Support Modules: panoply_cmap_annotate

panoply_cmap_annotate

Description

Annotates CMAP output from panoply_cmap_analysis by performing the following analyses. This module is already integrated into the panoply_cmap_analysis module.

• To identify how many trans-correlated genes for all candidate regulatory genes can be directly explained by gene expression changes measured in the CMAP shRNA perturbation experiments, knockdown gene expression consensus signature z-scores (knockdown/control) are used to identify regulated genes, followed by counting the number of trans-genes in this list of regulated genes.

• To obtain biological insight into the list of candidate driver genes, enrichment analysis is performed on samples with extreme CNA values (amplification or deletion) to identify statistically enriched sample annotation subgroups from annotation provided in the cmap_enrichment_groups file.

• Prepares input data for subsequent GSEA analysis on cis/trans-correlation values to find enriched pathways.

Input

Required inputs:

• tarball: (.tar file) tarball from panoply_cmap_connectivity (internal task)
• cmap_data_file: (String) CMAP level 5 gene knockdown data table in gctx format (gs://fc-de501ca1-0ae7-4270-ae76-6c99ea9a6d5b/cmap-data/annotated_GSE92742_Broad_LINCS_Level5_COMPZ_geneKDsubset_n36720x12328.gctx)
• yaml: (File) parameters file in yaml format

Optional inputs:

• cmap_grp: (String, default = "all") filename prefix used for files created during CMAP analysis
  • cmap_group: Internal parameter set by cmap_grp.
• cmap_typ: (String, default = "pome") omics data type; suppoted types are "pome" (all proteomics/PTM types) and "mrna" (for RNAseq data)
  • cmap_type: Internal parameter set by cmap_typ.
• cmap_enrichment_groups: (.csv File) subset of sample annotations, providing classes for enrichment analysis of candidate genes
• cna_threshold: (Float, default = 0.3) copy number up/down threshold; copy number is considered UP regulated if > cna_threshold and DOWN regulated if < -cna_threshold
• log_transform: (String, default = "FALSE") if TRUE, log2 transform input data
• alpha: (String, default = 0.05) p-value threshold for CMAP profile z-scores (see Description) and enrichments
• outFile: (String, default = "panoply_cmap-annotate-output.tar") output .tar file name

Output

• outputs: Tarball with annotated CMAP analysis results. See Data Analysis Modules: panoply_cmap_analysis for details.
• gsea_input: ("${cmap_group}-cmap-${cmap_type}-gsea-input.gct") GCT file with cis/trans-correlation values, used as input for subsequent GSEA analysis.