Endo
Repository for the TMEM184B Endoylysosomal Acidification paper
Adapted from source code used to analyze data in Dr. Martha Bhattacharya's lab at the University of Arizona
- The lab studies transmembrane protein 184b (TMEM184B), a protein involved in axon degeneration and cancer, across multiple neuroscience model systems
The Journal of Cell Science publication associated with this repository is the third to utilize function(s) from the
TMEM package. The first publication has
its own dedicated repository,
eriklarsen4/Itch,
and the second publication's repository, eriklarsen4/Hippo, is under
development. Please see those repositories for each paper's
respective URL. Among other datasets and analyses, they contain multiple, functionally validated bulk RNAseq datasets.
Please see the FIREpHly microscopy data vignette and the immunoprecipitation- label-free mass spec (IPMS) data vignette for more detail on each dataset's data cleaning and analysis.
Additional computational biology work on the published data is outlined in broad strokes here, with other vignettes in progress. This work improves upon the "gold standard" mixture modeling approach in affinity-precipitation mass spectrometry (APMS or IPMS) to infer proteins that truly interact with a target protein from a mixture of proteins.
Two packages are associated with this repository:
- A custom R package, TMEM, used for downstream gene set analyses and visualizations
- This repository's R package, Endo, which gathers the data used for the publication and documents it for reproducibility