gene and disease nework
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8.5 years ago
gbahramali ▴ 20

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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8.5 years ago
lkmklsmn ▴ 970

I am not aware of a single tool that will do this. I think you will have to do the mapping manually.

  1. PDB-ID-> Gene Symbol
  2. Gene Symbol -> Disease using OMIM

The biomart tool will probably facilitate these mappings.

I would recommend using Cytoscape to draw the network.

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thanks for your reply ,could you please tell me one tool for convert pdb-id to gene name (gene symbol)

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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.

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DisGeNET as an alternative source for the gene- disease mapping

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Thanks for your reply. Can I submit many name of gene(symbol gene name) in DisGeNET?

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8.5 years ago
gbahramali ▴ 20
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7.1 years ago
Felix Francis ▴ 580

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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