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[…] e less than median was considered as under expression. We then determined co-expression of putative target genes at the site of over expression/under expression of SIM2 and ETS2 and promoter sites of these genes were analyzed by GENEDOC and Promoter Scan tools respectively (http://www-bimas.cit.nih.gov/molbio/proscan/). Functions of these putative target genes along with SIM2 and ETS2 in various biological pathways was analyzed by Panther (http://www.pantherdb.org/pathway/) and KEGG pathway (http://www.genome.ad.jp/kegg/pathway.html). The entire process is presented schematically in Figure ., We used different web based tools namely SIFT (http://sift.jcvi.org), PolyPhen (http://coot.embl.de/PolyPhen/), SNPs3D (http://www.snps3d.org/), Pupasuite 2 (http://pupasuite.bioinfo.cipf.es), GlobPlot, FastSNP (http://fastsnp.ibms.sinica.edu.tw), [email protected] (http://variome.kobic.re.kr/SNPatPromoter), and dbSMR (http://miracle.igib.res.in/dbSMR) to identify fSNPs in the genomic regions of SIM2 and ETS2 as reported earlier []. fSNPs selected for genotyping in the present study are listed in Table . , aNS = Nonsynonymous, Syn = Synonymous, Cod = Coding, FS = Frame shift., bA1 = Major allele, A2 = Minor allele, allele mentioned in bold letter is the ancestral allele., cNK = Not known., dCEU: Caucasians from Utah with ancestry from western and northern Europe; YRI: Yoruba from Ibadan, Nigeria; HCB: Han Chinese from Beijing, China and J […]

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