PMC:3216508 / 18077-19622 JSONTXT

{"project":"2_test","denotations":[{"id":"22355539-14681366-135382476","span":{"begin":195,"end":197},"obj":"14681366"},{"id":"22355539-18842628-135382477","span":{"begin":207,"end":209},"obj":"18842628"},{"id":"22355539-12520026-135382478","span":{"begin":222,"end":224},"obj":"12520026"},{"id":"22355539-16952980-135382479","span":{"begin":802,"end":804},"obj":"16952980"},{"id":"22355539-16919236-135382480","span":{"begin":923,"end":925},"obj":"16919236"},{"id":"22355539-20861029-135382481","span":{"begin":1430,"end":1432},"obj":"20861029"}],"text":"To search for the SNPs with alleles that alter the putative transcription factor binding sites, we scanned the promoter region of the gene with annotated Position Weight Matrices (PWMs) in Jaspar33, UniPROBE34 and TRANSFAC35 databases. We first obtained the gene coordinates (txStart and txEnd) for human genome hg18 (NCBI36) from the RefSeq table of UCSC table browser (http://genome.ucsc.edu/). For the annotated SNPs in dbSNP129 that are within 2000 bp upstream to 500 bp downstream of the IL-22 gene, we extracted their flanking sequence (+-25bp) from the dbSNP website (http://www.ncbi.nlm.nih.gov/projects/SNP/). For each SNP, we kept the flanking sequence the same and changed the alleles, thus obtaining one sequence for each allele and forming a sequence set. We then used a PWM_SCAN algorithm36 to scan each sequence in the set to test whether it had a putative binding site (PBS), with the method we described in37. We considered sites with a probability score of p-value \u003c = 0.001 as PBS. If the SNP was within the PBS and any of the two alleles had differential p-values, we calculated the ratio (Sr) of p-values by dividing the bigger p-value by the smaller p-value. The Sr measures how the two alleles in the PBS change the binding scores between the PBS and putative binding protein. We then converted this Sr into a p-value based on a background distribution from a permutation test, based on the FastPval program38. If an SNP has Sr with p-value \u003c 0.01, we considered this SNP as functional and thus selected it for genotyping."}