Computational protocol: Investigation of single and synergic effects of NLRC5 and PD-L1 variants on the risk of colorectal cancer

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Protocol publication

[…] SNPs were selected using several in silico tools, such as UCSC browser (https://genome-euro.ucsc.edu/) to collect all potential functional SNPs in the regulatory regions, HaploReg (http://www.broadinstitute.org/mammals/haploreg/haploreg.php) and Regulome DB (http://www.regulomedb.org/) to explore the chromatin state, conservation, and regulatory motif alterations within sets of genetically linked variants, Gtex Portal (https://gtexportal.org/home/) to identify all cis-eQTL SNPs that affect the expression of genes of our interest and microRNA binding site prediction tools (http://www.microrna.org/microrna/home.do, http://epicenter.iefreiburg.mpg.de/services/microsniper/) to investigate the 3’-UTR and to predict if a SNP within the target site will disrupt/eliminate or enhance/create a microRNA binding site. PERFECTOS-APE (http://opera.autosome.ru/perfectosape/scan) and s-Transcription factor Affinity Prediction (s-TRAP, http://trap.molgen.mpg.de/cgi-bin/trap_two_seq_form.cgi) were used to identify transcription factors whose binding sites can be significantly affected by a given polymorphism. LD and the haplotype blocks within the genes were examined based on r2 (). […]

Pipeline specifications

Software tools HaploReg, MicroSNiPer, PERFECTOS-APE, TRAP
Databases RegulomeDB
Application sRNA-seq analysis
Organisms Homo sapiens
Diseases Neoplasms, Colorectal Neoplasms