Skip to main content

CLUMPS-PTM driver gene discovery using 3D protein structure (Getz Lab).

Project description

CLUMPS-PTM

An algorithm for identifying 3D clusters ("clumps") of post-translational modifications (PTMs). Developed for the Clinical Proteomic Tumor Atlas Consortium (CPTAC). Full project repoistory for pan-cancer project can be found here.

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. Once the mapping is performed once for a new data-set, the mapping file is used as the --maps flag in clumpsptm command (below).

  1. 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.

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.
  1. Post-Processing: post-processing (FDR correction) & visualization in Pymol.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

clumps-ptm-0.0.6.tar.gz (581.9 kB view details)

Uploaded Source

Built Distribution

clumps_ptm-0.0.6-py3-none-any.whl (25.5 kB view details)

Uploaded Python 3

File details

Details for the file clumps-ptm-0.0.6.tar.gz.

File metadata

  • Download URL: clumps-ptm-0.0.6.tar.gz
  • Upload date:
  • Size: 581.9 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.2 CPython/3.7.6

File hashes

Hashes for clumps-ptm-0.0.6.tar.gz
Algorithm Hash digest
SHA256 6a36b5599fa2702cd7bf48541ce842ee24c8ac27329590ef6acbeea748b09faf
MD5 087e11fb25f17e51a38c911f08babd92
BLAKE2b-256 5308c575be8645b0d0cc3ad0fa1a803830c0fb3a95057e0e8c7ee517f9c1658b

See more details on using hashes here.

Provenance

File details

Details for the file clumps_ptm-0.0.6-py3-none-any.whl.

File metadata

  • Download URL: clumps_ptm-0.0.6-py3-none-any.whl
  • Upload date:
  • Size: 25.5 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.2 CPython/3.7.6

File hashes

Hashes for clumps_ptm-0.0.6-py3-none-any.whl
Algorithm Hash digest
SHA256 96934b32fe4391c5250fd8baf5470d67ebd1ad5662dd44603f6252b9f9507f1d
MD5 90dee5c263c28e3369b5d4f5a90bec1a
BLAKE2b-256 82b263d7c145bc31c1d5c3c13fcb648479118164aa3d546fe5f5e62a6c5e55ae

See more details on using hashes here.

Provenance

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page