README.md

In richelbilderbeek/bianchi_et_al_2017: Bianchi Et Al Two Thousand Seventeen

bianchi_et_al_2017

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R code for 'Transmembrane Helices Are an Overlooked Source of Major Histocompatibility Complex Class I Epitopes', by Frans Bianchi, Johannes Textor and Geert van den Bogaart.

These R scripts make almost all figures in the paper "Transmembrane helices are an overlooked source of MHC class I epitopes" by Frans Bianchi, Johannes Textor, and Geert van den Bogaart. (DOI: 10.3389/fimmu.2017.01118)

Figure 3

Figure 3 as published

Figure 3 is made by tmh-predictions/HLA_predictions.xlsx.

Figure 3 in the Excel sheet

Usage

If you have all prerequisites installed, you should be able to create all figures by typing make. All necessary data will either be downloaded (such as the human proteome) or is included in the folder data/ (such as the transmembrane domain predictions).

Run test

make test

Run full

make

Be aware that the HLA binding predictions can take several hours. It can be useful to speed up the process by running e.g. 'make -j 8' to run 8 jobs in parallel.

Prerequisites

To run the code, you need:

• A working R installation and the R packages seqinr and data.table
• The R package EpitopePrediction, which can be installed from github using remotes::install_github("jtextor/epitope-prediction")
• GNU Make
• The program wget

If you do not have the program wget or do not wish to install it, you can also download the human proteome yourself and store it in the folder 'proteome/' before typing 'make'.

Files

The folder 'data' contains two files with peptide sequences that were eluted from B lymphoblastoid cell lines. These sequences are taken from the following publication, which is also cited in our paper:

"Comprehensive analysis of the naturally processed peptide repertoire: differences between HLA-A and B in the immunopeptidome" by Schellens et al, PLoS One (2015) 10:e0136417. (DOI: 10.1371/journal.pone.0136417)

Open questions

• Where does 'trans-membrane-analysis-shortened.txt' come from?

Makefile as a call graph

Create graph

make pic

Downloads

• Re-run done at 2020-09-29

Human proteome:

• Full proteome: download from: here, direct download from here, or use bianchietal2017::download_proteome
• Full proteome without selenocysteines: download from: http://richelbilderbeek.nl/UP000005640_9606_no_u.fasta,

Topology of human proteome:

• TMHMM topology of full proteome: impossible, due to selenocysteines, else it would be here
• TMHMM topology of full proteome without selenocysteines: at http://richelbilderbeek.nl/UP000005640_9606_no_u.tmhmm
• PureseqTM topology: here [1]

References

• [1] Changed the predicted topology of TRDD1_HUMAN from [nothing] to 00 (i.e. cytosolic)

richelbilderbeek/bianchi_et_al_2017 documentation built on Jan. 4, 2023, 1:36 a.m.