UniprotR: Retrieving and visualizing protein sequence and functional information from Universal Protein Resource (UniProt knowledgebase)
The package is avilable now online at https://proteomicslab57357.shinyapps.io/UniprotR/
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.
For the documentation see: UniprotR Documentation.
- link to package on CRAN: UniprotR
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)
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.
- Perform literature overview of given protein list.
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.