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XMotifs specifications

Information


Unique identifier OMICS_03486
Name XMotifs
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability No
Requirements
biclust, fabia, isa
Maintained No

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Publication for XMotifs

XMotifs in publications

 (6)
PMCID: 5660162
PMID: 29079755
DOI: 10.1038/s41598-017-13297-0

[…] tends to find sub-matrices having all ones (“1”), resulting in 10 clusters each with few pds that are present in all species of the cluster (size too small to be visible on the plot of fig. ), while xmotifs tends to identify sub-matrices whose rows have the same state (i.e. either “1” or “0”) over a set of columns, yielding five groups in which protein domains are “absent” in the group’s […]

PMCID: 5430742
PMID: 28432308
DOI: 10.1038/s41598-017-01064-0

[…] by maximizing mutual information between entries of bi-clusters. but this approach is restricted to non-negative data matrix. murali et al. proposed the concept of conserved gene expression motifs (xmotifs), each motif is defined as a subset of genes whose expressions are simultaneously conserved for a subset of samples. xmotifs aims to discover large conserved gene motifs that cover […]

PMCID: 5259837
PMID: 28114903
DOI: 10.1186/s12859-017-1487-1

[…] mean squared residue measure; order-preserving submatrix (opsm) [], which searches for biclusters with rows following the same linear order under the same columns; conserved gene expression motifs (xmotifs) [], a nondeterministic algorithm that finds submatrices with simultaneously conserved genes in subsets of experimental conditions in a discrete data matrix; iterative signature algorithm […]

PMCID: 3668234
PMID: 23433178
DOI: 10.1186/1748-7188-8-4

[…] modules, which are self-consistent regulatory unit consisting of a set of co-regulated genes and the experimental conditions that induce their co-regulation. murali and kasif [] proposed the use of xmotifs (conserved gene expression motifs) for the representation of gene expression data. their algorithm looks for large xmotifs in which genes are expressed in the same state across all samples […]

PMCID: 3037342
PMID: 21261986
DOI: 10.1186/1756-0381-4-3

[…] finding a remarkable number of biclusters with shifting and scaling patterns. in addition, the performance of the proposed method and fitness function are compared to that of cc, opsm, isa, bimax, xmotifs and samba using gene the ontology database., dna microarray technology measures the gene expression level of thousand of genes under multiple experimental conditions []. after several […]


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XMotifs institution(s)
Bioinformatics Program, Boston University, Boston, MA, USA

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