Mapping Affymetrix Medicago GeneChip

unknownlippsΤεχνίτη Νοημοσύνη και Ρομποτική

16 Οκτ 2013 (πριν από 3 χρόνια και 8 μήνες)

76 εμφανίσεις

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 90% BLASTN match)



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

25

5

10

15

20

1

25

5

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 GeneChip

Type

Num of
probe sets

Percent 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



Search IMGAG 3.5 splice Transcript or MTGI10
sequence against
Affy

Target Sequences by NCBI
BLASTN with e
-
value<1e
-
02



Only keep the hits whose HSP identical length / target
total length >= 0.9 as mapping between sequence and
probeset.

Mapping Approach

Originated from Affymetrix, Inc.

Matching probe
-
set

Num of Unigene

Percent (%)

0

30952

44.96

1

32308

46.93

>=2

5588

8.12

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

25968

53.07

1

15123

30.90

>=2

7845

16.03

Total

48936

100

Item

Num of
probesets

Matched To

Percent

1

9296


None

18.26

2

17909

Unigene only

35.18



3



21329

Unigene and
unique
IMGAGv3



41.90

Unigene and
multiple
IMGAGv3


+


4


2368

Unique
IMGAGv3 only


4.65

Multiple
IMGAGv3 only


++

50902

Total

100


EST
35.18






(
41.90)

IMGAG


4.65

18.26

Mtr

Probesets Map to IMGAG V3.5
and/or Gene Index V10

Medicago Data and Bioinformatics
Resources




http
://
bioinfo3.noble.org/medicago


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
)

… …