Integrated analysis of Cross-platform MicroArray and Pathway data

Release notes of InCroMAP version 1.5.1

  • Fixed a bug that prevented the integrated enrichment dialog from appearing.

Release notes of InCroMAP version 1.5

  • New feature: Support for metabolomics data.
  • New feature: Enrichmenet on metabolomics data and integrated enrichment on metabolomics and gene expression data.
  • New feature: Colour compounds in pathways according to metabolomics data.
  • New feature: Export tabular details of pathways and associated expression data (right mouse click on any row in a KEGG pathways enrichment).
  • Fixed a bug with filtering expression data based on absolute values.

Release notes of InCroMAP version 1.4

  • New feature: Import and visualization of GraphML and GML files, including all features of the cross-platform visualization technique for mRNA, miRNA, DNA methylation and proteins.
  • Fixed visualization of KEGG pathways. Updated KEGG adapter to the new REST interface.
  • Fixed bug in manual gene list importer.
  • Fixed p-value adjustment methods to now preserve monotonicity.
  • Improved some warning messages to better describe what is really missing.
  • Detection and conversion of old LocusLink identifiers to Entrez Gene identifiers when visualizing BioPAX pathways.
Since 2013-01-01, KEGG terminated the SOAP interface to retrieve data and started a REST interface. The amount of identifiers that can be resolved simultaneously has been reduced from 100 to 10. For many pathways this means that InCroMAP is now much slower in visualizing pathways. We're very sorry however we cannot change KEGG's restrictions. To overcome this issue, caching of information has been improved such that every information only needs to be downloaded once.

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.