PPI-Context

Contextualization of protein-protein interaction databases by cell line

Clone repository

$ git clone https://github.com/montilab/ppi-context

Install requirements

$ cd ppi-context
$ pip install -r requirements.txt

The data

If you just want the data it’s easy to load into R…

$ R

ppi <- read.delim("data/v_1_00/PPI-Context.txt", header=TRUE, sep="\t", stringsAsFactors=FALSE)

data.frame(sort(table(ppi$cell_name), decreasing=TRUE)) %>%
set_colnames(c("var", "freq")) %>%
head(30) %>%
ggbarplot(x="var", y="freq", fill="freq") +
labs(title="", x="Cell Line Name", y="PPI") +
scale_fill_viridis_c(option="inferno", begin=0, end=0.8) + 
theme(legend.position="none",
      axis.text.x=element_text(angle=45, hjust=1, size=12, face="bold"))

Pre-processing the data

| PPI - Context (v1.0)
usage: ppictx.py [-h] [-r] [-d]
                   [-fh PATH_HIPPIE] 
                   [-fp PATH_PUBTATOR]
                   [-fc PATH_CELLOSAURUS]
optional arguments:
  -h, --help            show this help message and exit
  -r, --run             run pipeline
  -d, --download        download raw data first
  -fh PATH_HIPPIE       path to downloaded Hippie data (optional)
  -fp PATH_PUBTATOR     path to downloaded Pubtator data (optional)
  -fc PATH_CELLOSAURUS  path to downloaded Cellosaurus data (optional)

In most cases you will need to download the latest bulk data first and
then process it…

$ python ppictx.py --download --run

| PPI - Context (v1.0)
| Downloading raw data...
| Processing raw data
  ~ [PPI]
  ~ [PID -> CLA]
  ~ [CLA -> CID]
  ~ [PPI -> PID -> CLA -> CID]

In other cases, you might have the previous versions of the data to
process…

$ python ppictx.py --run \
                   -fh path/to/HIPPIE.mitab \
                   -fp path/to/PUBTATOR.gz \
                   -fc path/to/CELLOSAURUS.txt

Special considerations

Cell lines that are primarily used in research due to their
efficiency as an expression vector (e.g. HeLa, HEK, CHO, Sf9) may
not be useful representations of cell-specific protein dynamics.
However it may be useful to filter out PPIs annotated with these
cell lines.
Cellosaurus contains synonymous cell lines, therefore some
annotations such as HEK (CVCL_M624) and HEK293 (CVCL_0045)
refer to the same cell line. Users should be aware of synonymous
cell lines relevant to their interests and filter accordingly.

Cite

Federico A, Monti S (2021) Contextualized Protein-Protein Interactions.
Patterns. https://doi.org/10.1016/j.patter.2020.100153.