InCroMAP

Integrated analysis of Cross-platform MicroArray and Pathway data

Clemens Wrzodek, Johannes Eichner, Andreas Dräger, Finja Büchel, Lars Rosenbaum, Michael Römer, and Andreas Zell

Center for Bioinformatics Tübingen (ZBIT), Germany




Start InCroMAP:
You may start InCroMAP directly here as Java webstart application on almost every operating system, or you can download a stand-alone version as runnable JAR file in our downloads section.


Short description:
Have you ever tried to integrate omics data from different biological layers? InCroMAP is a powerful, easy-to-use high-level cross-platform microarray dataset analysis tool. You can see example screenshots here. It provides several methods to analyze or visualize single datasets, as well as methods to perform integrated cross-platform analysis. Currently mRNA, miRNA (microRNA), DNA methylation and protein (modification) data are supported. InCroMAP can, for example, visualize all platforms at once in a pathway, provide detailed information, e.g., about promoter methylation or perform integrated mRNA and microRNA analysis. In general, InCroMAP is a tool for generic or pathway-based analysis and visualization of heterogeneous, cross-platform datasets.


Getting started:
This short screencast shows how to import data into InCroMAP and perform a first analysis on this data. First, the required tabular input file format is presented, secondly this mRNA dataset is opened and lastly, an enrichment analysis is performed and the dataset is visualized in a pathway.

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info
Update with new features: Released InCroMAP version 1.5 with new features. InCroMAP now supports metabolomics data and is able to perform integrated analysis (enrichments, pathway visualizations) on metabolomics and gene expression data. Please see the release notes for further information.  -   (wrzodek and rosenbaum - 2013-05-28 11:07)

Important update: Released InCroMAP version 1.4 with many important improvements. KEGG has changed its API such that previous releases cannot visualize pathways anymore. This has been fixed with this release. Please see the release notes for further information.  -   (wrzodek - 2013-01-10 10:25)

Applications note accepted: Our manuscript about the InCroMAP application has been accepted today by Oxford Bioinformatics. Please cite as:
Clemens Wrzodek, Johannes Eichner, Finja Büchel, and Andreas Zell. InCroMAP: Integrated analysis of Cross-platform MicroArray and Pathway data. Bioinformatics, 29(4):506-508, December 2012. [pdf ]   -   (wrzodek - 2012-12-16 13:49)

Methodology paper accepted: Our manuscript about the integrated visualization of omics data in a pathway, as implemented in InCroMAP, has been accepted by Oxford Bioinformatics. You can cite it as:
Clemens Wrzodek, Johannes Eichner, and Andreas Zell. Pathway-based visualization of cross-platform microarray datasets. Bioinformatics, 28(23):3021-3026, September 2012. [ DOI | details | link ]   -   (wrzodek - 2012-11-22 13:48)

Major Update: Released InCroMAP version 1.3 with many new features, improvements and bugfixes. InCroMAP can now visualize experimental omics data in BioPAX pathways, read data from many more platforms than before and contains multiple further enhancements. Please see the release notes for further information.  -   (wrzodek - 2012-09-28 16:25)

Update: Released InCroMAP version 1.2 with many new features, improvements and bugfixes. Please see the release notes for further information.  -   (wrzodek - 2012-08-07 10:58)

Documentation: The User's Guide and FAQ has been updated. For example, a description how to import data from GEO, using GEO2R has been added.  -   (wrzodek - 2012-08-06 15:11)

Screencast: A short video (screencast) is now available that shows how to open data in InCroMAP and perform a first analysis.  -   (wrzodek - 2012-08-06 15:08)

Documentation: A comprehensive documentation, including guides to format and import your expression data and a "Getting started" section is now available.  -   (wrzodek - 2012-03-15 12:31)

Examples: Example input datasets for mRNA, miRNA, protein and DNA methylation data are now available. Use them for testing the integration of omics data with InCroMAP.  -   (wrzodek - 2012-03-15 12:30)

FAQ: Updated the frequently asked questions.  -   (wrzodek - 2012-03-55 12:25)

Update: Version 1.1 now has an improved miRNA target mapping and allows to map DNA methylation data on gene promoters.  -   (wrzodek - 2012-03-05 14:54)

Update: Solved difficulties with saving pictures and added genome-region based DNA methylation plots.  -   (wrzodek - 2012-01-30 13:51)

First public release: Launch the application or download a stand-alone version as runnable JAR file.  -   (wrzodek - 2011-11-29 09:23)



This project is promoted by:

IMI MARCAR ZBIT