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Patrick X. Zhao, Ph. D.
The Zhao Bioinformatics Lab
Mapping Affymetrix Medicago GeneChip Probe sets to IMGAG 3.5
Genes
(Snapshot on May/12/2010, based on Affy Approach)
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• About Affymetrix Medicago GeneChip
• Mapping Approach
• Bioinformatics & Data Resources for Medicago IMGAG Release V3
Agenda
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Affymetrix GeneChip Probes
5’ UTR EXON-I EXON-II EXON-III 3’ UTR
mRNA
Probeset: 11 Probes
Target Sequence
25-mer
1 255 10 15 20
1 255 10 15 20
Perfect match - PM
Mismatch - MM
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• 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.
Probeset Types
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About Medicago GeneChipType Num of
probe setsPercent in the Mtr. set
Notes
Unique probe sets: e.g. Mtr.10097.1.S1_at
44182 86.80 Unique to one gene
Alternative (_a_), e.g.: Mtr.10267.1.S1_a_at
116 2.28 Alternative probe sets to one gene
Shared (_s_), e.g. Mtr.10146.1.S1_s_at
4795 9.42 Common to multiple genes
Others (_x_), e.g.:Mtr.10093.1.S1_x_at
1809 3.55 Other probe sets with complicated mapping
Total 50902 100
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Statistics on Original Medicago GeneChip Probe-sets vs. Gene Index V8 Mapping
Matching Probeset
Num of ESTs Percent (%)
0 6315 17.12
1 29038 78.74
>=2 1525 4.14
Total 36878 100
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• 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
Mapping Approach
1 255 10 15 20
[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]
Originated from Affymetrix, Inc.
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Matching probe-set Num of Unigene Percent (%)
0 29955 43.5
1 33185 48.2
>=2 5708 8.3
Total 68848 100
Overlapping mapping between our Probesets vs. Unigene mapping and the Affy original Probesets vs. Unigene mapping.
Statistics on Gene Index V10 vs. Probesets Mapping Results
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Statistics on Our IMGAG V3.5 vs. Probesets Mapping Results
# of matched probe_sets
# of Gene Models Percent (%)
0 25728 52.6
1 17077 34.9
>=2 6131 12.5
Total 48936 100
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Item Num of probesets
Matched To Percent
1 8556 None 16.8
2 18819 Unigene only 40.0
3 20474
Unigene and unique IMGAGv3
40.2
Unigene and multiple IMGAGv3
+
4 3053Unique IMGAGv3 only
6
Multiple IMGAGv3 only ++
50902 Total 100
EST 40.0
(40.2)IMGAG
6.0
16.8
Mtr Probesets Map to IMGAG V3.5 and/or Gene Index V10
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Medicago Data and Bioinformatics Resources
• http://bioinfo3.noble.org/medicago
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AcknowledgementZhao LabXinbin DaiRakesh KaundalHaiquan LiJun LiZhaohong ZhuangJoshua Smith
Collaborators:Michael K. UdvardiRick A. DixonKiran K. MysoreRujin ChenChris Town (JCVI)Greg D. May (NCGR)… …