NHR-scan protocols

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NHR-scan specifications

Information


Unique identifier OMICS_14042
Name NHR-scan
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data A DNA sequence, ensembl coordinates (species/database), probability features
Input format FASTA
Output data A graphical output with predicted nuclear hormone receptor binding sites
Output format HTML
Programming languages C++, Perl
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Wyeth Wasserman <>

Publication for NHR-scan

NHR-scan in pipeline

2013
PMCID: 3750112
PMID: 23990796
DOI: 10.1371/journal.pgen.1003689

[…] myc-rarαb1 mrna with respect to control uninjected embryos., the genomic sequence flanking zebrafish hoxb5b (−8 to +8 kb) was compared with the corresponding region for hoxb5 in mouse using mvista. nhr scan was used to identify binding sites for nuclear receptor., rarαb1 was identified by using blast against the zebrafish genome (ensemble_v7) with the human and mouse rarα1 a domains. macvector […]


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NHR-scan in publications

 (13)
PMCID: 5527017
PMID: 28743885
DOI: 10.1038/s41598-017-06679-x

[…] t3-regulated genes in vivo or under different treatment conditions.figure 4 , among the 278 tr target genes identified by chip-on-chip assay, 191 genes had 1 or more putative tre, as revealed by nhr scan analysis (http://www.cisreg.ca/cgi-bin/nhr-scan/nhr_scan.cgi), within the 8 kb sequences covered on the chip-on-chip slides (data not shown). to investigate if these tres were functional […]

PMCID: 5430760
PMID: 28432332
DOI: 10.1038/s41598-017-01183-8

[…] directly to gnih neurons.figure 5 , there are several putative th-response elements (tres) within 3 kb upstream region from the mouse gnih orf (fig. ; predicted by using the prediction programs; nhr scan, http://www.cisreg.ca/cgi-bin/nhr-scan/nhr_scan.cgi and alibaba2.1, http://www.gene-regulation.com/pub/programs/alibaba2/index.html). to determine whether trs directly act on the promoter […]

PMCID: 5362238
PMID: 28273073
DOI: 10.1371/journal.pgen.1006650

[…] performed at least two times., to predict nrs that interact with src-2, promoter regions (spanning 10kb on either side) of candidate src-2 target genes were screened for nr binding motifs using the nhr scan tool (http://www.cisreg.ca/cgi-bin/nhr-scan/nhr_scan.cgi). src-2 binding regions in candidate genes were overlapped with predicted nr binding motifs to predict potential src-2/nr […]

PMCID: 5295159
PMID: 28217257
DOI: 10.4254/wjh.v9.i4.191

[…] pgl3-basic vector, which was named as pgl3-hmir-194-2-pro and pgl3-hmir194-2 trim. the mutant 405-bp human mir-194-2 promoter had mutations of 3 putative hnf4-binding sites predicted by software of nhr-scan[] and hnf4 binding site scanner[] (for dna sequences see supplemental materials)., we pcr cloned a 2 kb fragment of the mouse mir-802 promoter (-2004 to -1 bp) into the mlui/xhoi sites […]

PMCID: 4014424
PMID: 24811540
DOI: 10.1371/journal.pgen.1004339

[…] this previous study , here we also found that the ets family motif was overrepresented (15%) in tr4-occupied peaks ()., we employed a second nuclear hormone receptor binding site prediction program, nhr-scan, to identify enriched repeat elements . of the dr elements, we identified dr1 sequences comprising the major site (29% of the 130 peaks at d11) with dr4 (5%) and dr0 (3%) motifs as minor […]


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NHR-scan institution(s)
Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden; Centre for Molecular Medicine and Therapeutics, British Columbia Children’s and Women’s Hospitals, and Department of Medical Genetics, University of British Columbia, Vancouver, Canada
NHR-scan funding source(s)
This work was supported by funds from the Pharmacia Corporation to the Center for Genomics and Bioinformatics, as well as funds from the Canadian Institutes of Health Research.

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