CisFinder protocols

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chevron_left Transcription factor binding site prediction Data analysis De novo motif discovery Over-representation analysis chevron_right
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CisFinder specifications

Information


Unique identifier OMICS_06290
Name CisFinder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Maintainers


  • person_outline Alexei Sharov <>
  • person_outline Minoru Ko <>

Information


Unique identifier OMICS_06290
Name CisFinder
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Alexei Sharov <>
  • person_outline Minoru Ko <>

Publication for CisFinder

CisFinder in pipelines

 (5)
2016
PMCID: 4891180
PMID: 27178982
DOI: 10.7554/eLife.12717.044

[…] was performed with macs 1.4.1 ) (default parameters). profiles of genomic regions were generated using d-peaks source code (). a de novo search for motifs enriched at peak summits was done with cisfinder () using default parameters and a background control set of 100 bp genomic regions located 3kp upstream input regions. calculation of p-values for the association between binding events […]

2014
PMCID: 3898017
PMID: 24417914
DOI: 10.1186/1471-2164-15-22

[…] de ciencia e innovación (spain), co-financed by feder, and grant p08-cvi-03838 from junta de andalucia (spain). the authors are very grateful to k. kornacker for carrying out the triform and cisfinder analyses, and to h. auer from the functional genomics core facility of the irb, barcelona (spain). we are indebted to j.w. golden for providing the processed files of the transcriptomic […]

2013
PMCID: 3732535
PMID: 23812588
DOI: 10.1038/nature12287

[…] libraries were constructed following the illumina protocol and sequenced on the illumina genome analyzer ii. peak-calling/annotation and consensus sequence analyses were performed with chipseeqer, cisfinder and cisgenome., the shrna against aml1-eto was designed to target the fusion site. other lentiviral shrna sets were purchased from open biosystems. virus preparation and cell infection […]

2013
PMCID: 3791401
PMID: 24055059
DOI: 10.1016/j.celrep.2013.08.012

[…] cluster3, and javatreeview were subsequently used to combine different chip/rna-seq data sets and visualize data as histograms, venn diagrams, or heat maps. de novo motif analysis was performed with cisfinder (). see for further details., the affinity of xbra binding to different dna motifs was measured on an octet red biolayer interferometer. biotinylated dna oligonucleotides () […]

2013
PMCID: 3878573
PMID: 24120743
DOI: 10.1016/j.stem.2013.09.003

[…] 70 bp. to identify peaks bound in one experiment but not another, we defined “nonbound” as the absence of a macs call in the nonfiltered list within 1 kb of that location. motif discovery used cisfinder () and meme () with default parameters; specific motifs were mapped back to peaks using fuzznuc (). peaks were assigned to the nearest transcription start site using cisgenome (). binary […]


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CisFinder in publications

 (22)
PMCID: 5719399
PMID: 29214996
DOI: 10.1038/s41598-017-16009-w

[…] were analyzed by high-throughput sequencing. using model-based chip-seq analysis, we found a total of 16736 confident peaks (supplementary table ). we performed de novo motif discovery with cisfinder. the main consensus-binding motif cluster turns out to be a known cdx motif (fig. ). this motif is overrepresented in chip-enriched regions, as we looked at motif counts across 4 kb windows […]

PMCID: 5569996
PMID: 28854641
DOI: 10.1093/gbe/evx127

[…] better suited to small-scale gene expression studies., other existing methods can be used to discover motifs and gene regulatory networks in daphnia, for example clover (), rsat peak-motifs (), or cisfinder (). a comprehensive comparison of the different methods is beyond the scope of this article and we refer the reader to the recent review by . because of differences in the underlying […]

PMCID: 5081483
PMID: 27777270
DOI: 10.15252/msb.20167131

[…] the ey1h network. randomization was done by edge switching so that overall network topology as well as individual node degree was preserved (martinez et al, )., motif predictions were derived using cisfinder (sharov & ko, ). briefly, for each tf, the 500 bp proximal promoter sequences of ey1h targets was used to identify motifs enriched compared to the sequences of promoters not bound […]

PMCID: 4576985
PMID: 26265007
DOI: 10.15252/embr.201540467

[…] low – batch – revcomp) on the complete set of peak sequences of sox2, oct6, brn1 and brn2 in nscs (this study), as well as oct4 and sox2 in escs (peaks obtained from http://lgsun.grc.nia.nih.gov/cisfinder), as well as oct4/sox2 in escs and brn2/sox2 in npcs . to exclude non-specific sequence patterns, we used dnasei hypersensitive sites from the encode project (http://genome.ucsc.edu/encode) […]

PMCID: 4509496
PMID: 26236718
DOI: 10.1155/2015/218068

[…] an unsolved problems of local optimum and the iteratively training also costs too much. additionally, consensus-based algorithms are designed based on word-enumeration methods, such as rast [] and cisfinder [], which can process whole chip-seq data set by two contrastive data sets. both rast and cisfinder are limited to find short motifs and may miss the useful information contained […]


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CisFinder institution(s)
Developmental Genomics and Aging Section, Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD, USA
CisFinder funding source(s)
Supported entirely by the Intramural Research Program of the NIH, National Institute on Aging.

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