Download SupplMaterialRefSeq102010

1
Introduction
The same analysis as in the paper presented at the BIOCOMP2011 has been performed. For this analysis the RefSeq database has been updated and the RefSeqIdentifieres XM ,XP ,NP are ignored in the analysis of cross-hybridzation. So
this study does an update of the data an shows the impact of the XM -RefSeqAccessions in comparision with the publication.
Additionally, the new RefSeq-accession lead to updated genes, which are represented in new gi-accession-number. For the CROP-Gene the official gene name
was also changed to LUC7L3. For the DUSP2 gene no matching Affymetrix
probes where found. It is therefore omitted from the results.
2
Datasets
For the detection of putative cross-hybridizations by sequence alignment, the
sequences of all Affymetrix probes (only the PM probes, the MM probes are discarded) are aligned against the RefSeq database using blastn. The gene annotations from RefSeq were downloaded on October,4th 2010 from ftp://ftp.ncbi.nih.gov/refseq/H sapiens/mRNA Prot/human.rna.fna.gz and ftp://ftp.ncbi.nih.gov/refseq/M musculus/mRNA Prot/mouse.rna.fna.gz.
1
2
Classification
Affymetrix Microarrays
HGUPlus
HGUA
HGUB
MG430
total number of probes
604258
247954
249502
496468
probes with a BLAST-hit
350537
210587
125766
316551
Unambiguous Probes
321272
185381
102726
269228
Ambiguous Probes
53511
25206
23040
47323
cross-hybridizing fraction
15340
9790
3849
38880
The probes were aligned against the RefSeq-Database. A large fraction did not have a identical 25mer-hit. The other probes
are classified if they are unambiguous or ambiguous. Ambiguity results from hits on the wrong strand or if they cross-hybridize.
The number of cross-hybridization probes is additionally shown.
3
4
Size of probesets
Affymetrix Microarrays
HGUPlus
HGUA
HGUB
MG430
5
former number of probesets
18800
12400
6500
16400
number of probesets
19381
12553
7484
16769
Correlation of Probesets with Etanercept and
MAQC dataset
Gene
Probeset
TNF
A: 207113 s at
D: NM 000594 at
F: GC06P031652
H: gi 25952110
A: 205067 at
A: 39402 at
D: NM 000576 at
F: GC02M113303
H: gi 27894305
A: 205207 at
D: NM 000600 at
F: GC07P022732
H: gi 224831235
A: 202859 x at
A: 211506 s at
D: NM 000584 at
F: GC04P074845
H: gi 28610153
A: 212657 s at
A: 212659 s at
A: 216243 s at
D: NM 173841 at
D: NM 000577 at
D: NM 173842 at
D: NM 173843 at
F: GC02P113591
H: gi 296010861
A: 202637 s at
A: 202638 s at
A: 215485 s at
D: NM 000201 at
F: GC19P010247
H: gi 16746619
A: 215223 s at
A: 216841 s at
D: NM 001024466 at
D: NM 000636 at
IL1B
IL6
IL8
IL1RN
ICAM1
SOD2
PCC
ETC
(RMA)
0.88
0.88
0.88
0.88
0.95
0.95
0.96
0.96
0.96
0.70
0.68
0.69
0.68
0.88
0.86
0.88
0.88
0.89
0.75
0.77
0.75
0.80
0.80
0.80
0.84
0.83
0.80
0.63
0.62
0.71
0.71
0.70
0.71
0.15
0.18
0.16
0.19
PCC
ETC
(MAS5)
0.89
0.89
0.89
0.89
0.95
0.96
0.96
0.96
0.96
0.72
0.73
0.72
0.73
0.89
0.87
0.92
0.92
0.92
0.77
0.71
0.69
0.80
0.80
0.80
0.76
0.76
0.80
0.64
0.68
0.62
0.71
0.71
0.71
0.13
0.24
0.21
0.23
3
PCC
MAQC
(RMA)
N/A
N/A
N/A
N/A
0.37
0.82
0.70
0.75
0.76
0.85
0.80
0.81
0.80
0.90
0.98
0.96
0.96
0.96
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
0.97
0.98
0.94
0.99
0.99
0.99
N/A
N/A
N/A
N/A
Number of
Probesetambiguous
size
probes
0
11
0
11
0
11
0
11
0
11
0
16
0
27
0
27
0
27
0
11
0
11
0
11
0
11
2
11
0
11
2
22
2
22
0
20
0
11
0
11
0
11
0
33
0
33
0
33
9
42
11
44
0
33
0
11
2
11
0
11
2
33
2
33
0
31
1
11
9
11
0
12
10
10
Continued on next page
number of covered genes
19381
12553
7484
16769
Gene
TRAF1
ZFP36
PTGS2
TNFAIP3
ADM
LUC7L3
NFκBIA
JUNB
Ø
Probeset
D: NM 001024465 at
F: GC06M160020
H: gi 67782308
A: 205599 at
D: NM 005658 at
F: GC09M122704
H: gi 300193046
A: 201531 at
D: NM 003407 at
F: GC19P044589
H: gi 141802261
A: 204748 at
D: NM 000963 at
F: GC01M184907
H: gi 223941909
A: 202643 s at
A: 202644 s at
D: NM 006290 at
F: GC06P138230
H: gi 26051241
A: 202912 at
D: NM 001124 at
F: GC11P010283
H: gi 4501944
A: 203804 s at
A: 208835 s at
A: 220044 x at
D: NM 016424 at
D: NM 006107 at
F: GC17P046151 at
H: gi 256542312
A: 201502 s at
D: NM 020529 at
F: GC14M034940 at
H: gi 168693660
A: 201473 at
D: NM 002229 at
F: GC19P012763 at
H: gi 44921611
all Affymetrix
all Dai
all Ferrari
Hummert
PCC
ETC
(RMA)
0.16
0.24
0.16
0.60
0.62
0.61
0.61
0.84
0.84
0.83
0.84
0.91
0.91
0.91
0.91
0.78
0.87
0.83
0.82
0.82
0.80
0.81
0.81
0.81
0.44
0.43
0.43
0.49
0.49
0.47
0.49
0.81
0.82
0.82
0.82
0.44
0.45
0.45
0.44
0.69
0.63
0.73
0.72
4
PCC
ETC
(MAS5)
0.20
0.27
0.26
0.55
0.56
0.54
0.55
0.79
0.80
0.79
0.79
0.94
0.94
0.94
0.94
0.80
0.85
0.84
0.83
0.84
0.84
0.84
0.84
0.84
0.58
0.34
0.46
0.54
0.49
0.52
0.49
0.68
0.69
0.67
0.69
0.39
0.40
0.39
0.39
0.68
0.67
0.72
0.67
PCC
MAQC
(RMA)
N/A
N/A
N/A
0.91
0.85
0.82
0.87
N/A
N/A
N/A
N/A
0.97
0.98
0.98
0.98
0.98
0.99
0.99
0.99
0.99
0.92
0.92
0.92
0.92
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
0.94
0.95
0.95
0.94
0.89
0.90
0.91
0.91
Number of
ambiguous
probes
1
11
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
3
0
0
2
0
3
0
2
2
2
0
0
0
0
0
0.79
1.13
1.06
0.00
Probesetsize
13
33
12
11
11
11
11
11
11
11
11
11
11
11
11
11
11
22
22
22
11
11
11
11
11
11
11
32
30
33
30
11
11
11
9
11
11
11
11
11.20
20.48
20.79
18.64