ABSTRACT

The recent discovery of long non-coding RNA as a regulatory molecule in the cellular system has altered the concept of the functional aptitude of the genome. Since our publication of the first version of LncRBase in 2014, there has been an enormous increase in the number of annotated lncRNAs of multiple species other than Human and Mouse. LncRBase V.2 hosts information of 549,648 lncRNAs corresponding to six additional species besides Human and Mouse, viz. Rat, Fruitfly, Zebrafish, Chicken, Cow and C.elegans. It provides additional distinct features such as (i) Transcription Factor Binding Site (TFBS) in the lncRNA promoter region, (ii) sub-cellular localization pattern of lncRNAs (iii) lnc-pri-miRNAs (iv) Possible small open reading frames (sORFs) within lncRNA. (v) Manually curated information of interacting target molecules and disease association of lncRNA genes (vi) Distribution of lncRNAs across multiple tissues of all species. Moreover, we have hosted ClinicLSNP within LncRBase V.2. ClinicLSNP has a comprehensive catalogue of lncRNA variants present within breast, ovarian, and cervical cancer inferred from 561 RNA-Seq data corresponding to these cancers. Further, we have checked whether these lncRNA variants overlap with (i)Repeat elements,(ii)CGI, (iii)TFBS within lncRNA loci (iv)SNP localization in trait-associated Linkage Disequilibrium(LD) region, (v)predicted the potentially pathogenic variants and (vi)effect of SNP on lncRNA secondary structure. Overall, LncRBaseV.2 is a user-friendly database to survey, search and retrieve information about multi-species lncRNAs. Further, ClinicLSNP will serve as a useful resource for cancer specific lncRNA variants and their related information. The database is freely accessible and available at http://dibresources.jcbose.ac.in/zhumur/lncrbase2/.

摘要

最近发现的长链非编码 RNA 作为细胞系统中的调节分子改变了基因组功能特性的概念。自从我们在 2014 年发布第一版 LncRBase 以来，除人类和小鼠之外的多个物种的注释 lncRNA 数量有了巨大的增加。LncRBase V.2 包含 549,648 个 lncRNA 的信息，对应于除人类和小鼠之外的其他六个物种，即。大鼠、果蝇、斑马鱼、鸡、牛和秀丽隐杆线虫. 它提供了额外的独特特征，例如 (i) lncRNA 启动子区域中的转录因子结合位点 (TFBS)，(ii) lncRNAs 的亚细胞定位模式 (iii) lnc-pri-miRNAs (iv) 可能的小开放阅读框（ sORFs) 在 lncRNA 中。(v) 人工管理的相互作用的靶分子信息和 lncRNA 基因的疾病关联 (vi) lncRNA 在所有物种的多个组织中的分布。此外，我们在 LncRBase V.2 中托管了 ClinicLSNP。ClinicLSNP 拥有从与这些癌症对应的 561 个 RNA-Seq 数据推断的乳腺癌、卵巢癌和宫颈癌中存在的 lncRNA 变体的综合目录。此外，我们检查了这些 lncRNA 变体是否与（i）重复元件、（ii）CGI、(iii) lncRNA 基因座内的 TFBS (iv) SNP 在性状相关连锁不平衡 (LD) 区域的定位，(v) 预测了潜在的致病变异和 (vi) SNP 对 lncRNA 二级结构的影响。总的来说，LncRBaseV.2 是一个用户友好的数据库，用于调查、搜索和检索有关多物种 lncRNA 的信息。此外，ClinicLSNP 将作为癌症特异性 lncRNA 变体及其相关信息的有用资源。该数据库可免费访问，可从 http://dibresources.jcbose.ac.in/zhumur/lncrbase2/ 获得。ClinicLSNP 将作为癌症特异性 lncRNA 变异及其相关信息的有用资源。该数据库可免费访问，可从 http://dibresources.jcbose.ac.in/zhumur/lncrbase2/ 获得。ClinicLSNP 将作为癌症特异性 lncRNA 变异及其相关信息的有用资源。该数据库可免费访问，可从 http://dibresources.jcbose.ac.in/zhumur/lncrbase2/ 获得。