PhosMap

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A Comprehensive R Package For Analyzing Quantitative Phosphoproteomics Data

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Functions summary

1. Extracting the confidence probability of phosphorylation sites at peptide level from identification results searched by Mascot.
2. Generating the quality control file of phosphorylation sites based on score of sites from Mascot.
3. Pre-processing phosphoproteomic data.
4. Kinase activity prediction.
5. Motif enrichment analysis.
6. Data visualization

Imports

graphics, grDevices, stats, utils, stringr, ggseqlogo, samr, limma, e1071, ClueR, Rtsne, glmnet, yaml, impute

External dependencies

• ksea (https://github.com/evocellnet/ksea)

install.packages('devtools')
require(devtools)
install_github('evocellnet/ksea')

• rmotifx (https://github.com/omarwagih/rmotifx)

install.packages('devtools')
require(devtools)
install_github('omarwagih/rmotifx')

Installation of PhosMap

install.packages('devtools')
require(devtools)
install_github('ecnuzdd/PhosMap')

User guide of PhosMap

• Tutorial of PhosMap (Tutorial_of_PhosMap.pdf)
• Functions manual of PhosMap (Manual_of_PhosMap.pdf)
• The help for installation (lnstallation_help.pdf)

Case study

You can go to this directory to find the files needed for the case study.

ftp://111.198.139.72:4000/PhosMap/data/

Or download them directly through the following links.

Complete workflow

This .zip contains PhosMap's demo code and raw datasets. After unzip, start the R program with setting the new folder as your working directory, and run the R script in it.

ftp://111.198.139.72:4000/PhosMap/data/PhosMap_Demo_With_BRAFi_Data.zip

Partial data

The .RData file stores the input objects required to invoke functions in the PhosMap script demo, which can be downloaded from the following link.

ftp://111.198.139.72:4000/PhosMap/data/BRAFi.RData

After downloading, put it into your working directory. Use the following command to introduce these objects into the global environment, then you can smoothly execute the statements in the script.

load(BRAFi.RData)

Source location of the built-in reference library

PhosMap_datasets https://github.com/ecnuzdd/PhosMap_datasets

• data (Demo data: BRAFi.RData)
• fasta_library
  • Refseq (Human, Mouse, Rattus)
  • Uniprot (Human, Mouse, Rattus)
• id_coversion_table
  • Human, Mouse, Rattus
• kinase_substrate_regulation_relationship_table
  • Human, Mouse, Rattus
• motif_library
  • Refseq (Human, Mouse, Rattus)
  • Uniprot (Human, Mouse, Rattus)

Complete demo data processed by Firmiana

Raw data from deposited in the ProteomeXchange Consortium

PXD007740

Processed data by Firmiana

ftp://111.198.139.72:4000/PhosMap/PhosMap_Demo_With_BRAFi_Data.zip

Reference

1. Ressa, A., et al. (2018) A System-wide Approach to Monitor Responses to Syner-gistic BRAF and EGFR Inhibition in Colorectal Cancer Cells, Molecular & cellular proteomics : MCP, 17, 1892-1908.
2. Feng, J., et al. (2017) Firmiana: towards a one-stop proteomic cloud platform for data processing and analysis, Nature biotechnology, 35, 409-412.