# CLUMPS-PTM
An algorithm for identifying 3D clusters ("clumps") of post-translational modifications (PTMs). Developed for the Clinical Proteomic Tumor Atlas Consortium ([CPTAC](https://proteomics.cancer.gov/programs/cptac)). Full project repoistory for pan-cancer project can be found [here](https://github.com/getzlab/CPTAC_PanCan_2021).
__Author__: Shankara Anand
__Email__: sanand@broadinstitute.org
_Requires Python 3.6.0 or higher._
## Installation
##### PIP
`pip3 install clumps-ptm`
or
##### Git Clone
```
git clone git@github.com:getzlab/CLUMPS-PTM.git
cd CLUMPS-PTM
pip3 install -e .
```
## Use
CLUMPS-PTM has 3 general phases of analysis:
1. __Mapping__: taking input PTM proteomic data and mapping them onto PDB structural data.
Mapping relies on the source data and involves programmatic calling of `blastp+` depending on the source data-base to map to UNIPROT and ultimately PDB structures. An example notebook that walks through the mapping and demonstrates use of `clumps-ptm` API for running these steps programmatically can be found [here](https://github.com/getzlab/CLUMPS-PTM/blob/main/examples/CPTAC_Mapping_Workflow.ipynb). Once the mapping is performed once for a new data-set, the mapping file is used as the `--maps` flag in `clumpsptm` command (below).
2. __CLUMPS__: running the algorithm for identifying statistically significant clustering of PTM sites.
CLUMPS-PTM was designed for use with differential expression proteomic data. Due to the nature of drop-out in Mass-Spectrometry data, we opt for using broad changes in PTM levels across sample groups to interrogate "clumping" of modifications. Thus, the input requires out-put from Limma-Voom differential expression.
```{python}
usage: clumpsptm [-h] -i INPUT -m MAPS -w WEIGHT -s PDBSTORE [-o OUTPUT_DIR]
[-x XPO] [--threads THREADS] [-v]
[-f [FEATURES [FEATURES ...]]] [-g GROUPING] [-q]
[--min_sites MIN_SITES] [--subset {positive,negative}]
[--protein_id PROTEIN_ID] [--site_id SITE_ID] [--alphafold]
[--alphafold_threshold ALPHAFOLD_THRESHOLD]
Run CLUMPS-PTM.
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
<Required> Input file.
-m MAPS, --maps MAPS <Required> Mapping with index as indices that overlap
input.
-w WEIGHT, --weight WEIGHT
<Required> Weighting for CLUMPS-PTM (ex. logFC).
-s PDBSTORE, --pdbstore PDBSTORE
<Required> path to PDBStore directory.
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
Output directory.
-x XPO, --xpo XPO Soft threshold parameter for truncated Gaussian.
--threads THREADS Number of threads for sampling.
-v, --verbose Verbosity.
-f [FEATURES [FEATURES ...]], --features [FEATURES [FEATURES ...]]
Assays to subset for.
-g GROUPING, --grouping GROUPING
DE group to use.
-q, --use_only_significant_sites
Only use significant sites for CLUMPS-PTM.
--min_sites MIN_SITES
Minimum number of sites.
--subset {positive,negative}
Subset sites.
--protein_id PROTEIN_ID
Unique protein id in input.
--site_id SITE_ID Unique site id in input.
--alphafold Run using alphafold structures.
--alphafold_threshold ALPHAFOLD_THRESHOLD
Threshold confidence level for alphafold sites.
```
3. __Post-Processing__: post-processing (FDR correction) \& visualization in Pymol.
Raw data
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