Porto-Sinusoidal Vascular Disease transcriptomics analysis workflow
Version 1

Workflow Type: Common Workflow Language
Work-in-progress

Workflow for gene set enrichment analsysis (GSEA) and co-expression analysis (WGCNA) on transcriptomics data to analyze pathways affected in Porto-Sinusoidal Vascular Disease.

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Inputs

ID Name Description Type
raw_counts Microarray data Illumina beadchip raw gene expression data -GSE77627
  • File
bgxfile Illumina beadchip array file Illumina HumanHT-12 WG-DASL V4.0 R2 expression beadchip
  • File
clinical_data Clinical data Clinical phenotype data
  • File

Steps

ID Name Description
pre_processing Data pre-processing Pre-processing input data
quality_control Quality control Quality control of input data
DEG Differential gene expression analysis Differential gene expression analysis using limma
wgcna Weighted gene co-expression network analysis Weighted gene co-expression network analysis for module identification
gsea_analysis Gene set enrichment analysis and visualisation Gene set enrichment analysis and visualisation in Cytoscape
ME_network Module eigenegene correlation network Module eigenegene correlation network and visualisation in Cytoscape
module_ora Module enrichment analysis Module enrichment analysis with significantly correlating modules

Outputs

ID Name Description Type
gsea_node_table GSEA node table Node table for GSEA network result visualisation in Cytoscape
  • File
gsea_edge_table GSEA edge table Edge table for GSEA network result visualisation in Cytoscape
  • File
net_data_table Network data table GSEA network data table
  • File
add_net_data_table Additional network data table GSEA network additional visualisation table
  • File
module_eigengene_net_nodetable Module eigengene node data Module eigenegene correlation network node table in Cytoscape
  • File
module_eigengene_net_edgetable Module eigengene edge data Module eigenegene correlation network edge table in Cytoscape
  • File

Version History

Version 1 (earliest) Created 11th Jun 2024 at 15:13 by Aishwarya Iyer

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Citation
Iyer, A., & Ehrhart, F. (2024). Porto-Sinusoidal Vascular Disease transcriptomics analysis workflow. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.1040.1
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Views: 584   Downloads: 65

Created: 11th Jun 2024 at 15:13

Last updated: 14th Jun 2024 at 13:23

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