Workflow Type: Common Workflow Language
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Workflow 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 |
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stringdb_input_file | STRING data | Table with Protein - protein interaction data as downloaded from STRING |
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mirtarbase_input_file | miRTarBase data | Table with miRNA - mRNA target data as downloaded from |
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entrez2string | STRING identifier mapping | Table with entrez mappings from STRING protein idenfitiers as downloaded from STRING |
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bridgedb | BridgeDB cache | directory with cached BridgeDB data |
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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 |
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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 |
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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 |
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de_miRNA | Differential miRNA expression | Output of differential miRNA expression testing from DESeq2, with miRBase ID's in the first column |
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variant_burden | Variant Burden | Output of variant burden testing using SKAT in the rvtests package, with HGNC symbols in the first column |
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stringdb_number_of_edges | STRING limit | The number of STRING edges to use, USE FOR TESTING ONLY |
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stringdb_min_weight | STRING filter | The minimum score for a STRING edge to be included in the analysis |
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mirtarbase_number_of_edges | miRTarBase limit | The number of miRTarBase edges to use, USE FOR TESTING ONLY |
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max_cor_edges | Correlation limit | The number of correlation edges to use, USE FOR TESTING ONLY |
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mogamun_generations | MOGAMUN generations | The number of generation to let the genetic algorithm in MOGAMUN evolve |
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mogamun_runs | MOGAMUN runs | The number of parallel runs to let MOGAMUN do, these parallel runs are combined in postprocessing |
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mogamun_cores | MOGAMUN cores | The number of cores to let MOGAMUN use |
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mogamun_min_size | Minimum subnetwork size | The minimum size of subnetworks during postprocessing |
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mogamun_max_size | Maximum subnetwork size | The maximum size of subnetworks during postprocessing |
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mogamun_merge_threshold | Subnetwork merge threshold | the minimum Jaccard Index overlap between two subnetworks to allow them to be merged |
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Steps
ID | Name | Description |
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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 |
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full_graph | Full network | The full disease network, which combines all data sources |
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subnetworks | Subnetworks | Folder with the resulting subnetworks and generation statistics |
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Version History
master @ 7e4122f (latest) Created 27th Nov 2023 at 16:19 by Daphne Wijnbergen
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master @ 5d0df39 (earliest) Created 27th Nov 2023 at 12:52 by Daphne Wijnbergen
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Creators and Submitter
Creators
Submitter
Citation
Wijnbergen, D., Johari, M., Udd, B., Roos, M., & Mina, E. (2024). Inclusion Body Myositis Active Subnetwork Identification Workflow. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.681.7
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Views: 2382 Downloads: 843
Created: 27th Nov 2023 at 12:52
Last updated: 1st Feb 2024 at 11:26
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