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.

How can I generate this table with given gene list? I am a new user of Bioconductor. Is there some luck? Thanks in advance? 

You may register to download tables with all OMIM diseases and genes from:

http://omim.org/downloads

Otherwise, I might recommend the following steps:

1. Convert your gene symbol such as "ACTN1" to an Entrez Gene ID "87".
2. Get the OMIM Gene ID for your Entrez Gene ID.
3. Get the disease names corresponding to your OMIM ID.

You'll have to write a few custom functions that make use of the mygene.info API. Try using the mygene package available from Bioconductor.

Regarding step 3, I haven't yet figured out how exactly to get the name of disorders for an OMIM Gene ID. You might find an API for that.

For example:

Get the Entrez Gene ID for "ACTN1": http://mygene.info/v2/query?q=symbol%3AACTN1&fields=entrezgene&species=human

{
  "hits": [
    {
      "entrezgene": 87,
      "_score": 92.2922,
      "_id": "87"
    }
  ],
  "max_score": 92.2922,
  "took": 4,
  "total": 1
}

Get the OMIM ID for Entrez Gene ID "87": http://mygene.info/v2/gene/87?fields=MIM

{
  "_id": "87",
  "MIM": "102575"
}

You are welcome to use addGeneIDs in ChIPpeakAnno package to get OMIDs for a list of gene IDs by setting IDs2Add = c("omim"). Currently, 6 different type of input gene IDs are supported, i.e., ensemble_gene_id, entrez_id, gene_symbol, gene_alias or refseq_id.  For more informations, please type ?addGeneIDs in a R session after load the package by library(ChIPpeakAnno).

Best regards,

Julie