StemMapper: a curated gene expression database for stem cell lineage analysis.
StemMapper: a curated gene expression database for stem cell lineage analysis.
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DOI：
10.1093/nar/gkx921
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发表时间：
2018-01-04
影响因子：
14.9
通讯作者：
Futschik ME
中科院分区：
文献类型：
--
作者：
Pinto JP;Machado RSR;Magno R;Oliveira DV;Machado S;Andrade RP;Bragança J;Duarte I;Futschik ME
转录组学数据已经成为干细胞（SC）生物学家以及更广泛的研究对象研究SC相关过程（如衰老，胚胎发育和包括癌症，糖尿病和神经退行性疾病在内的流行疾病）的基础资源。然而，获取和分析越来越多的免费的SCs转录组学数据集并不是一项简单的任务。在这里，我们介绍了StemMapper，这是一个人工编辑的基因表达数据库和SC研究的综合资源，建立在人类和小鼠不同谱系的SC的综合数据之上。它基于对相关转录组学数据集的仔细选择，标准化处理和严格的质量控制，以最大限度地减少人工制品，目前包括960多个转录组，涵盖广泛的SC类型。每个集成的数据集都是单独检查和手动整理的。StemMapper的用户友好的界面可以快速查询，比较，并以全面的方式对质量控制的SC基因表达数据进行交互式可视化。发现新的假定星形胶质细胞/神经SC谱系标记的原理验证分析举例说明了集成数据资源的效用。我们相信StemMapper可以通过大大简化SC转录组数据的获取和分析，为SC研究开辟新的见解和进步的道路。StemMapper可以免费访问http://stemmapper.sysbiolab.eu。
Transcriptomic data have become a fundamental resource for stem cell (SC) biologists as well as for a wider research audience studying SC-related processes such as aging, embryonic development and prevalent diseases including cancer, diabetes and neurodegenerative diseases. Access and analysis of the growing amount of freely available transcriptomics datasets for SCs, however, are not trivial tasks. Here, we present StemMapper, a manually curated gene expression database and comprehensive resource for SC research, built on integrated data for different lineages of human and mouse SCs. It is based on careful selection, standardized processing and stringent quality control of relevant transcriptomics datasets to minimize artefacts, and includes currently over 960 transcriptomes covering a broad range of SC types. Each of the integrated datasets was individually inspected and manually curated. StemMapper's user-friendly interface enables fast querying, comparison, and interactive visualization of quality-controlled SC gene expression data in a comprehensive manner. A proof-of-principle analysis discovering novel putative astrocyte/neural SC lineage markers exemplifies the utility of the integrated data resource. We believe that StemMapper can open the way for new insights and advances in SC research by greatly simplifying the access and analysis of SC transcriptomic data. StemMapper is freely accessible at http://stemmapper.sysbiolab.eu.
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影响因子：
4.4
作者：
Huminiecki L;Lloyd AT;Wolfe KH
通讯作者：
Wolfe KH
影响因子：
3
作者：
McCall MN;Irizarry RA
通讯作者：
Irizarry RA
影响因子：
14.9
作者：
Sánchez-Castillo M;Ruau D;Wilkinson AC;Ng FS;Hannah R;Diamanti E;Lombard P;Wilson NK;Gottgens B
通讯作者：
Gottgens B
影响因子：
14.9
作者：
Petryszak R;Keays M;Tang YA;Fonseca NA;Barrera E;Burdett T;Füllgrabe A;Fuentes AM;Jupp S;Koskinen S;Mannion O;Huerta L;Megy K;Snow C;Williams E;Barzine M;Hastings E;Weisser H;Wright J;Jaiswal P;Huber W;Choudhary J;Parkinson HE;Brazma A
通讯作者：
Brazma A
影响因子：
1.2
作者：
Mallon, Barbara S.;Chenoweth, Josh G.;Johnson, Kory R.;Hamilton, Rebecca S.;Tesar, Paul J.;Yavatkar, Amarendra S.;Tyson, Leonard J.;Park, Kyeyoon;Chen, Kevin G.;Fann, Yang C.;McKay, Ronald D. G.
通讯作者：
McKay, Ronald D. G.