How to Find OMIM id's of Disease Corresponding to a List of Gene Symbols in R?
I have list of dysregulated genes in a disease. I want to find OMIM ID of disease associated with this gene. Some thing like as below.
Disorder name Gene symbols OMIM ID Cytogenetic location Disease Class
Bleeding disorder, platelet-type, 15, 615193 (3) ACTN1 102575 14q24.1 Hematological
Mental retardation, X-linked nonsyndromic (3) AGTR2 300034 Xq22-q23 Neurological
Ichthyosiform erythroderma, congenital, nonbullous, 1, 242100 (3) ALOX12B 603741 17pter-p13.1 Dermatological
Asthma, dimished response to antileukotriene treatment in, 600807 (3) ALOX5 152390 10q11.2 Respiratory
Atherosclerosis, susceptibility to (3) ALOX5 152390 10q11.2 Cardiovascular
How can I generate this table with given gene list? I am a new user of Bioconductor. Please suggest any package in R. I know little about mygene package in R which can convert gene ID to Entrez ID. Thanks in advance.
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pankajnarula84 •
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pankajnarula84 •
2 answers
Hi, I had similar problem. I had list of gene names and ENSEMBL IDs and I wanted to get OMIM IDs. I used R package org.Hs.eg.db and following code, where overlapDf$gene are gene names.
library(org.Hs.eg.db)
cols <- c("SYMBOL", "GENENAME", "ENSEMBL", "OMIM" )
mappedGenes <- as.data.frame(select(org.Hs.eg.db, keys=overlapDf$gene, columns=cols, keytype="SYMBOL"))
Hope it helps, Nastia
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anastazie.d •
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anastazie.d •
Found some useful information here,
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