PermutMatrix protocols

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PermutMatrix statistics

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PermutMatrix specifications

Information


Unique identifier OMICS_13005
Name PermutMatrix
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data Subset of gene expression data
Input format TXT, XLS, EISEN’S CLUSTER (format)
Operating system Windows
Programming languages C++
Computer skills Advanced
Version 1.9.3
Stability Stable
Maintained Yes

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  • person_outline Gilles Caraux <>

Publication for PermutMatrix

PermutMatrix in pipelines

 (8)
2017
PMCID: 5206656
PMID: 28045125
DOI: 10.1038/srep39794

[…] software (addinsoft, new york, ny) to detect the common variations between variables and to visualize clusters of correlated observations. heatmap and hierarchical clustering were generated by permutmatrix program with euclidean distance for dissimilarity and complete linkage for aggregation criteria. the graphical representation is based on z-scores. normalized expression values […]

2016
PMCID: 4742245
PMID: 26844771
DOI: 10.1371/journal.pone.0148374

[…] by the sum of rpkm values in all libraries (rpkm threshold in unigene; > 2,129 or rpkm threshold in ensembl; > 4,389) were used for heat map analysis with hierarchical clustering using permutmatrix (http://www.lirmm.fr/~caraux/permutmatrix/en/). the excel statistical function chisq.test was used to obtain the p-values for differences between rpkm values within sex. theoretical […]

2016
PMCID: 4940487
PMID: 27374709
DOI: 10.3343/alm.2016.36.5.441

[…] again with the nucleotide basic local alignment search tool (blast) database []. the its and tvk sequences were also analyzed in blast because these sequences are not included in the rdp []. permutmatrix version 1.9.3 was used to draw a heat map for visualization of the taxonomy []. the shannon diversity index was calculated to estimate the alpha diversity []. two shannon diversity […]

2015
PMCID: 4849109
PMID: 27152109
DOI: 10.17179/excli2015-600

[…] fold change (rpkm-tr/rpkm-cont) ≥ 2 and the absolute ratio of log2 (rpkm-tr/rpkm-cont) ≥ 1 were used as threshold values. finally, the heat maps of hierarchical clustering were visualized with permutmatrix (caraux and pinloche, 2005[])., the seeds of ispir, a salt tolerant local common bean variety, were germinated in vermiculite containing plug trays. seedlings were incubated in growth […]

2014
PMCID: 3906094
PMID: 24450868
DOI: 10.1186/1471-2164-15-59

[…] a 2-fold change (fc) in expression between healthy and infected animals and had a p-value ≤ 0.05 were selected. these genes were clustered according to their euclidean distance coefficient using permutmatrix software []. a megablast search of the genbank database nr/nt was performed to identify genes that were similar to the differentially expressed probes. the molecular functions […]


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PermutMatrix in publications

 (100)
PMCID: 5915062
PMID: 29719595
DOI: 10.18632/oncotarget.24773

[…] epithelium. the ipa classified proteins were clustered individually in samples from the groups early and late stage cervical cancer and healthy epithelium. for hierarchical clustering analysis permutmatrix 1.9.3. was used (http://www.atgc-montpellier.fr/permutmatrix) selecting the euclidean distance for dissimilarity, wards’ method, as a cluster method and bipolarization seriation [, ]., […]

PMCID: 5867640
PMID: 29562624
DOI: 10.3390/md16030096

[…] into regular bins, i.e., chemical shift intervals of ∆δ = 0.2 ppm, and to associate the absolute intensity of each 13c nmr peak with the corresponding bin. the resulting table was imported into the permutmatrix version 1.9.3 software (lirmm, montpellier, france) for clustering analysis on raw peak intensity values. the classification was performed on the rows only, i.e., on the chemical shift […]

PMCID: 5815207
PMID: 29448950
DOI: 10.1186/s13567-018-0512-3

[…] and p value of each mirna in each sample pair were calculated using previously published criteria [–]. a hierarchical clustering analysis of the mirna expression levels was performed using permutmatrix software. the relative expression level of each mirna was calculated as the total number of reads in the four libraries., differentially expressed mirna and target mrna were validated […]

PMCID: 5812622
PMID: 29444183
DOI: 10.1371/journal.pone.0192562

[…] and primers on the other. afterwards the plate was run using the biomark fluidigm system. data was obtained by fluidigm real-time pcr analysis software. heatmaps were produced using the software permutmatrix v.1.9.3., analysis of mg63 cell rna levels in response to antaogmir-31-gnp incubation was performed using the fluidigm biomark hd system. this system allows for automated pcr reactions […]

PMCID: 5794915
PMID: 29391556
DOI: 10.1038/s41598-018-20473-3

[…] the remaining residuals of the phenotypes and gene expression values corrected for the corresponding effects were used to obtain the pairwise correlations. the hierarchical clustering option of permutmatrix software was used to visualize the results of both traits and genes., , maria ballester and josep m. folch contributed equally to this work., electronic supplementary material , […]


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PermutMatrix institution(s)
Laboratoire d’Informatique de Robotique et de Microélectronique de Montpellier, Montpellier, France; Ecole Nationale Supérieure Agronomique de Montpellier, Montpellier, France; Research School of Biological Sciences, Australian National University, Canberra, Australia

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