MAJIQlopedia: an encyclopedia of RNA splicing variations in human tissues and cancer.
MAJIQlopedia: an encyclopedia of RNA splicing variations in human tissues and cancer.
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MAJIQlopedia：人体组织和癌症中RNA剪接变异的百科全书。
DOI：
10.1093/nar/gkad1043
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发表时间：
2024-01-05
影响因子：
14.9
通讯作者：
Barash, Yoseph
中科院分区：
文献类型：
--
作者：
Quesnel-Vallieres, Mathieu;Jewell, San;Lynch, Kristen W.;Thomas-Tikhonenko, Andrei;Barash, Yoseph
基于RNA测序的RNA剪接变异的量化可以揭示组织和疾病特异的剪接模式。为了研究这种剪接变异，我们引入了MAJIQlopedia，这是一本关于剪接变异的百科全书，包括86个人类组织和41个癌症数据集。MAJIQlopedia报告了正常组织中总共486-175个可选剪接连接和癌症中338-317个可选剪接连接的有注释和无注释的剪接事件。这个数据库可在https://majiq.biociphers.org/majiqlopedia/，上获得，它包括一个用户友好的界面，它提供了所有组织或癌症类型中每个连接的连接使用量化的图形表示。为了说明MAJIQlopedia的用法，我们回顾了WT1、MAPT和BIN1基因的剪接变异，这些基因都有已知的组织或癌症特异性剪接变异。我们还使用MAJIQlopedia来强调正常组织中FDX1和MEGF9的新剪接变异，并在RPS6KA6中发现了一个新的外显子包含事件，该事件只在两种癌症类型中发生。用户可以下载数据库，请求将数据添加到WebTool，或安装MAJIQlopedia服务器以集成专有数据。MAJIQlopedia可以作为一个参考数据库，供寻求了解感兴趣基因中存在哪些剪接变异的研究人员以及那些希望了解组织或癌症特异性剪接亚型使用的人使用。
Quantification of RNA splicing variations based on RNA-Sequencing can reveal tissue- and disease-specific splicing patterns. To study such splicing variations, we introduce MAJIQlopedia, an encyclopedia of splicing variations that encompasses 86 human tissues and 41 cancer datasets. MAJIQlopedia reports annotated and unannotated splicing events for a total of 486 175 alternative splice junctions in normal tissues and 338 317 alternative splice junctions in cancer. This database, available at https://majiq.biociphers.org/majiqlopedia/, includes a user-friendly interface that provides graphical representations of junction usage quantification for each junction across all tissue or cancer types. To demonstrate case usage of MAJIQlopedia, we review splicing variations in genes WT1, MAPT and BIN1, which all have known tissue or cancer-specific splicing variations. We also use MAJIQlopedia to highlight novel splicing variations in FDX1 and MEGF9 in normal tissues, and we uncover a novel exon inclusion event in RPS6KA6 that only occurs in two cancer types. Users can download the database, request the addition of data to the webtool, or install a MAJIQlopedia server to integrate proprietary data. MAJIQlopedia can serve as a reference database for researchers seeking to understand what splicing variations exist in genes of interest, and those looking to understand tissue- or cancer-specific splice isoform usage.
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遗传对人体组织基因表达的影响。
影响因子：
64.8
作者：
GTEx Consortium;Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group;Statistical Methods groups—Analysis Working Group;Enhancing GTEx (eGTEx) groups;NIH Common Fund;NIH/NCI;NIH/NHGRI;NIH/NIMH;NIH/NIDA;Biospecimen Collection Source Site—NDRI;Biospecimen Collection Source Site—RPCI;Biospecimen Core Resource—VARI;Brain Bank Repository—University of Miami Brain Endowment Bank;Leidos Biomedical—Project Management;ELSI Study;Genome Browser Data Integration &Visualization—EBI;Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz;Lead analysts:;Laboratory, Data Analysis &Coordinating Center (LDACC):;NIH program management:;Biospecimen collection:;Pathology:;eQTL manuscript working group:;Battle A;Brown CD;Engelhardt BE;Montgomery SB
通讯作者：
Montgomery SB
影响因子：
15.1
作者：
Lai MC;Bechy AL;Denk F;Collins E;Gavriliouk M;Zaugg JB;Ryan BJ;Wade-Martins R;Caffrey TM
通讯作者：
Caffrey TM
影响因子：
6
作者：
Jiang W;Chen L
通讯作者：
Chen L
DOI：
10.1146/annurev-cancerbio-030617-050407
发表时间：
2019-01-01
期刊：
ANNUAL REVIEW OF CANCER BIOLOGY, VOL 3
影响因子：
--
作者：
Escobar-Hoyos, Luisa;Knorr, Katherine;Abdel-Wahab, Omar
通讯作者：
Abdel-Wahab, Omar
影响因子：
14.9
作者：
Hubbard, T;Barker, D;Clamp, M
通讯作者：
Clamp, M