Workflow Type: Common Workflow Language
Frozen
Frozen
Frozen
Frozen
Frozen
Frozen
Frozen
Workflow for Creating a large disease network from various datasets and databases for IBM, and applying the active subnetwork identification method MOGAMUN.
Click and drag the diagram to pan, double click or use the controls to zoom.
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
Added remaining metadata
Frozen
master
7e4122f
master @ fbe3ed5 Created 27th Nov 2023 at 16:10 by Daphne Wijnbergen
More metada
Frozen
master
fbe3ed5
master @ 7fd2fb2 Created 27th Nov 2023 at 16:04 by Daphne Wijnbergen
More metadata
Frozen
master
7fd2fb2
master @ 7fd2fb2 Created 27th Nov 2023 at 16:00 by Daphne Wijnbergen
More metadata
Frozen
master
7fd2fb2
master @ 7fd2fb2 Created 27th Nov 2023 at 15:59 by Daphne Wijnbergen
More metadata
Frozen
master
7fd2fb2
master @ 7fd2fb2 Created 27th Nov 2023 at 15:50 by Daphne Wijnbergen
More metadata
Frozen
master
7fd2fb2
master @ 5d0df39 (earliest) Created 27th Nov 2023 at 12:52 by Daphne Wijnbergen
Update README.md
Frozen
master
5d0df39
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
License
Activity
Views: 2722 Downloads: 962
Created: 27th Nov 2023 at 12:52
Last updated: 1st Feb 2024 at 11:26
Annotated Properties
Operation annotations
Attributions
None