Cell map analysis scripts

Scripts are currently being migrated to GO and can be found at this repo: https://github.com/knightjdr/cmgo

Scripts used for analyzing data at the cell-map.org. All perl scripts can be run with the -h flag for command line options.

Script order

For third-party datasets, see data-sets README for instructions on getting and/or reformatting files.

Setup up an ENV variable CMSCRIPTS pointing to this repo. Run any script as "$CMSCRIPTS"/folder/script.pl

1. saint-processing

• merge files
• filter files to remove contaminants and poorly performing baits

2. assessment

• summary statistics: no. preys, unique preys, etc.
• r-squared between replicates
• bait GO enrichment
• prey overlap between baits using the Jaccard index
• bait localization summary (from known information)
• baits recovered as preys
• overlap with BioPlex

3. interaction-assessment

• known interaction recovery per FDR
• known and new interactions recovered per bait

4. prey-prey

• prey-prey correlation
• generate list of preys in network
• generate Cytoscape files
• prey-prey interaction recovery
• prey-prey complex recovery

5. cytoscape

• generate network for SAFE

6. safe

• create annotation matrix
• run SAFE with a collection of networks, annotation matrices and parameters
• assess results
• generate Cytoscape network coloured by SAFE domain

7. nmf

• create matrix for NMF
• run NMF in batch
• summarize NMF ranks by GO terms
• assess NMF ranks
• assess prey localizaiton at varying NMF thresholds
• assess prey moonlighting
• report top three localizations (ranks) per prey
• generate heat map for viewing NMF matrices
• generate Cytoscape network based on correlation
• create t-SNE map from basis matrix

8. localization assessments

• assess NMF, SAFE and published dataset localizations against GO
• compare NMF and SAFE for overlap
• compare two datasets
• calculate the recovery of known terms per bait and avgspec
• assess primary and secondary NMF localizations

9. enrichments

• enriched domains for NMF or SAFE compartments
• enriched motifs for NMF or SAFE compartments

10. organelle assessments

• assess bait overlap for ER
• assess bait overlap for Mito
• assess bait overlap for ER-mito

11. networks (for website)

• create NMF tSNE network
• create correlation networks for NMF or SAFE

12. hierarchy

• build a localization hierarchy for retrieving parent and child terms

13. Upload related

• summary of prey values for evaluating localizations