Inclusion Body Myositis Active Subnetwork Identification Workflow
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Download RO CrateWorkflow for Creating a large disease network from various datasets and databases for IBM, and applying the active subnetwork identification method MOGAMUN.
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Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| stringdb_input_file | STRING data | Table with Protein - protein interaction data as downloaded from STRING |
|
| mirtarbase_input_file | miRTarBase data | Table with miRNA - mRNA target data as downloaded from |
|
| entrez2string | STRING identifier mapping | Table with entrez mappings from STRING protein idenfitiers as downloaded from STRING |
|
| bridgedb | BridgeDB cache | directory with cached BridgeDB data |
|
| mRNA-mRNA_bicor | mRNA expression correlation | Tab separated edge list with Ensembl gene ID's in the first two columns, and their bi-weight midcorrelation as defined by Langelder et al. in the third column |
|
| miRNA-mRNA_bicor | miRNA mRNA correlation | Tab separated edge list with Ensembl gene ID's in the first column, miRBase ID's in the second column. and their bi-weight midcorrelation as defined by Langelder et al. in the third column |
|
| de_mRNA | Differential gene expression | Output of differential mRNA expression testing from DESeq2, with Ensembl gene ID's concatened with gene symbols with ";" inbetween in the first column |
|
| de_miRNA | Differential miRNA expression | Output of differential miRNA expression testing from DESeq2, with miRBase ID's in the first column |
|
| variant_burden | Variant Burden | Output of variant burden testing using SKAT in the rvtests package, with HGNC symbols in the first column |
|
| stringdb_number_of_edges | STRING limit | The number of STRING edges to use, USE FOR TESTING ONLY |
|
| stringdb_min_weight | STRING filter | The minimum score for a STRING edge to be included in the analysis |
|
| mirtarbase_number_of_edges | miRTarBase limit | The number of miRTarBase edges to use, USE FOR TESTING ONLY |
|
| max_cor_edges | Correlation limit | The number of correlation edges to use, USE FOR TESTING ONLY |
|
| mogamun_generations | MOGAMUN generations | The number of generation to let the genetic algorithm in MOGAMUN evolve |
|
| mogamun_runs | MOGAMUN runs | The number of parallel runs to let MOGAMUN do, these parallel runs are combined in postprocessing |
|
| mogamun_cores | MOGAMUN cores | The number of cores to let MOGAMUN use |
|
| mogamun_min_size | Minimum subnetwork size | The minimum size of subnetworks during postprocessing |
|
| mogamun_max_size | Maximum subnetwork size | The maximum size of subnetworks during postprocessing |
|
| mogamun_merge_threshold | Subnetwork merge threshold | the minimum Jaccard Index overlap between two subnetworks to allow them to be merged |
|
Steps
| ID | Name | Description |
|---|---|---|
| import_stringdb | Import STRING | Imports STRING database file |
| import_mirtarbase | Import miRTarBase | Imports miRTarBase database file |
| map_stringdb | Map STRING | Maps STRING identifiers to identifiers consistent with datasets |
| map_mirtarbase | Map miRTarBase | Maps miRTarBase identifiers to identifiers consistent with datasets |
| integrate_graph | Integrate network | Integrates all datasources into a single disease network |
| igraph_to_mogamun | Convert igraph to MOGAMUN | Converts the igraph network format to the MOGAMUN input format |
| run_mogamun | Run MOGAMUN | runs the MOGAMUN software with selected paramters |
| postprocess_mogamun | Postprocess MOGAMUN | processes output from MOGAMUN, and merges overlapping subnetwork |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| full_graph | Full network | The full disease network, which combines all data sources |
|
| subnetworks | Subnetworks | Folder with the resulting subnetworks and generation statistics |
|
Version History
master @ 7e4122f (latest) Created 27th Nov 2023 at 16:19 by Daphne Wijnbergen
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Creators and SubmitterViews: 646
Created: 27th Nov 2023 at 12:52
Last updated: 1st Feb 2024 at 11:26
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