Workflow Type: Common Workflow Language

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
stringdb_input_file STRING data Table with Protein - protein interaction data as downloaded from STRING
  • File
mirtarbase_input_file miRTarBase data Table with miRNA - mRNA target data as downloaded from
  • File
entrez2string STRING identifier mapping Table with entrez mappings from STRING protein idenfitiers as downloaded from STRING
  • File
bridgedb BridgeDB cache directory with cached BridgeDB data
  • Directory
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
  • File
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
  • File
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
  • File
de_miRNA Differential miRNA expression Output of differential miRNA expression testing from DESeq2, with miRBase ID's in the first column
  • File
variant_burden Variant Burden Output of variant burden testing using SKAT in the rvtests package, with HGNC symbols in the first column
  • File
stringdb_number_of_edges STRING limit The number of STRING edges to use, USE FOR TESTING ONLY
  • int
stringdb_min_weight STRING filter The minimum score for a STRING edge to be included in the analysis
  • int
mirtarbase_number_of_edges miRTarBase limit The number of miRTarBase edges to use, USE FOR TESTING ONLY
  • int
max_cor_edges Correlation limit The number of correlation edges to use, USE FOR TESTING ONLY
  • int
mogamun_generations MOGAMUN generations The number of generation to let the genetic algorithm in MOGAMUN evolve
  • int
mogamun_runs MOGAMUN runs The number of parallel runs to let MOGAMUN do, these parallel runs are combined in postprocessing
  • int
mogamun_cores MOGAMUN cores The number of cores to let MOGAMUN use
  • int
mogamun_min_size Minimum subnetwork size The minimum size of subnetworks during postprocessing
  • int
mogamun_max_size Maximum subnetwork size The maximum size of subnetworks during postprocessing
  • int
mogamun_merge_threshold Subnetwork merge threshold the minimum Jaccard Index overlap between two subnetworks to allow them to be merged
  • int

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
  • File
subnetworks Subnetworks Folder with the resulting subnetworks and generation statistics
  • Directory

Version History

master @ 7e4122f (latest) Created 27th Nov 2023 at 16:19 by Daphne Wijnbergen

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help Creators and Submitter
Creators
  • Daphne Wijnbergen
  • Mridul Johari
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: 232

Created: 27th Nov 2023 at 12:52

Last updated: 1st Feb 2024 at 11:26

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