Integrated analysis of Cross-platform MicroArray and Pathway data

Release notes of InCroMAP version 1.3

  • BioPAX (Level 2 and Level 3) pathways can now be visualized. Thus, pathways from a plethora of different databases can now be visualized together with experimental cross-platform datasets within InCroMAP.
  • Added a generic gene-based and generic region-based data reader that can be used to read many different types of data.
  • Added support for SNP/GWAS data with dbSNP identifiers.
  • Added support for proxy servers.
  • Added a novel &Custom annotation& column type that can be used with all importers to read arbitrary user data.
  • Added support for filtering the multiple heterogeneous data integration table.
  • Added support for Uniprot identifiers.
  • Large, uninformative terms can now be removed in an enrichment.
  • Many dialogs are now resizable.
  • Captions of group nodes or complexes in pathways are now wrapped and displayed inside the node. The node size is changed to fit the caption.
  • Captions of metabolites (small molecules, compounds) are now wrapped across two lines.
  • Enhanced the layout of many graphs (and added support for edge routing, bundling, etc).
  • Fixed a bug that shows incorrect column contents in the pair data table.
  • Fixed a bug that prevented the pair data table from displaying correctly.
  • Fixed problem with sorting the GeneID column in any table.

Release notes of InCroMAP version 1.2

  • New feature: probeset identifiers from Affymetrix, Agilent and Illumina can now be used to import data.
  • Improved graph layout: Edges are now on top of nodes, DNA methylation is depicted in grey and edges to group nodes and at their border.
  • Improved: auto-detection of column contents when opening new expression data files.
  • Added feature: apply an edge-routing layout algorithm after pathway translation (see preferences).
  • Fixed: wrong pathway-based visualization of DNA methylation p-values.
  • Renamed group nodes from "undefined" to "Group".
  • Note: we have made changes to the InCroMAP cache. Therefore, you'll get the following error message the first time you start InCroMAP after the update: java.lang.ClassNotFoundException: de.zbit.kegg.KeggInfoManagement. Please simply ignore this message!
  • Many further bugfixes and improvements in general.

Release notes of InCroMAP version 1.1

  • Many bugfixes and improvements in general.
  • Enhanced microRNA target mapping (example: "let-7" targets now also get assigned to "let-7c"
  • DNA methylation data not requires gene identifiers anymore. Based on chromosomal locations, InCroMAP now includes a promoter mapping procedure that can be used to map DNA methylation data to gene promoters.