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Patrick X. Zhao, Ph. D. The Zhao Bioinformatics Lab pzhao@noble

Mapping Affymetrix Medicago GeneChip Probe sets to IMGAG 3.0 Genes. Patrick X. Zhao, Ph. D. The Zhao Bioinformatics Lab pzhao@noble.org. Agenda. About Affymetrix Medicago GeneChip Mapping Approach Bioinformatics & Data Resources for Medicago IMGAG Release V3. Affymetrix GeneChip Probes.

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Patrick X. Zhao, Ph. D. The Zhao Bioinformatics Lab pzhao@noble

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  1. Mapping Affymetrix Medicago GeneChip Probe sets to IMGAG 3.0 Genes Patrick X. Zhao, Ph. D. The Zhao Bioinformatics Lab pzhao@noble.org

  2. Agenda • About Affymetrix Medicago GeneChip • Mapping Approach • Bioinformatics & Data Resources for Medicago IMGAG Release V3

  3. Affymetrix GeneChip Probes mRNA EXON-I EXON-II EXON-III 3’ UTR 5’ UTR Target Sequence Probeset:11 Probes 25-mer Perfect match - PM 1 5 10 15 20 25 Mismatch - MM 1 5 10 15 20 25

  4. Probeset Types • id_at: Designates probe sets that uniquely recognize target transcripts • id_a_at: Designates probe sets that recognize alternative transcripts from the same gene. • id_s_at: Designates probe sets with common probes among multiple transcripts from different genes. • id_x_at: Designates probe sets where it was not possible to select either a unique probe set or a probe set with identical probes among multiple transcripts. Rules for cross-hybridization were dropped in order to design the _x probe sets. These probe sets share some probes identically with two or more sequences and, therefore, these probe sets may cross-hybridize in an unpredictable manner. GeneChip® Expression Analysis Data Analysis Fundamentals.

  5. About Medicago GeneChip

  6. Statistics on Original Medicago GeneChip Probe-sets vs. Gene Index V8 Mapping

  7. Mapping Approach • IMGAG V3 gene sequences were matched to corresponding Affymetrix probe sets using a position-weighted scoring index in which mismatches near the middle of a probe were most heavily penalized as follows: A perfect match for a probe set yields a score of 45 • Matches were declared when at least 8 of 11 probe sets had scores of 43 or higher [1,1,1,1,1,2,2,2,2,2,3,3,3,3,3,2,2,2,2,2,1,1,1,1,1] 1 5 10 15 20 25 Originated from Affymetrix, Inc.

  8. Statistics on Our Probesets vs. Gene Index V8 Mapping Results Overlapping mapping between our Probesets vs. Unigene mapping and the Affy original Probesets vs. Unigene mapping. 37872 ∩ 32108=32106. Our method covered 32106/32108=99.9993% of the Affymetrix original mapping.

  9. Statistics on Our IMGAG V3 vs. Probesets Mapping Results

  10. Probesets Map to IMGAG V3 and/or Gene Index V9 9.55 EST 38.72 (47.83) IMGAG 3.90

  11. Medicago Data and Bioinformatics Resources • http://bioinfo3.noble.org/medicago

  12. Acknowledgement Zhao Lab Xinbin Dai Rakesh Kaundal Haiquan Li Jun Li Zhaohong Zhuang Joshua Smith Collaborators: Michael K. Udvardi Rick A. Dixon Kiran K. Mysore Rujin Chen Chris Town (JCVI) Greg D. May (NCGR) … …

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