SNPeQTLrSNPWe describe a statistical method for prioritizing candidate causal noncoding single nucleotide polymorphisms (SNPs) in regions of the genome that are detected as trait-associated in a population-based genome-wide association study (GWAS). Our method's key step is to combine, within a ...
3e, PCAWG RPKM), 2.15-fold enriched for germline cancer-associated small nucleotide polymorphism (SNP) in their gene body (4.7% vs 2.5%) (Fig. 3e, SNPs per MB), and enriched in orthologues of driver lncRNAs carrying common insertion sites (CIS), discovered by transposon insertional ...
The HGMD regulatory mutation model was trained with L1 regularization parameter 20 and L2 regularization parameter 2,000 for ten iterations. eQTL and GWAS SNP models were trained with L1 regularization parameter 0 and L2 regularization parameter 10 for 100 iterations. 可以看到这两个数据是分开train的,...
(SNP) rs7134599 (Padua et al.99). There is a positive link between IFNG-AS1 over-expression and the crucial inflammatory cytokine IFNG expression in immune cells99. Moreover, Rankin et al.100illustrated that the IFNG-AS1 gene is located beside the inflammatory cytokine IL-22 gene and ...
For example, the CACNA1C index SNP (rs1006737) and eSNP (rs758170) are in close proximity (16.2 kb) and have an RTC score of 1. Furthermore, the risk allele is associated with decreased CACNA1C gene expression (p = 1.88 × 10−5 at false discovery rate [FDR] 0.7%). We ...
et al. Mice lacking a Myc enhancer that includes human SNP rs6983267 are resistant to intestinal tumors. Science 338, 1360–1363 (2012). Article CAS PubMed Google Scholar Ulitsky, I., Shkumatava, A., Jan, C. H., Sive, H. & Bartel, D. P. Conserved function of lincRNAs in ...
The structure of aeukaryoticprotein-codinggene. Regulatory sequence controls when and where expression occurs for theprotein coding region(red).Promoterandenhancerregions (yellow) regulate thetranscriptionof the gene into a pre-mRNA which ismodifiedto removeintrons(light grey) and add a 5' cap and ...
Population differentiation of genetic variants associated with complex diseases or traits. Thirty-five complex trait-/disease-associated SNP (cSNP) sets from GWASdb are listed. The color of the left-most bars represents the different types of diseases/traits, and the length of the bars represents ...
For example, an SNP in the first intron of ABO at the putative promoter of an antisense lncRNA was significantly associated with elevated fasting glucose levels (29). Mechanistically, how this noncoding region may be conferring disease risk or whether biological effects could be attributed to ...
systematically assessed the binding of 270 human transcription factors to 95,886 noncoding variants in the human genome using an ultra-high-throughput multiplex protein–DNA binding assay, termed single-nucleotide polymorphism evaluation by systematic evolution of ligands by exponential enrichment (SNP-...