Demo Workflows

Here, we list workflows that were used to prove the capabilities of the geneXplain platform, for instance in the cited publications. The links given direct you straight into the platform without requiring any registration.
Using these demo workflows, you will be able to reproduce the published results and to learn more about the platform’s look and feel. To work with your own data, however, registration is required. Additional licensing is necessary for certain third-party products such as TRANSFAC® or TRANSPATH®.
Workflows 1-3 are from our recent publication Koschmann et al., Microarrays 4, 270-286.
1. Workflow “Identify enriched motifs in promoters“,
applied to datasets of naphthalene-treated mouse liver and lung tissue.
Find further instructions and explanations here.
Origin of datasets:
GEO GSE18858 and GSE17933
Thomas, R.S., et al. (2011) Application of transcriptional benchmark dose values in quantitative cancer and noncancer risk assessment. Toxicol. Sci. 120, 194-205. PMID: 21097997
Thomas, R.S., et al. (2009) Use of short-term transcriptional profiles to assess the long-term cancer-related safety of environmental and industrial chemicals.Toxicol. Sci. 112, 311-321. PMID: 19776212
2. Workflow “Find master regulators in the TRANSPATH® network“,
applied to datasets of naphthalene-treated mouse liver and lung tissue.
Find further instructions and explanations here.
The data sources are as for Workflow 1.
3. Workflow “Enriched upstream analysis with TRANSFAC® and TRANSPATH® network“,
applied to datasets of naphthalene-treated mouse liver and lung tissue.
Find further instructions and explanations here.
The data sources are as for Workflow 1.
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