dreamBase: DNA modification, RNA regulation and protein binding of expressed pseudogenes in human health and disease.
dreamBase: DNA modification, RNA regulation and protein binding of expressed pseudogenes in human health and disease.
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RBase v2.0：从表观转录组测序数据中解读 RNA 修饰图谱
DOI：
10.1093/nar/gkx972
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发表时间：
2018-01-04
影响因子：
14.9
通讯作者：
Qu LH
中科院分区：
文献类型：
--
作者：
Zheng LL;Zhou KR;Liu S;Zhang DY;Wang ZL;Chen ZR;Yang JH;Qu LH
摘要尽管人类基因组中已经注释了成千上万的假基因，但它们的转录调控、表达谱和功能机制仍不清楚。在本研究中，我们开发了dreamBase（http：//rna.sysu.edu.cn/dreamBase），以便于从多维高通量测序数据中研究潜在表达假基因的DNA修饰、RNA调控和蛋白结合。基于125500 ChIP-seq和DNase-seq数据集，我们确定了假基因位点周围各种转录相关因子的全基因组结合谱。通过整合近18000个RNA-seq数据，我们分析了假基因的表达谱，并探索了它们与32种癌症和31种正常组织中的亲本基因的共表达模式。通过结合microRNA结合位点，我们展示了涉及275个microRNA和1201个假基因的复杂转录后调控网络。我们生成了ceRNA网络来说明假基因和它们的亲本基因之间通过竞争性结合microRNA的串扰。此外，我们基于458个CLIP-seq数据集研究了RNA结合蛋白（RBP）和假基因之间的转录组范围的相互作用。结合epitranscriptome测序数据，我们还将1039个RNA修饰位点映射到635个假基因上。该数据库将提供对假基因的转录调控、表达、功能和机制以及它们在生物过程和疾病中的作用的见解。
Abstract Although thousands of pseudogenes have been annotated in the human genome, their transcriptional regulation, expression profiles and functional mechanisms are largely unknown. In this study, we developed dreamBase (http://rna.sysu.edu.cn/dreamBase) to facilitate the investigation of DNA modification, RNA regulation and protein binding of potential expressed pseudogenes from multidimensional high-throughput sequencing data. Based on ∼5500 ChIP-seq and DNase-seq datasets, we identified genome-wide binding profiles of various transcription-associated factors around pseudogene loci. By integrating ∼18 000 RNA-seq data, we analysed the expression profiles of pseudogenes and explored their co-expression patterns with their parent genes in 32 cancers and 31 normal tissues. By combining microRNA binding sites, we demonstrated complex post-transcriptional regulation networks involving 275 microRNAs and 1201 pseudogenes. We generated ceRNA networks to illustrate the crosstalk between pseudogenes and their parent genes through competitive binding of microRNAs. In addition, we studied transcriptome-wide interactions between RNA binding proteins (RBPs) and pseudogenes based on 458 CLIP-seq datasets. In conjunction with epitranscriptome sequencing data, we also mapped 1039 RNA modification sites onto 635 pseudogenes. This database will provide insights into the transcriptional regulation, expression, functions and mechanisms of pseudogenes as well as their roles in biological processes and diseases.
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影响因子：
2.9
作者：
Kim TK
通讯作者：
Kim TK
starBase v2.0：从大规模 CLIP-Seq 数据中解码 miRNA-ceRNA、miRNA-ncRNA 和蛋白质-RNA 相互作用网络
影响因子：
14.9
作者：
Li JH;Liu S;Zhou H;Qu LH;Yang JH
通讯作者：
Yang JH
影响因子：
4.8
作者：
Han, Yoo Jeong;Ma, Shwu Fan;Garcia, Joe G. N.
通讯作者：
Garcia, Joe G. N.
影响因子：
7
作者：
Harrow J;Frankish A;Gonzalez JM;Tapanari E;Diekhans M;Kokocinski F;Aken BL;Barrell D;Zadissa A;Searle S;Barnes I;Bignell A;Boychenko V;Hunt T;Kay M;Mukherjee G;Rajan J;Despacio-Reyes G;Saunders G;Steward C;Harte R;Lin M;Howald C;Tanzer A;Derrien T;Chrast J;Walters N;Balasubramanian S;Pei B;Tress M;Rodriguez JM;Ezkurdia I;van Baren J;Brent M;Haussler D;Kellis M;Valencia A;Reymond A;Gerstein M;Guigó R;Hubbard TJ
通讯作者：
Hubbard TJ
影响因子：
64.5
作者：
Kalyana-Sundaram S;Kumar-Sinha C;Shankar S;Robinson DR;Wu YM;Cao X;Asangani IA;Kothari V;Prensner JR;Lonigro RJ;Iyer MK;Barrette T;Shanmugam A;Dhanasekaran SM;Palanisamy N;Chinnaiyan AM
通讯作者：
Chinnaiyan AM