UniprotR: Retrieving and visualizing protein sequence and functional information from Universal Protein Resource (UniProt knowledgebase)

Installation

The package is avilable now online at https://proteomicslab57357.shinyapps.io/UniprotR/

install.packages("UniprotR")

Description

Connect to Uniprot to retrieve information about proteins using their accession number such information could be name or taxonomy information,The package provides a powerful data retrieval capabilities in addition to screening visualization tool, and ID conversion tool that helps researchers for analyzing their proteomics data as well as subsequent downstream analysis.

Documentation

For the documentation see: UniprotR Documentation.

Package information

• link to package on CRAN: UniprotR

Usage

Example

library(UniprotR) 
#Read Accessions from csv file , Note : Accessions must be in the first column. 
Accessions <-GetAccessionList("https://s3.amazonaws.com/csvpastebin/uploads/9571fa356c67a0c7c95e8431799a051a/Accessions.csv") 
#Get Taxanomy Information 
TaxaObj <- GetNamesTaxa(Accessions) 
#Visualize Chromosomes localization
PlotChromosomeInfo(TaxaObj)
#Visualize protein's gene name as Network 
PlotGenesNetwork(TaxaObj)

Gene ontology of protein list

#Get Gene ontolgy Information 
GeneOntologyObj <- GetProteinGOInfo(Accessions) 
#Plot Biological process information top 10 go terms  
PlotGOBiological(GeneOntologyObj, Top = 10) 
#Plot molecular function information top 20 go terms
Plot.GOMolecular(GeneOntologyObj, Top = 20)
#Plot subcellualr localization information 
Plot.GOSubCellular(GeneOntologyObj) 
#Combine Gene ontology plots into one plot 
PlotGoInfo(GeneOntologyObj)
#Handy visualization for publications 
PlotGOAll(GOObj = GeneOntologyObj, Top = 10, directorypath = getwd(), width = 8, height = 5)

Enrichment analysis using KEGG, Reactome of protein list

Pathway.Enr(Accessions)
#For ready graphs for publications 
PlotEnrichedGO(Accs = Accessions, Path = getwd(), theme = "lancet", width = 9, height = 5)
PlotEnrichedPathways(Accs = Accessions, Path = "Your local path to save graph", theme = "jama", w = 9, h = 5)

Get diseases associated with protein list

PathologyObj <- GetPathology_Biotech(Accessions)
Diseases <- Get.diseases(PathologyObj)

Get fasta file for protein list

#This feature could be used to create a databse search for MS/MS
GETSeqFastaUniprot(Accessions = Accessions, FileName = "Acclist")

Protein- Protein interaction using STRING

#Get Protein-Protein Interaction within input data 
#Path example = "E:/Users/Network.pdf"
GetproteinNetwork(Accessions , Path to save your pdf file) 

Contribution Guidelines

For bugs and suggestions, the most effective way is by raising an issue on the github issue tracker. Github allows you to classify your issues so that we know if it is a bug report, feature request or feedback to the authors.

Email: [email protected]

Future plans

• Perform literature overview of given protein list.

Citation

Soudy, Mohamed, Ali Mostafa Anwar, Eman Ali Ahmed, Aya Osama, Shahd Ezzeldin, Sebaey Mahgoub, and Sameh Magdeldin. 2020. “UniprotR: Retrieving and Visualizing Protein Sequence and Functional Information from Universal Protein Resource (UniProt Knowledgebase).” Journal of Proteomics 213 (February). Elsevier B.V. doi:10.1016/j.jprot.2019.103613.