SNP-SIG 2013: from coding to non-coding-new approaches for genomic variant interpretation. BMC Genomics. 2014;15 Suppl 4:S1.Bromberg Y, Capriotti E. SNP-SIG 2013: from coding to non-coding--new approaches for genomic variant interpretation. BMC Genomics. 2014; 15 (Suppl 4):S1. doi: ...
x-axis: offset from SNP position (bp), y-axis: stranded read count. (f) Replication of the effect at time 0 (mesenchymal stem cells) with ATAC-seq. (g) BMI-dependent variant association analysis. Bar plots represent the beta of the ...
这两大类的分析方法截然不同,coding主要直接影响了mRNA和蛋白;而noncoding,主要是影响调控。 coding编码区如何分析? 通常有很多pipeline来预测WGS等得到的SNP的功能,如annovar等数据库。 protein binding domain 综述: Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation:...
As a causal SNP could alter chromatin accessibility via the different binding of a TF, we adopted formaldehyde-assisted isolation of regulatory element (FAIRE) allele-specific qPCR (AS-qPCR) to examine the risk allele and non-risk allele FAIRE signal in this rs2431697 heterozygous cell clone. Th...
Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits. Nature genetics. 2012;44(4):369–75, s1-3. Article CAS PubMed PubMed Central Google Scholar Maller JB, McVean G, Byrnes J, Vukcevic D, Palin K, Su Z, et al....
Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits. Nature genetics. 2012;44(4):369–75, s1-3. Article CAS PubMed PubMed Central Google Scholar Maller JB, McVean G, Byrnes J, Vukcevic D, Palin K, Su Z, et al....
In inflammatory breast cancer, this SNP is associated with the occurrence of metastasis and independently predicts outcome [47]. Another study showed that CCAT2 increases cell invasion and motility in vitro and in vivo, correlating with shorter MFS in colon and breast cancer [46]. Even if the ...
(derived from SNP arrays or whole genome sequencing; “Methods”), and RNA-seq data for hundreds of individuals in five cell types: LCLs (n = 317), fibroblasts (FIB,n = 78), monocytes (n = 172), neutrophils (n = 164), and T cells (n = 93) [19,28]. ...
Very inter- estingly, a study reported that lncRNA PTCSC3 (Papillary Thyroid Carcinoma Susceptibility Candidate 3), located 3.2 kb downstream of SNP rs944289 at 14q.13.3, is strongly downregulated in papillary thyroid carcinoma (PTC). The overexpression of lncRNA PTCSC3 could in- hibit PTC ...
human SNP variationsOne of the surprising revelations of the initial stage of the ENCODE project was the conclusion that more than 90% of human genome is transcribed. A major component of this vast transcriptional output is represented by highly heterogeneous families of transcripts defined as short...