Commit 5ea550cd authored by Matt Rogon's avatar Matt Rogon

Update README.md

parent 3302c927
# Integration_transcriptome_proteome_2020_d2
Day 2 Integration of Transcriptome and Proteome Data
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Day 1 Introduction to Network Biology and Cytoscape
1. Introductory Lecture 9-10am Matt
2. 10:30 - Practical introduction with Livia
- Introductory Cytoscape
- interface
- loading of networks into CS from files
- loading of attributes into networks
- merging networks
- extracting subnetworks
- editing attributes in CS node and edge table
- layouts
- manipulation of the style
- apps/installation and launching
3. Lunch
4. Enrichment analysis, Clustering and String database access
Day 2 Integration of Transcriptome and Proteome Data
Section 1: Pre-process input files into formats needed for the analysis.
- Load and clean up the datasets
- Apply thresholds for significant hits
Section 2 BioMart and merging
- Threshold data and add identifiers for quick data filtering
- Annotate datasets using BioMaRt
- Merge proteomic and transcriptomic datasets
Section 3 STRING
- Extract known interactions for proteins using STRING database
- String Plot interactions for top 100 significantly (<0.05) up-regulated
proteins
Section 4 iGraph
- Process the STRING output into Cytoscape
- Conversion to an iGraph object
- Deleting edges and nodes
- Converting to different formats e.g. edge lists, adjacency matrices.
- Filtering using edge attributes e.g. combined score from String
- Creating output files for further analysis
Section 5 iGraph to Cytoscape
- Transferring networks to Cytoscape using the REST interface
Section 6 integration analysis in Cytoscape
- at this stage we will run Cytoscape to integrate and visualise datasets and
generate biologically relevant results.
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