Hi everyone,

I am trying to upload a prefiltered data from Illumina HT_12_v4 beadchip. I have performed the normalization and differential analysis.

Now I want to do pathway analysis together with network anaylsis using PathVisio and Cytoscape.

Unfortunately the Ensembl bridge files :http://bridgedb.org/data/gene_database/

http://www.bridgedb.org/mapping-databases/ensembl-gene-mappings/

containing the mapping database are missing some 9300 accessions (ILMN_) identifiers for the chip I used for microarray.

I have loaded the bridge files from 2007 till 2016 and still some genes are unrecognized. 

This is why I am asking if there is a way to translate/convert all of the ILMN_ identifiers into another platform like Agilent/Affymetrix/RefSeq which I could use when uploading my expression data in PathVisio.

Is there any R package and script that might help me in this respect. I am not IT and have minimum experience with R so your help would be very much appreciated.

Thanks in advance.

Regards

Hi,

There are certainly ways of doing this from R using bioconductor packages. If you start by importing your data into R you can then use the annotation package "illuminaHumanv4.db" to convert illumina probe names to other identifiers.

# install the package
source("https://bioconductor.org/biocLite.R")
biocLite("illuminaHumanv4.db")

# load library
library(illuminaHumanv4.db)

# your_probe_ids <- import(expressiondata)
# The below function call will return a datafram with probe_id, gene symbol
# and ŕefgene_id for your data
select(illuminaHumanv4.db, 
       keys = your_probe_ids, 
       columns=c("SYMBOL","REFGENE"), 
       keytype="PROBEID")

Note that there are probes on the array that can not be converted
to gene ids, there is for example many control probes on the
array.

This is more or less directly from the vignette "1. Introduction
To Bioconductor Annotation Packages" that is part of the
AnnotationDbi package

so make sure to check this out for more examples.

BiocManager::install("illuminaHumanv4.db")

library("illuminaHumanv4.db")

probeID=c("ILMN_1690170", "ILMN_2410826", "ILMN_1675640", "ILMN_1801246",
          "ILMN_1658247", "ILMN_1740938", "ILMN_1657871", "ILMN_1769520",
          "ILMN_1778401")

df = data.frame(Gene=unlist(mget(x = probeID,envir = illuminaHumanv4SYMBOL)))

Outout: df

             Gene
ILMN_1690170 CRABP2
ILMN_2410826   OAS1
ILMN_1675640   OAS1
ILMN_1801246 IFITM1
ILMN_1658247   OAS1
ILMN_1740938   APOE
ILMN_1657871  RSAD2
ILMN_1769520 UBE2L6
ILMN_1778401  HLA-B