Expander version 8 includes the following improvements: =========================================================== 1)ChIP-Seq data analysis support including: * Loading BED/GFF3 peaks file * Mapping peaks to closest gene * Visualization of peaks chromosomal positions * Visualization of peaks genomic region distribution * Human/Mouse regions enrichment within hits * Visualization of gene expression distribution within ChIP-Seq hits * Analysis of ChIP-Seq hits enrichment within gene groups * Enrichment analysis within ChIP-Seq hits 2) Support for simultaneous analysis of more than one data set (same organism) 3) Addition of Cytoscape interface for improved network visualization 4) Improved GSEA visualization 5) Updated PPI data for all orgainsms Version 8.0 additions ========================== 1) Updated organism data for the following supported species: Human, mouse, rat, s.cerevisiae, s.pombe, tomato, zebrafish, rice, fly, chicken, arabidopsis, c.elegans, e.coliK12, and a.fumigatus 2) We now support JASPAR position weight matrices (PWMs) in Prima and Amadeus. We no longer support TRANSFAC PWMs in Prima. 3)Pathway enrichments - (1) Fixed a bug preventing to change the minimal overlap of genes in target and in pathway sets. (2) Added q-values column to the output table result in case FDR multiple correction was chosen. (3) Added additional descriptions to the output info panel – "Minimal required number of genes in pathway and target sets" and "Corrected p-values are the FDR q-values" in case the FDR multiple correction was chosen. (4) Default threshold p-value was changed from 1E-4 to 0.05 and a FDR multiple testing option is performed. 4)PRIMA promoter analysis – Added q-values column to the output table result. 5)TANGO GO enrichment – added empirical p-Value column to the output table result. Empirical p-Values were computed on all p-values from all clusters before threshold filtering by corrected p-value. 6)miRNA enrichment analysis (FAME) - added empirical p-values column to the output table result. 7)GSEA – fixed a bug preventing running Kegg pathways as gene sets in Fly organism. 8)Display options - Added Black-Yellow heatmap color display option. 9)Exapnder save session option - Amadeus motif finding tabs will not be saved.