How to Find OMIM id's of Disease Corresponding to a List of Gene Symbols in R?

Question

[pankajnarula84]

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.

Answer 1

[anastazie.d]

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

Answer 2

[EagleEye]

Found some useful information here,

Help with OMIM disease categories, filtering, etc