High throughput microarray based analysis methods e.g. gene expression profiling, Matrix CGH (comparative genom hybridization), miRNA profiling, protein profiling, or high density tissue microarrays are now routinely used in molecular oncology. However, these methods generate large amounts of data that have to be evaluated and analyzed. Further, the array data have to be linked with anonymized patients clinical and pathologic records or with corresponding information on experimental settings deposited in diverse type of databases. Our goal is to offer scientists easy to use statistics, data analysis, and bioinformatics data management tools. Molecular biologists as well as clinicians should be able to retrieve install and use these tools without prior extensive training or teaching.
Onco-Express tools are a
collection of software applications helping scientists to easily
manage, pre-process, analyse and visualise their 'omics data.
Onco-Express tools are compact MS-Windows based stand alone programs which do not need any additional supporting software libraries or installations.
Use of the rich graphical Windows user interface as well as a web-based context specific help system allow non-bioinformaticians to perform complex statistitics analyses with huge data-sets.
Onco-Express tools are composed of the main components:
|GeneSkipper||A sequence assembly and analysis|
|ChipSkipper||Micro array image analysis|
|MO-MEX||Micro array database / LIMS|
|TableButler||Data table pre-processing and handling|
|SUMO||A Statistical Utility for Micro array and Omics data|
|CS-Clust||Hierarchical clustering tool|
|bfDICOM||A tool for analysis of ultra sound contrast images|
|Utilities||CS-Cal: A tool for evaluation of clonogenic survival experiments|
|ChroMap: A tool for viewing and analysis of CGH-data|
|SeedScan: A tool for analyses of gene targeted/ClonTracer screens.|
|CircleGraph: A generic tool to generate circular maps|
Onco-Express tools were developed in a collaboration between
|Heidelberg University (Radiation Oncology)|
|Translational Radiation Oncology, DKFZ|
|Centre of Cancer Systems Biology, TUFTS University|