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F-Match specifications

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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 citations

 (25)
library_books

Exploring gene expression biomarker candidates for neurobehavioral impairment from total sleep deprivation

2018
BMC Genomics
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 […]

library_books

Computational master regulator search reveals mTOR and PI3K pathways responsible for low sensitivity of NCI H292 and A427 lung cancer cell lines to cytotoxic action of p53 activator Nutlin 3

2018
BMC Med Genomics
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 […]

library_books

Accurately tracking single cell movement trajectories in microfluidic cell sorting devices

2018
PLoS One
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 […]

library_books

Nucleotide patterns aiding in prediction of eukaryotic promoters

2017
PLoS One
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) […]

library_books

Relevance of iPSC derived human PGC like cells at the surface of embryoid bodies to prechemotaxis migrating PGCs

2017
Proc Natl Acad Sci U S A
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 […]

library_books

Metformin induces cell cycle arrest at the G1 phase through E2F8 suppression in lung cancer cells

2017
Oncotarget
PMCID: 5731892
PMID: 29254182
DOI: 10.18632/oncotarget.21552

[…] dickinson)., the transcription factors (tfs) responsible for downregulation of genes (<1.5) by metformin were analyzed using transfac and explain (qiagen, germany). transfac and explain use f-match to search for putative tfbss and tfs by a weight matrix-based algorithm through comparing a yes-set (experimental set) to a no-set (control or background set) []. promoter regions from -2000 […]


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