Cellmap analysis modules

Cellmap analysis modules written in GO. This was built with GO modules.

Build

git clone https://github.com/knightjdr/cmgo.git
cd cmgo
go build ./...

Run an analysis module

An options file in JSON format can be used to define run time arguments. Arguments can also be supplied on the command line (these will override corresponding arguments specified in the options file).

A module name must always be supplied for analysis.

cmgo -options="config.json" -module="module-name"

Module specific parameters can be found in the README files in the corresponding folder.

Analysis

Module name

Modules for generating files for upload and query file processing.

Module name: analysis-dbgenes

• folder analysis/dbgenes

Generates a txt file of official genes used for SAINT

Assessment

Module name: assessment-compartment-recovered

• folder assessment/localization/recovered

Get the genes assigned to a specific compartment by GO and report on those seen from a list of genes.

Module name: assessment-countgo

• folder assessment/countgo

Count the number of genes with a GO term specified by the supplied namespace.

Module name: assessment-go

• folder assessment/go

Perform GO analysis on baits in a SAINT file

Module name: bait-gradient

• folder assessment/bait/gradient

Takes an ordered bait list and expected localizations for the baits and outputs a gradient showing adjacent bait similarity: black if the two adjacent baits share an expected localization, grey if only one does and white otherwise.

Module name: assessment-hydropathy

• folder assessment/hydropathy

Measures the average hydropathy of proteins in a SAINT file and a BioPlex dataset

Module name: assessment-localization

• folder assessment/localization/evaluate

Report on which localizations are previously known.

Module name: assessment-prediction

• folder assessment/localization/prediction

Assign a prediction score for every prey localized by NMF or SAFE

Module name: assessment-transmembrane

• folder assessment/transmembrane

Information about the transmembrane proteins residing between two NMF compartments.

Control

• folder assessment/controls/preys

Module name: control-preys

Output statistics on prey proteins in controls using SAINT input files.

Enrichment

Modules for calculating term enrichment in compartments and lists.

Module name: enrichment-genes

• folder enrichment/genes

Perform a g:Profiler enrichment on a list of genes

Module name: enrichment-heatmap

• folder enrichment/heatmap

Creates a heat map visualizing region (domain/motif) fold enrichment (scaled to Log2) across NMF or SAFE compartments.

Interactors

Module name: interaction-knownbyrank

• folder interaction/knownbyrank

Calculates the proportion of known interactors for the Nth best prey across all baits in a SAINT report. Prey spectral counts are control subtracted and length normalized to determine their rank.

Module name: interaction-rankaverage

• folder interaction/rankaverage

Calculates the average bait interaction rank for a list of preys.

Module name: interaction-rankmetrics

• folder interaction/rankmetrics

Calculates metrics for preys by interaction rank, including expression level, number of lysines and turnover rate.

LBA

Module name: lba-correlation

• folder lba/correlation

Calculate correlation between LBA profiles and output Cytoscape formatted file for viewing network.

Module name: lba-enrichment

• folder lba/enrichment

Enrichment performs GO enrichments of preys from a SAINT file using LBA.

Module name: lba-localize

• folder lba/localize

Localize preys based on enriched terms for LBA

Module name: nmf-v-safe

• folder assessment/localization/nmfsafe

Check concordance between NMF and SAFE localizations

Network

Modules for creating networks

Module name: network-svg

Create an svg network for NMF or SAFE

Module name: network-tsnecytoscape

Convert a tSNE coordinate system into a .cyjs file for Cytoscape

NMF

Modules for NMF (and related) analysis.

Module name: nmf-moonlighting

• folder nmf/moonlighting

Calculates a moonlighting score for preys in an NMF basis matrix

Module name: nmf-robustness

• folder nmf/robustness

Evaluates how robust each rank's GO terms are based on the genes used to define it. It will first define the rank by performing a GO enrichment using at most maxGenesPerRank, and then repeat this when using 90%, 80%... of the maxGenesPerRank. For each evaluation it will calculate the RBD between the list generated for maxGenesPerRank and the fractional list.

Module name: nmf-subset

• folder nmf/subset

Subset an NMF basis (prey) matrix to only include preys enriched in specified compartments.

Module name: nmf-uv

• folder nmf/uv

For all prey genes not used to define an NMF rank, it calculates what proportion are being assigned to a previously known localization. UV: unused validation

Organelle comparison

Modules for comparing cell map compartments.

Module name: organelle-isolation

• folder organelle/isolation

Calculates how isolated an NMF compartment is, i.e. for genes localizing to the compartment the number of edges between members of the compartment relative to the number of edges to proteins outside the compartment.

Module name: organelle-overlap

• folder organelle/overlap

Takes two lists of proteins and a txt file with similarity scores between proteins and outputs metrics on the similarity within and between the lists.

Module name: organelle-sharedregion

• folder organelle/shared

Takes two lists of proteins and outputs metrics on the regions (domains/motifs) shared between common preys.

Prey prey

Modules for prey-prey analysis

Module name: preyprey-subset

• folder preyprey/subset

Subset a ProHits-viz interactive file to grab a cluster

Summary

SAINT file summaries and information

Module name: summary-crapome

• folder summary/crapome

Generates a CRAPome matrix from SAINT input files

Module name: summary-notsignificant

• folder summary/notsignificant

Generates a list of preys that were not significant with any bait in a SAINT file.

Files for website

1. CRAPome matrix

• module: summary-crapome
• filename: crapome-matrix-v1.txt
• destination: client/resources/downloads

2. preys detected in samples that are not significant

• module: summary-notsignificant
• filename: not-significant-v1.txt
• destination: client/resources/downloads

3. sequence database

• download FASTA database from ProHits
• filename: sequence-database-v1.txt
• destination: client/resources/downloads

4. genes in database

• module: analysis-dbgenes
• filename: v1_dbgenes.txt
• destination: api/app/data/genes