Biology Reference
In-Depth Information
Table 1.
(Continued)
Microarray data
qRT-PCR data
Gene
name
Pig
homologene
Primer sequences
(5'-3')
Brain
(n-fold change)
Lung
(n-fold change)
Brain
(n-fold change)
Lung
(n-fold change)
PIK3RI
Ssc.49949
F: cccaggaaatccaaatga
R: ggtcctcctccaaccttc
-
-
0.61
0.45
SERPI-
NEI
Ssc.9781
F: ccagcagcagatccaaga
R: cggaacagcctgaagaagt
-1.66
2.36
-0.64
4.28
a
ND, not done;
b
-, not changed or absent.
Microarray Analysis of Gene Expression Profiles in Brain and Lung
Six brain samples and four lung samples were used for microarray hybridization and
qRT-PCR, and two of the lung samples were excluded as they were found to be de-
graded. Table 2 shows the number of differentially expressed human probe sets ini-
tially identified in brain and lung tissues (
p
-value < 0.01 and
p
-value < 0.05). Based
on BLAST analysis, those probes with putative pig gene homologues have been con-
sidered for further analysis and numbers are shown in Table 2. This avoids making as-
sumptions about other probes that detect expression changes but have weaker matches
to pig ESTs. Most probes with porcine homologues remained unchanged, and few
showed a reduction in transcription level by microarray analysis. For example, expres-
sion of only four (6070 bp human match category) and one (5059 bp human match
category) were decreased in infected lung tissue (
p
-value < 0.01). In contrast, a large
number of host transcripts were induced in response to wild type PRV infection (Table
2). Here we identified 120 and 866 up-regulated transcripts in brain and lung (
p
-value
< 0.01) with pig: human matches ≥ 60 bp, and 42, and 259 genes with matches of 5059
bp for further gene ontology and pathway classification (Table 2).
Table 2.
Number of probe sets and pig gene homologues in brain and lung tissues affected by wild
type PRV infection.
p- value
Up/down regulated
Brain
Lung
A
B
C
D
A
B
C
D
p-value <
0.0 1
down
253
35(34)
14(14)
17
195
4(4)
1 (1)
11
up
528
132(120)
44(42)
115
2283
888(866)
261(259)
424
p-value <
0.05
down
588
77(76)
26(26)
43
1657
25(24)
4(4)
51
up
879
209(196)
69(67)
173
3284
1122(1075)
357(355)
545
A= Total number of differentially expressed human probes.
B =Total number of pig Unigene matches of 60-70 basepairs (subset of verifi ed gene or thologues).
C =Total number of pig Unigene matches of 50-59 basepairs (subset of verifi ed gene or thologues).
D =Total number of EST matches >50 basepairs with no assigned Unigene ID.
Of the transcripts with matches ≥ 60 bp, 76, corresponding to 74 unique pig gene
homologues, are up-regulated in common between the two tissues. Forty-four probe
