Patrick X. Zhao, Ph. D.

The Zhao Bioinformatics Lab

pzhao@noble.org

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)… …