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Ortho2ExpressMatrix—a web server that interprets cross-species gene expression data by gene family information

Thomas Meinel12*, Michal R Schweiger2, Andreas H Ludewig3, Ramu Chenna4, Sylvia Krobitsch5 and Ralf Herwig2

Author Affiliations

1 Structural Bioinformatics Group, Institute for Physiology, Charité - University Medicine Berlin, Thielallee 71, 14195 Berlin, Germany

2 Vertebrate Genomics Department, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany

3 Institute of Human Nutrition and Food Science, Christian-Albrechts-University of Kiel, Heinrich-Hecht-Platz 10, 24118 Kiel, Germany

4 Biotechnology Center, Technical University Dresden, Tatzberg 47-49, 01307 Dresden, Germany

5 Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany

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BMC Genomics 2011, 12:483  doi:10.1186/1471-2164-12-483

Published: 4 October 2011

Additional files

Additional file 1:

Supplementary tables and figures. Table S1 lists the genome builts for five organisms with respective Ensembl versions integrated into Ortho2ExpressMatrix at the time of publication. Table S2 lists the implemented Microarray platforms and respective and GEO platform identifiers at the time of publication. Table S3 reports the assessment of numbers of proteins in families and protein families for pairs of organisms of four protein family inferring approaches basing on sequence data of Ensembl version 59, Table S4 reports the assessment of Ensembl 49. Figure S5 displays O2EM output examples for miRBase and TargetScan families. Figure S6 displays variations of the ratio threshold as significance criterion, which is an important O2EM selection parameter.

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