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Fig. 3 | BMC Bioinformatics

Fig. 3

From: ADAGE signature analysis: differential expression analysis with data-defined gene sets

Fig. 3

ADAGE web server interface and analysis workflow. The ADAGE web server interface has six tabs on the top. The signature analysis pipeline starts with choosing a machine learning model on the homepage (step1) and choosing to explore assays and experiments (step2). In the Analyze page, users can search datasets or samples using keywords (step3). After clicking the “+” button beside each dataset or sample, the dataset with all samples in it or an individual sample is added into the analysis basket (step4). After users add samples, clicking the basket brings users to the Sample page (step5). The Sample page provides experimental information about each sample and a signature activity heatmap. Users can define a two-group comparison by selecting samples and assigning them to either treatment (yellow) group or control (purple) group (step6). The signatures that are differentially active between two groups of samples can be examined in a volcano plot (step7). Next users select signatures in the volcano plot (step8) and further inspect them in the Signature page (step9). The Signature page provides information about gene composition, gene set association, and related datasets of a signature. Lastly, users can visualize their interested signatures in a gene-gene network (step10). Users can also directly examine genes in the gene-gene network through the GeneNetwork tab and examine a signature through the Signature tab

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