ExAtlas: An interactive online tool for meta-analysis of gene expression data.
ExAtlas: An interactive online tool for meta-analysis of gene expression data.
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DOI：
10.1142/s0219720015500195
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发表时间：
2015-12
影响因子：
1
通讯作者：
Ko MS
中科院分区：
文献类型：
--
作者：
Sharov AA;Schlessinger D;Ko MS
我们已经开发了ExAtlas，一个在线软件工具，用于基因表达数据的荟萃分析和可视化。与现有的软件工具相比，ExAtlas比较多组分数据集并生成所有组合的结果（例如，所有基因表达谱对所有基因本体注释）。ExAtlas既处理用户自己的数据，也处理从公共储存库（GEO/NCBI数据库）半自动提取的数据。ExAtlas为荟萃分析提供了多种工具：（1）标准荟萃分析（固定效应、随机效应、z分数和Fisher方法）;（2）基因表达数据集之间的全局相关性分析;（3）基因集富集;（4）基因集重叠;（5）通过表达谱的基因关联;（6）基因特异性;（7）统计分析（ANOVA、成对比较和PCA）。ExAtlas生成图形输出，包括热图、散点图、条形图和三维图像。一些最广泛使用的公共数据集（例如，GNF/BioGPS、Gene Ontology、KEGG、GAD表型、BrainScan、ENCODE ChIP-seq和蛋白质-蛋白质相互作用）已预加载，可用于功能注释。
We have developed ExAtlas, an on-line software tool for meta-analysis and visualization of gene expression data. In contrast to existing software tools, ExAtlas compares multi-component data sets and generates results for all combinations (e.g., all gene expression profiles vs. all Gene Ontology annotations). ExAtlas handles both users’ own data and data extracted semi-automatically from the public repository (GEO/NCBI database). ExAtlas provides a variety of tools for meta-analyses: (1) standard meta-analysis (fixed effects, random effects, z-score, and Fisher’s methods); (2) analyses of global correlations between gene expression data sets; (3) gene set enrichment; (4) gene set overlap; (5) gene association by expression profile; (6) gene specificity; and (7) statistical analysis (ANOVA, pair-wise comparison, and PCA). ExAtlas produces graphical outputs, including heatmaps, scatter-plots, bar-charts, and 3-deminsional images. Some of the most widely used public data sets (e.g., GNF/BioGPS, Gene Ontology, KEGG, GAD phenotypes, BrainScan, ENCODE ChIP-seq, and protein-protein interaction) are pre-loaded and can be used for functional annotations.