biotinIDR : Contains code and input files for Biotin IDR study

Main code : R and Python code for analysing data

Note: Before you run this code, you will need to download the following scripts

1. R installed on your computer
2. Python installed on your computer
3. GO.R from https://github.com/TomSmithCGAT/CamProt_R/blob/master/GO.R (if running from scratch you'll need to modify the code to be able to read in the column "to.id" instead of "GO.ID". Alternatively, you can change the coloumn names in your input dataframe to be "GO.ID"
4. 'd2p2.py' and 'protinfo.py' from https://github.com/TomSmithCGAT/CamProt/tree/master/camprot/proteomics (needs to be complied)

File	Description	Language/Format
biopepFunctions.R	Functions required for the R code to run	R
biopep.pub.Rmd	R markdown file that contains the main code used in the data analysis	R
nods.pub.html	HTML rendering of R markdown file biopep.pub.Rmd	Html
Get_IDRs-DM-v2.py	Adds IDR info for all proteins in each of the biotin studies	Python
runpy.sh	Calls Get_IDRs-DM-v2.py using various inputs and parameters	Shell
printUrl.py	Uses Protter URLs generated by Get_IDRs-DM-v2.py and retrieved PDF files into specific folders	Python
runUrl.sh	Calls printUrl.py on a file of interest	Shell
GO.R	Tom's code to add ancestor terms to existing GO terms	R
d2p2.py	Tom's code to use the d2p2 API to use 9 different callers to identify intrinsically disordered regions	Python
protinfo.py	Tom's code to query uniprot/swissprot database on Ensembl	Python

Input : Folder containing all input files needed for code to run

File	Contents
Ab-APEX-with-biotins-ptms-by-gene.rds	Biotinylation sites from Ab-APEX study summarised by gene with IDR and PTM information added in
BioSITe-with-biotins-ptms-by-gene.rds	Biotinylation sites from BioSITE study summarised by gene with IDR and PTM information added in
DiDBIT-with-biotins-ptms-by-gene.rds	Biotinylation sites from DiDBIT study summarised by gene with IDR and PTM information added in
SpotBioID-with-biotins-ptms-by-gene.rds	Biotinylation sites from Ab-APEX study summarised by gene with IDR and PTM information added in
Biotin-PTM-IDR-data-for-all-studies-and-callers.rds	Biotin,IDR and PTM information for all studies and caller combinations
HEK293-annotated-list-of-proteins.rds	HEK293 list of proteins from Geiger et al
HEK293-GO-annotation-with-ancestors.rds	GO annotations with ancestor terms for the HEK293 background protein list from Geiger et al
HEK293-with-IDR-VSL2b-and-PTMs.rds	HEK293 peoteins from Geiger et al with PTMs and IDRs based on the algorithm VSL2b
PTMs-by-gene-from-Phosphositeplus.rds	PTM data from PhosphositePlus summarised by gene and for phosphorylation, ubiquitination, sumoylation, acetylation
go-pro-kegg.rda	An object that contains all GO, Interpro and KEGG annotations for proteins in each of the 4 studies

RDS files can be read using the command readRDS as shown below

readRDS("Input/Biotin-PTM-IDR-data-for-all-studies-and-callers.rds")

RDA files can be loaded using the command "load" as shown below

load("Input/go-pro-kegg.rda")

Output : A description of all files generated by running nods_final.Rmd.

Date_Output : Date-tagged output folder This folder should contain the following files
Date = Date of the analysis in format yyyy-mm-dd ; Time = Time of analysis in format hh:mm:ss
Most of these files are related to the Figures in the main manuscript with some additional information

File	Contents
Figure3A_Number.biotins.vs.FractionIDR-VSL2b.pdf	Violin plots comparing fraction of IDR and biotin number in each protein
Figure3B_Distribution-of-Biotins-in.out.of.IDRs-by-caller-and-study.pdf	Bar plot showing expected and observed rates of biotin for all studies and callers
Figure3B_Binomial-test-stats.txt	Bionomial test values and parameters for all studies and callers looking at obs biotins in IDRs
Figure3C_Distribution-of-FPU-by-caller-parameters-and-study.pdf	Number of proteins in FPU categories in each study and by caller
Figure3D_VSL2b_Biotins-in-IDR.vs.IDR-classes.violinPlots.pdf	Violin plots showing biotins in IDRs separated by FPU for caller VSL2b
Figure4A_Num.idrs.vs.num.ptms_HEK293-vs-biotin.pdf	Correlation plot between number of PTMs and Biotins for HEK293 proteome (Geiger) and HEK203 biotinome
Figure4B_Distribution-of-PTM-types-in-HEK-vs-in-Biotin-studies.pdf	Boxplots showing PTM counts by type in HEK293 proteome and biotinome
Figure4C_Binomial-test-stats.txt	Bionomial test values and parameters for all studies and callers looking at obs PTMs in IDRs
Figure4C_Distribution-of-PTMs-in.out.of.IDRs-by-study-VSL2b.pdf	Bar plot showing expected and observed rates of all types of PTMs for all studies
Figure4D_VSL2b_PTMs-in-IDR.vs.IDR-classes.violinPlots.pdf	Violin plots showing all PTMs in IDRs separated by FPU for caller VSL2b
Figure4D_VSL2b_Acytelation.vs.IDR-classes.violinPlots.pdf	Violin plots showing acetylation marks in IDRs separated by FPU for caller VSL2b
Figure4D_VSL2b_Phosphorylation.vs.IDR-classes.violinPlots.pdf	Violin plots showing phosphorylation marks in IDRs separated by FPU for caller VSL2b
Figure4D_VSL2b_Sumoylation.vs.IDR-classes.violinPlots.pdf	Violin plots showing sumoylation marks in IDRs separated by FPU for caller VSL2b
Figure4D_VSL2b_Ubiquitination.vs.IDR-classes.violinPlots.pdf	Violin plots showing ubiquitination marks in IDRs separated by FPU for caller VSL2b
FigureS1A_VennDiagrams-for-biotinylation-data.pdf	Venn diagram showing overlap of proteins in biotinylation data
FigureS1C_Biotin-GO-CC-enrichment-with-anc-terms_8_enricher-dotplot.pdf	Bubble plots showing top 8 GO enrichment terms (including ancestors) for "cellular component" for each of the 4 studies
Biotin-GO-enrichment-with-anc-terms_8_enricher-dotplot.pdf	Bubble plots showing top 8 GO enrichment terms (including ancestors) for each of the 4 studies
Biotin-GO-enrichment_8_enricher-dotplot.pdf	Bubble plots showing top 8 GO enrichment terms for each of the 4 studies. No ancestor terms used.
Biotin-GO-CC-enrichment_8_enricher-dotplot.pdf	Bubble plots showing top 8 GO enrichment terms for "cellular component" for each of the 4 studies. No ancestor terms used.
GO-KEGG-enrichment-with-whole-human-genome-bg.pdf	GO enrichment plotting using clusterProfiler's inbuilt code and whole human genome as background
Effect-size-for-pairwise-comparison-of-PTMs-in-IDRs-VSL2b.pdf	Effect size plot based on Tukey's HSD for PTMs in IDRs
Effect-size-for-pairwise-comparison-of-biotin-in-IDRs-VSL2b.pdf	Effect size plot based on Tukey's HSD for PTMs in IDRs
Date_Time_Effect-size-for-pairwise-comparison-of-IDR-classes-and-parameters-VSL2b.pdf	Effect size plot based on Tukey's HSD for multiple parameters and IDR classes using VSL2b calls for IDR
Date_Time_VSL2b_Pairwise-t-test-pvals.txt	P-values for pairwise t-tests for all groups U-P, P-F, U-F across all studies
Date_Time_VSL2b_Tukey-HSD-ci-pvals.txt	P-values for Tukey's HSD tests following an ANOVA for all groups U-P, P-F, U-F across all studies

Figures : Folder containing all main and supplementary Figures from the paper

SupplTables.xlsx :

Supplementary tables referred to in the manuscript. Contain data that can be queried/used. Contains 5 datasheets and an "Index" sheet describing each of the data sheets.