A Tentative Mapping between Medicago truncatula Affymetrix Probe-sets and  IMGAG 2.0  Genes /  Medicago Gene Index 8.0 Unigenes

May 07, 2008

Haiquan Li, Xinbin Dai, et al. (authors from Michael Udvardi's group) and Patrick X. Zhao*
Plant Biology Division, The Samuel Robert Noble Foundation, Ardmore OK 73401 , USA
Tel: + 1 580 224 6725; Fax: + 1 580 224 6692
* Corresponding Author

Email: pzhao@noble.org, Lab Website: bioinfo.noble.org

This webpage hosts our tentative mapping between Medicago truncatula Affymetrix Probe-sets vs. IMGAG 2.0 genes and Medicago Gene Index 8.0 unigenes.

The Medicago truncatula Affymetrix gene chip was developed based on Medicago truncatula Gene Index 8.0 release and pre-IMGAG 1.0 gene prediction. We believe that re-analyzing Affymetrix Probe-sets vs. newly released IMGAG gene 2.0 and original Medicago Gene Index 8.0 will be beneficial to legume community to get the most out of our recent published Medicago truncatula Gene Expression Atlas.

1. Original Data with Links:

• IMGAG 2.0 was downloaded from ftp://ftpmips.gsf.de/plants/medicago/MT_2_0/MT2.0_medicago_chrX_20080303_NoOverlap.xml.tar.gz. This is a slightly updated version (some errors have been fixed) of the IMGAG 2.0 release originally hosted on www.medicago.org.
• Medicago truncatula 8.0 (01-19-05) was downloaded from http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl?gudb=medicago.


• [ Original design downloaded from Affymetrix, inc.] Medicago_Affy_Consensus_Seqs.fasta: Consensus sequences assembled based on the original MTGI 8.0 unigenes and pre-IMGAG 1.0 predicted  genes.
• [ Original design downloaded fromAffymetrix, inc.] Medicago_Affy_Target_Seqs.fasta: probe-sets' target sequences were designed based on the above consensus sequences.
• [ Original design downloaded from Affymetrix, inc.] medicago_probes.fasta: probes that are presented on Medicago gene chip. They were designed by Affymetrix, Inc. based on the original MTGI 8.0 and pre-IMGAG 1.0 gene prediction.

2. Analysis and Discussion:

• 20080227_imgag_cdna.fasta: The UTRs+CDs (mRNA) of predicted genes in Medicago 2.0, downloaded from above internal link and further parsed using an internal script.
• MtAffyprobeset_MTGI80_IMGAG20_mapping0326.ppt: The PowerPoint presentation generated for discussion and evaluation of the quality of M.t. Affymetrix probe-set vs. IMGAG 2.0 and MTGI 8.0 gene mapping.

3. Mapping results:

• probe_mapping.xls: tentative mapping between probe-sets, IMGAG genes and Unigenes, analyzed by the Zhao bioinformatics lab.

Note: Although, we've done our best to ensure the quality of mapping between Affymetrix probe-sets and IMGAG 2.0 / MTGI 8.0 genes, please consider this as a tentative mapping release. We advise to use them at your own risk.

© 2008 by The Samuel Roberts Noble Foundation, Inc.