F-Match protocols

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F-Match specifications

Information


Unique identifier OMICS_18427
Name F-Match
Interface Web user interface
Restrictions to use None
Input data A DNA sequence.
Input format FASTA
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

Additional information


A registration is needed to access to tool. https://portal.biobase-international.com/archive/documents/GSG_ExPlain_Match_FAQ.pdf

F-Match in pipelines

 (2)
2018
PMCID: 5941663
PMID: 29739334
DOI: 10.1186/s12864-018-4664-3

[…] 25 had z-scores <− 2. the largest absolute value of the rif score again was for elk3, with rif z-score = − 6.36., to further characterize potential regulators of the response to tsd, the biobase f-match algorithm was used to assess potential transcription factor binding sites in the promoters of transcript clusters from the treatment and pvt lists. seven transcription factor matrices […]

2012
PMCID: 3504713
PMID: 22790872
DOI: 10.1038/cdd.2012.89

[…] of about 600 positional weight matrices (pwms) from the transfac database for vertebrate tfs. overrepresentation of tf-binding sites and composite elements (tf site pairs) were computed by the f-match algorithm and composite module analyst program (composite module analysts) that is implemented in the genexplain platform (www.genexplain.com)., expression profiling of mcf7 cells […]


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F-Match in publications

 (25)
PMCID: 5941663
PMID: 29739334
DOI: 10.1186/s12864-018-4664-3

[…] the input gene list, and once with the pvt effect transcript clusters. in each run the two conditions consisted of c and tsd., in addition to the rif differential co-expression analysis, the biobase f-match tool (http://www.biobase-international.com) was utilized to search for regulatory transcription factors based on the promoter sequence of differentially expressed genes. the tool scanned […]

PMCID: 5836833
PMID: 29504919
DOI: 10.1186/s12920-018-0330-5

[…] genes that were not differentially regulated under the condition of the experiment. we denote study and background sets briefly as yes and no sets. the algorithm for tfbs enrichment analysis, called f-match, has been initially described in []. briefly, as it has been described in detail previously [], the procedure finds a critical value (a threshold) for the score of each pwm in the library […]

PMCID: 5802930
PMID: 29414993
DOI: 10.1371/journal.pone.0192463

[…] “multiple” forms a pairwise matrix of maximum distances, which represents evidence of whether these “multiple” events in frame f have been separated in previous frames. since these events in frame f match to one event in frame f + 1, we define a threshold using the radius of the “one” event. if the smallest element of this pairwise matrix is smaller than the threshold, meaning the two […]

PMCID: 5687710
PMID: 29141011
DOI: 10.1371/journal.pone.0187243

[…] reference nucleotide or alternative nucleotide; the “no” set is the set created by random nucleotide substitutions in random genomic positions). the algorithm for tfbs enrichment analysis, called f-match, has been described in kel, konovalova [] and koschmann, bhar []. briefly, the procedure finds a critical value (a threshold) for the differences between scores q and q* (the threshold δ0) […]

PMCID: 5699045
PMID: 29087313
DOI: 10.1073/pnas.1707779114

[…] to cd38+ hpgclcs, we examined enrichment of tf binding motifs in promoter sequences of degs between cd38+ and cd38− cells in day 5 ebs using the transcription factor (transfac) database and the f-match algorithm (). we identified 13 tf binding motifs that were significantly enriched in promoters of 537 genes expressed more strongly in cd38+ hpgclcs than cd38− eb cells (), whereas […]


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