Sample Output

Download sample output result files

Below are links to download sample results for the different modules of the Mergeomics pipeline as well as the input files/parameters overview file (all inputs are available as sample inputs in the pipeline). These results are the same as displayed in the pipeline workflow below.

View pipeline workflow sample results display

Below is the pipeline workflow with results for individual GWAS enrichment (meta-MSEA results are also included). For this sample analysis, the top 50% of coronary artery disease GWAS associations were mapped to genes using the 'Distance 50kb' (SNPs mapped to genes based on chromosomal distance) file and corrected with CEU linkage disequilibrium over 70% dependency ('CEU LD70'), and MSEA was run with KEGG, BioCarta, and Reactome marker sets. wKDA was run with an adipose gene regulatory network, and PharmOmics was run with all genes from the wKDA generated subnetwork.

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Marker Dependency Filtering
Type Description Filename/Parameters
Files Association Data CARDIOGRAM_CAD.txt
Marking Mapping Data gene2loci.050kb.txt
Marker Dependency File ld70.ceu.txt
Parameters Percentage of Markers 50
Download Output Files
Corrected Marker Associations 'MARKER' and 'VALUE' file with marker with lower value in linkage disequilibrium filtered out Download
Corrected Marker Mappings 'GENE' and 'MARKER' file with mappings subsetted to those matching markers in the association file Download
MDF input files and parameters File listing chosen files and parameters for this MDF run Download
Marker Set Enrichment Analysis
Type Description Filename/Parameters
Files Association Data MDF_corrected_association.txt
Marking Mapping Data MDF_corrected_mapping.txt
Gene Sets KEGG_Reactome_BioCarta.txt
Gene Sets Description KEGG_Reactome_BioCarta_info.txt
Parameters Permutation Type gene
Max Genes in Gene Sets 500
Min Genes in Gene Sets 10
Max Overlap Allowed for Merging 0.33
Min Overlap Allowed for Merging 0.33
Number of Permutations 2000
MSEA to KDA export FDR cutoff 25
Download MSEA Result Files
Modules Details Lists for each module the genes that contributed to the module's enrichment, the corresponding markers in the association file and their association strengths Download
Modules Results Summary Records for each module the enrichment p-value, FDR, and number of genes and markers contributing to the enrichment Download
File and Parameter Selection Lists chosen files and parameters for this MSEA run Download
Runtime job log Runtime outputs and errors (if any) of job Download
Download Merged Modules Result Files
Merged Modules Results Summary Records MSEA results for merged modules (same data fields as the 'Modules Results Summary File'). Merged modules contain supersets of individual modules that share genes at a ratio above the 'Max Overlap Allowed for Merging' parameter (some modules may remain independent). MSEA is rerun on these merged modules and the results are recorded in this file. Download
Merged Modules Nodes for KDA Lists the genes (nodes) of non-redundant supersets (merged modules) that will automatically be used as input for the next optional step of the analysis, key driver analysis (KDA). These genes are members of modules that passed the user specified FDR cutoff ('MSEA to KDA export FDR cutoff'; default is 25%). If no modules passed this significance, then the top 10 modules are used. Please refer to your results if this was the case and interpret results from KDA accordingly. You may rerun the analysis with a different threshold. Download

Module ID MSEA: P-Value MSEA: FDR Description Module Top Gene Module Top Marker Module Top Association Score
Merge Module ID Merge Module P-Value Frequency Number of Genes Number of Markers Density Overlap Description
Meta-MSEA
Click for Parameters Type of Enrichment Association File Mapping File Modules File Descriptions File
Download Output Files
Meta Modules Details File Lists for each module the genes that contributed to the module's enrichment, the corresponding markers in the association file and their association strengths Download
Meta Modules Results Summary Records for each module the enrichment p-value, FDR, and number of genes and markers contributing to the enrichment Download
Meta Merged Modules Results File Records MSEA results for merged modules (same data fields as the 'Modules Results Summary File'). Merged modules contain supersets of individual modules that share genes at a ratio above the 'Max Overlap Allowed for Merging' parameter (some modules may remain independent). MSEA is rerun on these merged modules and the results are recorded in this file. Download
Meta Merged Modules Nodes for KDA Lists the genes (nodes) of non-redundant supersets (merged modules) that will automatically be used as input for the next optional step of the analysis, key driver analysis (KDA). These genes are members of modules that passed the user specified FDR cutoff ('MSEA to KDA export FDR cutoff'; default is 25%). If no modules passed this significance, then the top 10 modules are used. Please refer to your results if this was the case and interpret results from KDA accordingly. You may rerun the analysis with a different threshold. Download
Individual Study P and FDR Results File Combined summary file containing the P and FDR values for each individual MSEA run. Refer to the file and parameter selection file below for the individual MSEA run codes Download
Individual MSEA Result Files Zip file containing individual MSEA result files. Refer to the file and parameter selection file below for the individual MSEA run codes Download
Meta MSEA File and Parameter Selection File Lists chosen files and parameters for this Meta MSEA run for each study Download
Meta MSEA Job log Runtime outputs and errors (if any) of job Download

Module ID Meta P-Value Meta FDR Cochran.Q Cochran.P I2 Module Top Gene Module Top Marker Module Top Association Score
Merge Module ID Merge Module P-Value Frequency Number of Genes Number of Markers Density Overlap Description
Module P.values FDR.values Meta.P Meta.FDR
Weighted Key Driver Analysis
Type Description Filename/Parameters
Files Gene Sets Sample.MSEA_merged_modules.txt
Gene Sets Description KEGG_Reactome_BioCarta_info.txt
Network networks.hs.adipose.txt
Parameters Search Depth 1
Edge Type Incoming and Outgoing
Min Overlap 0.33
Edge Factor 0.5
Download KDA Output and Cytoscape Visualization Files
Key Drivers Results Lists for each key driver its P and FDR values, the module of which it is a key driver for, the total number of neighbors ('N.neigh'), the number of neighbors that are members of the module ('N.obsrv'), and the expected number of neighbors that are members of the module as calculated by permutation. Download
Cytoscape Edges Cytoscape-ready edges file describing network connections of the top 5 key drivers from each module and their neighbors Download
Cytoscape Nodes Cytoscape-ready nodes file listing each node of the edges file and their detailed attributes which can be modified by the user Download
Cytoscape Module Color Mapping File describing module colors. A node pie chart image (Google Chart API) will have the color(s) of the module(s) they are members of. Download
File and Parameter Selection Lists chosen files and parameters for this KDA run Download
Runtime job log Runtime outputs and errors (if any) of job Download
Merge Module ID Module Description Key Driver Node P-Value FDR Module Genes KD Subnetwork Genes Module and Subnetwork Overlap Fold Enrichment

KDA to PharmOmics Network Based Drug Repositioning
Drug Repositioning Analysis Description Parameters
Network Based Drug Repositioning Network Selection Sample liver network
Species Selection Human
Module and Gene Selection All genes from the subnetwork
Download Output Files
Network Based Drug Repositioning Analysis File Download
Genes used for repositioning Download
Parameters overview Download
Drug Species Tissue Z-Score Rank P-value Visualization Link Network files
KDA to PharmOmics Overlap Based Drug Repositioning
Drug Repositioning Analysis Gene selection
Overlap Based Drug Repositioning All genes from the subnetwork
Download Output Files
Overlap Based Drug Repositioning Analysis File Download
Genes used for repositioning Download
Database Method Drug Species Tissue or Cell Line Study Dose Treatment Duration Jaccard Score Odds Ratio P value Within Species Rank