Mfuzz protocols

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chevron_left Gene expression microarray data visualization Gene expression clustering Time course chevron_right
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Mfuzz specifications

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Unique identifier OMICS_02012
Name Mfuzz
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.40.0
Stability Stable
Requirements
Biobase(>=2.5.5), marray, tcltk, R(>=2.5.0), e1071, tkWidgets
Maintained Yes

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Publication for Mfuzz

Mfuzz in pipelines

 (10)
2018
PMCID: 5941663
PMID: 29739334
DOI: 10.1186/s12864-018-4664-3

[…] of the inflammatory response, cell adhesion, and calcium ion binding. there were no significantly enriched functional clusters for the up-regulated transcript clusters of the treatment list (mfuzz treatment group 2, fig. ) or pvt list (mfuzz pvt group 3, fig. ), likely due to the small number of up-regulated transcript clusters. most transcript clusters were down-regulated.table 3table […]

2017
PMCID: 5560543
PMID: 28817560
DOI: 10.1371/journal.pgen.1006930

[…] seven developmental stages (six stages for columella tissue). the identification of co-expressed genes with csr was done separately with csr-d and csr-wt alleles. the data was first pre-processed by mfuzz [] for normalization. the heatmap.2 function in r was then employed to generate a heatmap based on the normalized rpkm. twelve clusters for csr-d and 10 clusters for csr-wt were identified […]

2016
PMCID: 4866773
PMID: 27175901
DOI: 10.1371/journal.pone.0155671

[…] fold changes. differentially expressed genes were identified based on fold change values. the time-course expression patterns during conidiation were clustered into 10 groups using the r package mfuzz with default setting, which performs fuzzy c-means clustering []., sexual and asexual reproduction are commonly induced together in various fusarium species, including f. graminearum []. […]

2016
PMCID: 4931018
PMID: 27339440
DOI: 10.1038/ncomms11708

[…] homeobox, far1-like and mads-box family (). expression analysis revealed that many tf families were more highly expressed in pollen () and the 5,423 tf isoforms were classified into 20 clusters by mfuzz based on their expression value ()., in addition to protein-coding rnas, non-coding rnas constitute a major component of the transcriptome. recently, 1,704 high-confidence long non-coding rnas […]

2016
PMCID: 5389521
PMID: 27899593
DOI: 10.1093/nar/gkw1156

[…] cut-off at 1.5-fold averaged over the two replicate experiments and a p-adjusted value <0.05. clustering of the temporal profile of h3k4me3 regions during differentiation was performed with mfuzz, as described above (). homer was used for counting tags at identified regions, annotating binding sites to refseq genes, generating average profiles, and count matrices for heat maps as well […]


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Mfuzz in publications

 (86)
PMCID: 5941663
PMID: 29739334
DOI: 10.1186/s12864-018-4664-3

[…] of the top hub transcript cluster for each module, namely, the most highly connected transcript cluster within the module., a second, temporal clustering approach was performed using r/mfuzz v. 2.28.0 [] to visualize gene expression shifts over time in response to tsd, for those not fatigue resistant. thus, mfuzz was used to cluster and plot the mean expression of differentially […]

PMCID: 5922017
PMID: 29699496
DOI: 10.1186/s12864-018-4657-2

[…] expression list, the fold changes of expression levels between the treated and time-matched control samples across all five time points were analyzed by the r (http://www.r-project.org) package mfuzz (http://mfuzz.sysbiolab.eu) to identify clusters of distinct time profiles following injury presented in figs.  and . targetscan version 7.0 [] was queried to compile a list of computationally […]

PMCID: 5885395
PMID: 29765976
DOI: 10.1155/2018/7691794

[…] of each time series gene and lncrna, principal component analysis (pca) was performed with the aid of the “prcomp” module in r., the time series genes identified were clustered using the r package mfuzz [] that performs soft clustering based on the fuzzy c-means algorithm. the advantage of soft clustering is that the algorithm clearly reflects the strength of association of an individual gene […]

PMCID: 5848805
PMID: 29608722
DOI: 10.1093/gbe/evy041

[…] we searched for all homo sapiens motifs on both + and – strands and specified a minimum score of 100% using r packages tfbstools () and jaspar2016 ()., we performed soft clustering of dhs data using mfuzz (), using standardized expression sets prepared from log2 values of mean dhs activity among replicates for shared or species-specific dhs sites. the fuzzifier for each expression set […]

PMCID: 5813207
PMID: 29445139
DOI: 10.1038/s41467-018-03024-2

[…] state.fig. 2, to further understand the dynamic changes at the gene expression level during the metastasis progression, we classified all degs into six patterns (cluster 1,…,cluster 6) using mfuzz (fig. ). genes in clusters 1 and 2 were continuously and monotonically downregulated and upregulated from the second to fourth weeks after orthotropic implantation, respectively. genes […]


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Mfuzz institution(s)
Institute of Medical Informatics and Biometry, Charite, Humboldt University, Berlin, Germany

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