SwissRegulon statistics

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Number of citations per year for the bioinformatics software tool SwissRegulon
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SwissRegulon specifications

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Unique identifier OMICS_00543
Name SwissRegulon
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Maintainer


Publications for SwissRegulon

SwissRegulon citations

 (12)
library_books

TFAP2A is a component of the ZEB1/2 network that regulates TGFB1 induced epithelial to mesenchymal transition

2017
Biol Direct
PMCID: 5392957
PMID: 28412966
DOI: 10.1186/s13062-017-0180-7

[…] 51 for ZEB2 in human, and 0.18 and 0.52, respectively in mouse). To validate the interaction between TFAP2A and the Zeb2 promoter we performed an Electrophoretic Mobility Shift Assay (EMSA). From the SwissRegulon database of transcription factor binding sites that were predicted based on evolutionary conservation (www.swissregulon.ch), we found that the region around the second exon of the Zeb2 ge […]

library_books

Layer specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex

2017
eLife
PMCID: 5325622
PMID: 28112643
DOI: 10.7554/eLife.21883.061

[…] lyze fragment size statistics, and preseq v0.1.0 () to analyze library sequencing saturation. The CENTIPEDE package for R () was used to analyze insertions near ATF2 motif locations obtained from the SwissRegulon database (RRID:SCR_005333) (, ). To downsample BAM files, the data were sorted by name instead of location using Samtools sort in SAM format, then the R sample function was used to select […]

library_books

Characterisation of the global transcriptional response to heat shock and the impact of individual genetic variation

2016
Genome Med
PMCID: 4995779
PMID: 27553423
DOI: 10.1186/s13073-016-0345-5

[…] the promoter region (1200 bp upstream–300 bp downstream of the transcriptional start site (TSS)) of differentially expressed genes. The scan was based on the position weight matrices (PWM) defined by SwissRegulon [] and carried out with the Bioconductor package PWMEnrich []. […]

library_books

Transcription factor motif quality assessment requires systematic comparative analysis

2016
F1000Res
PMCID: 4821295
PMID: 27092243
DOI: 10.5256/f1000research.7983.r11604

[…] algorithms and DBs. It also shows that no single database currently outperforms the others for all TFs. There is agreement in ranking of the best (ZLAB and HOCOMOCO) and worst performing (TF2DNA and SWISSREGULON) DBs. We observe that, compared with GOMER ( ), the ranks for most DBs remain the same when using energy ( ) except for POUR and JOLMA. This shows that motifs from these DBs, or at least […]

library_books

Mapping Mammalian Cell type specific Transcriptional Regulatory Networks Using KD CAGE and ChIP seq Data in the TC YIK Cell Line

2015
Front Genet
PMCID: 4650373
PMID: 26635867
DOI: 10.3389/fgene.2015.00331

[…] al., ) found significant enrichment for the relevant motifs (NeuroD1/Homer motif was found in 46% of NEUROD1 peaks, 7.4% of background; Lmx1a-mouse/Jaspar–9% of LMX1A peaks, 4.7% of background; PAX6/SwissRegulon–11% of PAX6 peaks, 2.2% of background, Supplementary Figure ). For RFX6 there is no known motif; however, the motifs of other RFX family members, and in particular RFX5, were enriched (37 […]

library_books

Reconstruction of novel transcription factor regulons through inference of their binding sites

2015
BMC Bioinformatics
PMCID: 4576408
PMID: 26388177
DOI: 10.1186/s12859-015-0685-y

[…] We used Tomtom [] to quantify the similarity between TF motifs. It calculates statistical measures between the given query motifs and a database of known motifs. In this study, we used the SwissRegulon’s motif database [] for E. coli TFs. For each motif, we displayed the results for the best hit obtained by Tomtom in its default settings. […]


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SwissRegulon institution(s)
Biozentrum, University of Basel, Basel, Switzerland, Swiss Institute of Bioinformatics, Basel, Switzerland
SwissRegulon funding source(s)
Supported by Swiss Institute of Bioinformatics; Swiss National Science Foundation [31003A-118318, in part]; and by SystemsX.ch through the CellPlasticity project.

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