README for Probe ID -> RGD Gene ID mapping files


The files in this directory and its subdirectories contain microarray probe ID to gene RGD ID mapping data.  Each line contains one probe ID-RGD Gene ID pair.

Mappings were imported into RGD from Affymetrix and Ensembl in July 2008.

Annotation files for Affymetrix assignments were downloaded from the Affymetrix website at http://www.affymetrix.com/analysis/downloads/na25/ivt/.  Ensembl assignments were downloaded using the Ensembl BioMart tool at http://www.ensembl.org/biomart/martview/.  For information about how Ensembl maps probe sets to genes, see http://www.ensembl.org/info/docs/microarray_probe_set_mapping.html


PLEASE NOTE:  We have found that the Affymetrix data, which was produced when the microarrays were first designed, contains some inconsistencies.  Many of the Affymetrix assignments were based on UniGene IDs and some of those IDs are no longer in use, or have been assigned to different genes than what they were originally associated with.  We therefore recommend that care be taken when using this data.


Files in this directory:
Nonredundant_Probe-RGDgene_Affymetrix.txt
Nonredundant_Probe-RGDgene_Ensembl.txt
Each of these is a non-redundant list of Affymetrix probe ID to gene RGD ID mappings.  They are listed without regard to what chip/platform the probe can be found on.

array_id_agilent_probe_Ensembl.txt
array_id_codelink_Ensembl.txt
These files contain the Ensembl-assigned probe ID to gene RGD ID mappings for microarrays from companies other than Affymetrix (i.e.Agilent Technologies, and Applied Microarrays/CodeLink)


The two subdirectories, Affy_Platforms_Affymetrix and Affy_Platforms_Ensembl, include lists of Affymetrix probe ID to gene RGD ID mappings separated into separate files based on Affymetrix platform/chip--one file per directory per chip.  The files are divided into the two directories based on where the mappings came from.  File names include the name of the chip (e.g. "rae230b") and the name of the data source (either Ensembl or Affymetrix).  An example of a file name for the Affymetrix rae230b array with probe IDs mapped to RGD IDs by Ensembl would be:  array_id_affy_rae230b_Ensembl.txt.  The file for the same array with mappings from Affymetrix is:  array_id_rae230b_Affymetrix.txt

For questions about these files, please contact RGD using the "Contact Us" form at http://rgd.mcw.edu/contact/index.shtml


COMPLETE LIST OF AVAILABLE FILES:

Lists of Non-redundant probe ID to RGD ID mappings		
Folder:	RGD_Gene-Microarray_Probe_ID_Mappings		
URL:	ftp://rgd.mcw.edu/pub/data_release/RGD_Gene-Microarray_Probe_ID_Mappings/ 
	
Files:							Array type	Source of Mapping Data
	Nonredundant_AffyProbe-RGDgene_Affymetrix.txt	Affymetrix	Affymetrix
	Nonredundant_AffyProbe-RGDgene_Ensembl.txt	Affymetrix	Ensembl
	array_id_agilent_probe_Ensembl.txt		Agilent		Ensembl
	array_id_codelink_Ensembl.txt			CodeLink	Ensembl
			
Platform-specific lists of probe ID to RGD ID mappings		
Folder:	Affy_Platforms_Affymetrix/		
URL:	ftp://rgd.mcw.edu/pub/data_release/RGD_Gene-Microarray_Probe_ID_Mappings/Affy_Platforms_Affymetrix/ 
	
Files:						Array type	Source of Mapping Data
	array_id_rae230a_Affymetrix.txt		Affymetrix	Affymetrix
	array_id_rae230b_Affymetrix.txt		Affymetrix	Affymetrix
	array_id_rat230_2_Affymetrix.txt	Affymetrix	Affymetrix
	array_id_rg_u34a_Affymetrix.txt		Affymetrix	Affymetrix
	array_id_rg_u34b_Affymetrix.txt		Affymetrix	Affymetrix
	array_id_rg_u34c_Affymetrix.txt		Affymetrix	Affymetrix
	array_id_rn_u34_Affymetrix.txt		Affymetrix	Affymetrix
	array_id_rt_u34_Affymetrix.txt		Affymetrix	Affymetrix
			
Folder:	Affy_Platforms_Ensembl/		
URL:	ftp://rgd.mcw.edu/pub/data_release/RGD_Gene-Microarray_Probe_ID_Mappings/Affy_Platforms_Ensembl/ 
	
Files:						Array type	Source of Mapping Data
	array_id_affy_rae230a_Ensembl.txt	Affymetrix	Ensembl
	array_id_affy_rae230b_Ensembl.txt	Affymetrix	Ensembl
	array_id_affy_raex_1_0_st_Ensembl.txt	Affymetrix	Ensembl
	array_id_affy_rat230_2_Ensembl.txt	Affymetrix	Ensembl
	array_id_affy_rg_u34a_Ensembl.txt	Affymetrix	Ensembl
	array_id_affy_rg_u34b_Ensembl.txt	Affymetrix	Ensembl
	array_id_affy_rg_u34c_Ensembl.txt	Affymetrix	Ensembl
	array_id_affy_rn_u34_Ensembl.txt	Affymetrix	Ensembl
	array_id_affy_rt_u34_Ensembl.txt	Affymetrix	Ensembl