patrick x. zhao, ph. d. the zhao bioinformatics lab mapping affymetrix medicago genechip probe sets...
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Patrick X. Zhao, Ph. D.
The Zhao Bioinformatics Lab
pzhao@noble.org
Mapping Affymetrix Medicago GeneChip Probe sets to IMGAG 3.0
Genes
• 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
4793 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 50900 100
Statistics on Original Medicago GeneChip Probe-sets vs. Gene Index V8 Mapping
Num of ESTs
Matching Probeset
Percent
6315 0 17.12
29038 1 78.74
1525 >=2 4.14
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.
Num of EST
Matching probe-set
Percent
3304 0 8.96
29535 1 80.09
4039 >=2 10.95
36878 1000
10
20
30
40
50
60
70
80
90
0 probset 1 probeset 2 probesets
OriginOurs
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.
Statistics on Our Probesets vs. Gene Index V8 Mapping Results
Statistics on Our IMGAG V3 vs. Probesets Mapping Results
Num of cDNA Matching probe_set Percent
29755 0 55.70
16384 1 30.67
7284 >=2 13.63
53423 Total 100
Item Num of probesets
Matched To Percent
1 4860 None 9.552 19709 Unigene only 38.723 24348 19949 Unigene and
unique IMGAGv3
39.19 47.83
4399 Unigene and multiple IMGAGv3
8.64+
4 1983 1698 Unique IMGAGv3 only
3.34 3.90
285 Multiple IMGAGv3 only
0.56++
50900 Total 100
EST 38.72
(47.83)IMGAG
3.90
9.55
Probesets Map to IMGAG V3 and/or Gene Index V9
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)… …
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