for either inactive or activated mor conformations suggest a preference for mor homodimerization through tm4,5,6,7 or tm1,2,h8 contacts, respectively. notably, the region around α1, α2 ≈ π presents a broader distribution in the inactive mor simulations (see larger dark red area in fig. ) compared […]

PMCID: 5942774
PMID: 29742107
DOI: 10.1371/journal.pone.0195869

[…] for the anderson-darling test and the bioconductor biostrings package was used to process dna sequence data., hierarchical clustering of cib using average linkage was carried out by means of the tm4 mev v4.9.0 stand-alone local client using the pearson product correlation coefficient as the distance metric []., mining sites are characterized by the presence of low-ph and the prevalence […]

PMCID: 5941469
PMID: 29739322
DOI: 10.1186/s12870-018-1296-3

[…] q ≤ 0.05 was used as the threshold for significant enrichment of deg kegg pathways. hierarchical clustering analysis of degs was carried out using multi experiment viewer (http://mev.tm4.org/#/welcome)., fresh hazel ovary or stigma samples from four different developmental stages were fixed in 4% paraformaldehyde for 16 h at 4 °c, then washed with phosphate-buffered saline (pbs) […]

PMCID: 5941172
PMID: 29735731
DOI: 10.1098/rstb.2017.0177

[…] can be traced back to the global modes, or the signature profile, uniquely defined by the leut-fold., a closer inspection shows differences at certain regions, such as tm1, the ic loop between tm4 and tm5, and the ec loop el4 between tm7 and tm8. the latter participates in regulating ec gating and substrate access [], a role fulfilled by substrate-specific residues, hence the heterogeneity […]

PMCID: 5935748
PMID: 29728569
DOI: 10.1038/s41598-018-25349-0

[…] spikelets with bracts removed at 5 dpa (car5) and 15 dpa (car15). a heat map of the expression of hvspls was generated by the average hierarchical clustering method using the mev tool (http://www.tm4.org/mev.html)., the mirex2.0 web portal (http://www.combio.pl/mirex) provides a comprehensive platform for the examination of microrna expression data based on next generation sequencing (ngs) […]


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