系统生物学软件（王栋）manual.docVIP

? ??? Expander 6 Online Documentation ? Table of Contents ? Introduction. 1 Starting EXPANDER.. 2 Input Data. 3 Tabular Data File. 3 CEL Files. 5 Working on Gene Groups with no associated expression data. 7 Preprocessing GE Data. 9 Viewing Data Plots. 13 Differential Expression Analysis. 15 Defining a group according to a rule. 16 Defining a group according to similarity to a selected probe. 17 Clustering GE Data. 17 Biclustering GE Data. 20 Network Based Grouping of GE Data. 25 Group Analysis Tools. 27 Functional Analysis. 27 Promoter Analysis. 31 Location Enrichment Analysis. 35 miRNA Targets Enrichment Analysis. 39 Pathway Enrichment Analysis. 43 General Enrichment Analysis. 43 Network Based Group Analysis. 46 Matrix Visualizations. 47 Hierarchical Clustering and Visualization. 49 PCA Transformation. 51 Analysis Wizard. 51 Additional Options. 52 File Formats. 55 Sample Input Files. 57 Supplied Files. 58 Settings. 63 R External Application. 64 FAQ.. 65 Copyrights Information. 68 References. 69 ? Introduction ? EXPANDER (EXpression Analyzer and DisplayER) is a java-based tool for analysis of gene expression data. It is capable of (1) preprocessing (2) visualizing (3) clustering (4) biclustering and (5) performing downstream analysis of clusters and biclusters such as functional enrichment and promoter analysis (i.e. analysis of gene groups?for enrichment of transcription factor binding sites in their promoters). EXPANDER incorporates several conventional?gene expression?analysis algorithms and custom ones that have been developed in the computational genomics group in Tel-Aviv University, and provides them with an easy-to-operate user interface. EXPANDER?versions are available for Windows OS and for Linux/Unix OS and require the?pre-installation of?the Java Runtime Environment (JRE) 5.0 (or higher). The Java Runtime Environment can be installed via: /javase/downloads/index.jsp. The CEL file preprocessing and the newly added SAM filter utilities require the pre