1. iPlant Omics Data Analysis and Visualization System iPlant Viz Team, Lecong Zhou, demo, 7-8-10

2. GUIGUI input output AffyGen Analyser ® AffyGen Analyser ® BiNGO (Cytoscape plugin) GO® Analyser GO® Analyser Enriched GOterms GeneMANIA (Cytoscape plugin) GeneMANIA (Cytoscape plugin) Gene List(s) Gene List(s) GenAV --Analysis & Visualization of Affymetrix Gene Expression Data User Output (text files, graphs) Output (text files, graphs)

3. GUIGUI AffyGen Analyser ® AffyGen Analyser ® BiNGO (Cytoscape plugin) GO® Analyser GO® Analyser Enriched GOterms GeneMANIA (Cytoscape plugin) GeneMANIA (Cytoscape plugin) Gene List(s) Gene List(s) GenAV --Analysis & Visualization of Affymetrix Gene Expression Data Output (text files, graphs) Output (text files, graphs) input output User

4. AffyGenAnalyser Design file GEO # (or alternatives) CEL files summarizing limma expr values of present genes present genes RMA PMAcalls QC DEG sets(.txt files) Summary(.txt) QCreport(.pdf) GOanalyser ViVA R

5. GOanalyser Design file DEG sets Heatmap.R Multi-lists organisor.pl Goanalyser.R(GO hyperGAll) DEGs [At#] heatmaps(.pdf) GeneMANIA Args : Idtype, FDR, cutoff Outputs (.txt, with GOid, At#s, p-values, etc) Args : GOterm(s) Notes: Goanalyser is based on GOhyperGAll package, which is for “Global Hypergeometric Test Using Custom Gene-to- GO Mappings Plus GO Slim Analysis” (Thomas Girke, UC Riverside) Added FDR option “qvalue”. Heatmap uses converted p-values (cPval, negative log10). Show the top 50 terms with highest sum of cPvals of all the listed contrasts.