Identification of cis-regulatory variants that may be causal for disorders

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1618400/



In Silico Detection of Sequence Variations
Modifying Transcriptional Regulation
* https://bora.uib.no/bitstream/1956/2703/1/In_Silico_PLOMed.pdf
* RAVEN (regulatory analysis of variation in enhancers).
* http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.0040005
* http://www.cisreg.ca
* In this paper we present a Web-based tool for the identification of genetic variation in
potential transcription factor binding sites.


https://depace.med.harvard.edu/work.html


ORegAnno
JASPAR
dbSNP
Phylofoot - Tools for phylogenetic footprinting 
sTRAP - http://strap.molgen.mpg.de/
TRANSFAC - transcription factor motifs



A traditional bioinformatics approach to
predict TFBSs is through the application of binding site
profile models known as position-specific weight matrices
(PWMs) [24]. Such matrix models assign a score to each
candidate binding sequence.


Thomas Manke, Matthias Heinig, and Martin Vingron, “Quantifying the effect of sequence variation on regulatory interactions,” Human Mutation 31, no. 4 (April 2010): 477-483.
* sTRAP - http://strap.molgen.mpg.de/



is-rSNP: a novel technique for in silico regulatory SNP detection Macintyre G, Bailey J, Haviv I, Kowalczyk ABioinformatics 2010 26(18): i524. doi:10.1093/bioinformatics/btq378


Predicting functional regulatory polymorphisms [Get the full text PDF from Pubget] Torkamani A, Schork NJBioinformatics 2008 24(16): 1787. doi:10.1093/bioinformatics/btn311


Impact of DNA-binding position variants on yeast gene expression [Get the full text PDF from Pubget] Swamy KBS, Cho C, Chiang S, Tsai ZT, Tsai HNucleic Acids Research 2009 37(21): 6991. doi:10.1093/nar/gkp743


Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP Ameur A, Rada-Iglesias A, Komorowski J, Wadelius CNucleic Acids Research 2009 37(12): e85. doi:10.1093/nar/gkp381