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Contains code and input files for Biotin IDR study by David Paul Minde and Manasa Ramakrishna

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ComputationalProteomicsUnit/biotinIDR

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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.

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Contains code and input files for Biotin IDR study by David Paul Minde and Manasa Ramakrishna

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