Porto-Sinusoidal Vascular Disease transcriptomics analysis workflow Version 1
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Download RO-CrateWorkflow 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 |
|
| bgxfile | Illumina beadchip array file | Illumina HumanHT-12 WG-DASL V4.0 R2 expression beadchip |
|
| clinical_data | Clinical data | Clinical phenotype data |
|
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 |
|
| gsea_edge_table | GSEA edge table | Edge table for GSEA network result visualisation in Cytoscape |
|
| net_data_table | Network data table | GSEA network data table |
|
| add_net_data_table | Additional network data table | GSEA network additional visualisation table |
|
| module_eigengene_net_nodetable | Module eigengene node data | Module eigenegene correlation network node table in Cytoscape |
|
| module_eigengene_net_edgetable | Module eigengene edge data | Module eigenegene correlation network edge table in Cytoscape |
|
Version History
Version 1 (earliest) Created 11th Jun 2024 at 15:13 by Aishwarya Iyer
Initial commit
Frozen
Version-1d0fc23d
Creators and Submitter
Views: 1237 Downloads: 184
Created: 11th Jun 2024 at 15:13
Last updated: 14th Jun 2024 at 13:23
AttributionsNone
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https://orcid.org/0000-0002-7770-620X
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