Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.
Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.
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DOI：
10.1093/nar/gkv1045
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发表时间：
2016-01-04
影响因子：
14.9
通讯作者：
Brazma A
中科院分区：
文献类型：
--
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
表达图谱（http：//www.ebi.ac.uk/gxa）提供了关于不同细胞类型、生物体部分、发育阶段、疾病和其他状况的动物和植物样品中基因和蛋白质表达的信息。它由ArrayExpress的精选微阵列和RNA测序研究组成，这些研究已经过手动管理，用本体术语注释，检查高质量并使用标准化分析方法进行处理。自上次更新以来，Atlas已经增长了7倍（截至2015年8月，已有1572项研究），并纳入了来自Human Protein Atlas、GTEx和FANTOM 5的组织基线表达谱，以及来自ENCODE、CCLE和Genentech项目的癌细胞系基线表达谱。植物研究占Atlas数据的四分之一。对于感兴趣的基因，用户可以查看组织中的基线表达，以及生物学上有意义的成对比较的差异表达-使用所有Atlas的一致方法进行估计。我们在人体组织中的第一个蛋白质组学研究现在与相同组织中的转录组学数据一起显示。新的分析和可视化包括：在GO术语、Reactome、植物Reactome途径和InterPro结构域的每个差异比较中的“富集”;大多数可变基因和实验条件的分层聚类（通过基线表达）;以及对于给定的基因条件，跨生物重复的基线表达的分布。
Expression Atlas (http://www.ebi.ac.uk/gxa) provides information about gene and protein expression in animal and plant samples of different cell types, organism parts, developmental stages, diseases and other conditions. It consists of selected microarray and RNA-sequencing studies from ArrayExpress, which have been manually curated, annotated with ontology terms, checked for high quality and processed using standardised analysis methods. Since the last update, Atlas has grown seven-fold (1572 studies as of August 2015), and incorporates baseline expression profiles of tissues from Human Protein Atlas, GTEx and FANTOM5, and of cancer cell lines from ENCODE, CCLE and Genentech projects. Plant studies constitute a quarter of Atlas data. For genes of interest, the user can view baseline expression in tissues, and differential expression for biologically meaningful pairwise comparisons—estimated using consistent methodology across all of Atlas. Our first proteomics study in human tissues is now displayed alongside transcriptomics data in the same tissues. Novel analyses and visualisations include: ‘enrichment’ in each differential comparison of GO terms, Reactome, Plant Reactome pathways and InterPro domains; hierarchical clustering (by baseline expression) of most variable genes and experimental conditions; and, for a given gene-condition, distribution of baseline expression across biological replicates.