Difference between revisions of "Explain my genes (workflow)"
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== Workflow overview == | == Workflow overview == | ||
[[File:Explain-my-genes-workflow-overview.png|400px]] | [[File:Explain-my-genes-workflow-overview.png|400px]] | ||
| + | == Description == | ||
| + | This workflow is designed to find effector molecules downstream of an input gene set. | ||
| + | |||
| + | At the next step the input gene table is subjected to the ''Regulator search'' method. | ||
| + | |||
| + | |||
| + | |||
| + | in the GeneWays network. For each potential master regulator, FDR, Score, and Z-score are calculated. | ||
| + | |||
| + | The results are filtered by '''Z_Score>1 and Score>0.2''' to select statistically significant Effector nodes. | ||
| + | |||
| + | Further, the filtered Effector molecules are converted to both Ensembl Gene IDs and a list of UniProt protein IDs. The table with Ensembl Gene Ids is annotated with additional information, gene description and gene symbols. | ||
| + | |||
| + | Finally, the filtered Effector nodes table is sorted by Score and networks for the three top effectors are visualized as diagrams in the hierarchical layout. | ||
| + | |||
| + | The same steps are repeated for the next input table, and several cycles are performed automatically corresponding to the number of tables in the input folder. | ||
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== Parameters == | == Parameters == | ||
;Input gene set | ;Input gene set | ||
Latest revision as of 16:34, 12 March 2019
- Workflow title
- Explain my genes
- Provider
- geneXplain GmbH
[edit] Workflow overview
[edit] Description
This workflow is designed to find effector molecules downstream of an input gene set.
At the next step the input gene table is subjected to the Regulator search method.
in the GeneWays network. For each potential master regulator, FDR, Score, and Z-score are calculated.
The results are filtered by Z_Score>1 and Score>0.2 to select statistically significant Effector nodes.
Further, the filtered Effector molecules are converted to both Ensembl Gene IDs and a list of UniProt protein IDs. The table with Ensembl Gene Ids is annotated with additional information, gene description and gene symbols.
Finally, the filtered Effector nodes table is sorted by Score and networks for the three top effectors are visualized as diagrams in the hierarchical layout.
The same steps are repeated for the next input table, and several cycles are performed automatically corresponding to the number of tables in the input folder.
[edit] Parameters
- Input gene set
- Species
- Results folder
