Patrick X. Zhao, Ph. D. The Zhao Bioinformatics Lab [email protected] Mapping Affymetrix Medicago...
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Transcript of Patrick X. Zhao, Ph. D. The Zhao Bioinformatics Lab [email protected] Mapping Affymetrix Medicago...
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)
• About Affymetrix Medicago GeneChip
• Mapping Approach
• Bioinformatics & Data Resources for Medicago IMGAG Release V3
Agenda
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
• 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
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
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
• 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.
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
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
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
Medicago Data and Bioinformatics Resources
• http://bioinfo3.noble.org/medicago
AcknowledgementZhao LabXinbin DaiRakesh KaundalHaiquan LiJun LiZhaohong ZhuangJoshua Smith
Collaborators:Michael K. UdvardiRick A. DixonKiran K. MysoreRujin ChenChris Town (JCVI)Greg D. May (NCGR)… …