Note: Before you run this code, you will need to download the following scripts
- R installed on your computer
- Python installed on your computer
- 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"
- '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 |
| 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 |
readRDS("Input/Biotin-PTM-IDR-data-for-all-studies-and-callers.rds")
load("Input/go-pro-kegg.rda")
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 |
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.