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SYstems Genetic Network AnaLysis (SYGNAL) pipeline

We developed the transcription factor (TF)-target gene database and the Systems Genetics Network Analysis (SYGNAL) pipeline to decipher transcriptional regulatory networks from multi-omic and clinical patient data. SYGNAL is widely applicable for integrating genomic and transcriptomic measurements from other human cohorts and also mouse studies. We provide a lot of details about applying the SYGNAL pipeline to glioblastoma multiforme (GBM) in our recent paper Plaisier et al., 2016 with a lot of details in the supplementary information.

Outline

1. Installation
   • Dependencies
     • Python
     • R
     • Stand alone programs
   • Installing SYGNAL
2. Preparing for SYGNAL run
   • Overview of SYGNAL method
   • Directory structure for running cMonkey₂ and SYGNAL
   • Running cMonkey₂
   • Overlaying SYGNAL on alternative clustering methods
3. Running SYGNAL
   • Command line parameters
   • Input files
     • sygnal_config.json
     • cMonkey₂ output database
     • User supplied cMonkey₂ expression matrix
     • Complete user supplied expression matrix
     • Gene ID thesaurus
     • TF-target gene regulatory interactions
     • TF family information
     • miRNA-target gene regulatory interactions
     • Promoter and 3' UTR sequences for organism of study
     • Background sequence information for motif callers
   • Typical run of SYGNAL
   • Typical output from running SYGNAL
4. Results from SYGNAL
   • output directory
   • postProcessed_.csv
5. Troubleshooting