I have 1000 pdbid and I want to know that which one of this pdb- id contribute in disease. Could you please tell me which tools give all of pdb id and then draw the network in output
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gbahramali •
thanks for your reply ,could you please tell me one tool for convert pdb-id to gene name (gene symbol)
You can use the "biomaRt" R package if you are familiar with R.
Code for this operation would look like this (not run):
library(biomaRt)
ensembl <- useMart("ensembl",dataset="hsapiens_gene_ensembl")
proteinIDs<- #A character vector of Ensembl Protein IDs. (I am assuming Ensembl Protein IDs is what you are talking about, please make sure that this is the case!)
tab<-getBM(attributes=c("hgnc_symbol","ensembl_peptide_id"),filters="ensembl_peptide_id",values=proteinIDs,mart=ensembl)
tab will now be a table with two columns, where the first column will be the gene symbol and the second column protein ID.
DisGeNET as an alternative source for the gene- disease mapping
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written
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Georg Summer
Thanks for your reply. Can I submit many name of gene(symbol gene name) in DisGeNET?
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gbahramali •
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gbahramali •
If you have a list of proteins/genes and their aggregate p-values from a GWAS study or transcriptome analysis study, you could use HotNet2 to prioritize significantly mutated subnetworks.
Also, see FunSeq2
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Felix Francis
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