Expander version 7 includes the following improvements:
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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 7.01 additions
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1) Fixed bug that prevented using the new condition order when performing clustering or enrichement analysis.
2) Fixed bug that prevented showing KEGG pathway names in GSEA dispaly.
3) Fixed bug that prevented selection of top enriched probes when performing RankSum test.
4) Addition of explanatory comments "NA=Not Available", "P-Value is not calculated for the intergenic category" to the "Peaks Distribution" bar chart
after loading ChIP-Seq data.
5) Renamed in the GSEA table "Number of Hits" to "Set genes in ranking".
6) Added "Top hits genes" column to the GSEA table showing the number of hits until the maximum enrichment score.
 
Version 7.1 additions
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1) AMADEUS - Full graphical representation of the AMADEUS motif finder output.
2) DESeq2 – Option to perform DESeq2 for differential expression analysis of RNA-Seq  data with respect to a given classification.
3) GSEA - Addition of another dashed line showing the maximum cumulative enrichment score (ES) in the GSEA output plot. Indication of the maximum cumulative enrichment score (ES) on the plot.
4) GSEA – Fixed a bug preventing to choose a ChIP-Seq solution as a set of genes under "Grouping solution" field.
5) Fixed a bug preventing running R scripts in EXPANDER Linux version.

Version 7.11 additions
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1) "ChIP-Seq Analysis" menu item – This menu allows performing all related ChIP-Seq analyses in Expander including enrichment analysis (GSEA, Tango and Prima), 
	integration analyses with a given GE data and extracting peaks sequences for De-Novo motif finding in AMADEUS
2) AMADEUS - Option to extract ChIP-Seq peaks sequences and to apply De-Novo motif searching on them using AMADEUS.
3) ChIP-Seq Enrichment – Changed the output result name from "<gene set name> Custom Enrich." To ""<gene set name> ChIP-Seq Enrich.", for example: "K-Means 1.1 Custom Enrich.1" was changed to "K-Means 1.1 ChIP-Seq Enrich.1"
4) "ChIP-Seq GE distribution" – 
   (1) operation name was changed to "ChIP-Seq vs. GE analysis". 
   (2) added Wilcoxon 2 sample test P-Value in the "Visualization Info" panel on the left view. 
   (3) added number of target/background genes in the "Visualization Info" panel on the left view. 
   (4) added y-axis label "Fold-Change (log2)" on the boxplot view on the right view. 
   (5) changed the title of the boxplot view on the right from "distributions" to "Response of ChIP-Seq target genes vs. background genes".
5) PCA plot – cross symbol color was changed to dark grey when performing PCA on the input data
6) Enrichment Analysis – In all dialog boxes, the "Background set" section was changed: 
  (1) In case a GE data was loaded, the names "Original data" and "Filtered data" were changed to "Original GE data" and "Filtered GE data" respectively. 
  (2) If the GE's probes were not filtered then the field "Filtered GE data" is not available. 
  (3) In case that no GE data was loaded, For ChIP-Seq data analysis only "All genes" option is available as background, For loaded "Gene Groups" file only "All genes" and "Original data" options are available. 
7) Fetch ChIP-Seq Sequences – 
  (1) In the dialog box, "Sequence Length" was changed to "Sequence Width". 
  (2) Added option to select target/background sequences by peak width from the file (peak widths are limited up to 1000 bp).  
8) GSEA – added option to rank genes by ratio using selected test/base conditions. 
  (1) In case the GE values are relative expression then only a test condition can be selected. 
  (2) In case the GE values are absolute expression then both test and base conditions should be selected.