Difference between revisions of "Find common effectors for multiple gene sets (GeneWays) (workflow)"
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== Workflow overview == | == Workflow overview == | ||
[[File:Find-common-effectors-for-multiple-gene-sets-GeneWays-workflow-overview.png|400px]] | [[File:Find-common-effectors-for-multiple-gene-sets-GeneWays-workflow-overview.png|400px]] | ||
| + | == Description == | ||
| + | This workflow is designed to find effector molecules downstream of an input list of genes. The Input is a folder containing several gene or protein tables, and these tables are taken automatically by the workflow, one input table after another, in a cycle. | ||
| + | |||
| + | At the first step, the input table is converted into a table with Entrez Gene IDs. At the next step the Entrez genes are subjected to Effector search 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. | ||
| + | |||
| + | |||
| + | |||
== Parameters == | == Parameters == | ||
;Input folder | ;Input folder | ||
Latest revision as of 16:34, 12 March 2019
- Workflow title
- Find common effectors for multiple gene sets (GeneWays)
- Provider
- geneXplain GmbH
[edit] Workflow overview
[edit] Description
This workflow is designed to find effector molecules downstream of an input list of genes. The Input is a folder containing several gene or protein tables, and these tables are taken automatically by the workflow, one input table after another, in a cycle.
At the first step, the input table is converted into a table with Entrez Gene IDs. At the next step the Entrez genes are subjected to Effector search 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 folder
- Input folder containing differentially expressed genes
- Species
- MaxSteps
- Maximal number of downstream steps/radius
- Results folder
