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Table 1 Most significant differentially regulated transcripts

From: Profile of whole blood gene expression following immune stimulation in a wild passerine

Uniprot-SwissProt annotation

RPKM

 

Baggerley's test

 

Gene name

Accession

Identity %

Transcript name

LPS ± SD

Saline ± SD

Fold change

Test statistic

P-value

Known or possible functions

GAL2

P46158

91

Gallinacin-2 (Beta-defensin 2)

4.7 ± 2.3

0.02 ± 0.03

221.00

21.4

<0.00001

antimicrobial activity[55]

AVID

P02701

70

Avidin

12.3 ± 5

0.2 ± 0.3

53.26

4.8

<0.00001

antimicrobial activity[56]

SAA

P02740

73

Serum amyloid A protein

16.1 ± 8.3

0.6 ± 0.3

28.63

3.8

0.00017

chemoattractant for immune cells, induction of pro-inflammatory cytokines and extracellular matrix degrading enzymes [53, 57]

M126

P28318

78

Protein MRP-126

183 ± 76.8

24.1 ± 28.8

7.58

3.9

0.00011

leukocyte chemoattractant, oxidant scavenging, antimicrobial activity[58]

DNAJC12

Q9UKB3

78

DnaJ (Hsp40) homolog, subfamily C 12

10.4 ± 5.7

4.5 ± 2.4

2.30

3.7

0.00028

co-chaperone for Hsp70 proteins [59]

HPS5

Q9UPZ3

80

Ruby-eye protein 2

13.5 ± 6.2

6 ± 1.4

2.25

9.1

<0.00001

eumelanin synthesis [60]

LY75

O60449

56

Lymphocyte antigen 75 (C-type lectin, CD205)

62.9 ± 23.2

29.8 ± 12.1

2.14

5.0

<0.00001

antigen uptake of antigen presenting cells [61, 62]

GTF2H1

P32780

90

General transcription factor IIH subunit 1

69.8 ± 32.9

33.8 ± 7.9

2.07

7.5

<0.00001

part of DNA repair complex TFIIH [63]

SLC25A6

P12236

90

ADP/ATP translocase 3 (ANT3)

67.6 ± 15.7

32.9 ± 8

2.06

4.0

0.00008

cellular energy metabolism, mediation of T-cell survival [64]

ATP7A

P70705

90

Copper-transporting ATPase 1

10.6 ± 1.6

5.1 ± 1.3

2.05

7.6

<0.00001

regulation of macrophage function and extracellular superoxide dismutase activity [65]

DSCR3

O14972

88

Down syndrome critical region protein

25.9 ± 2.7

12.9 ± 1.3

2.01

16.3

<0.00001

part of polymeric immunoglobulin receptor transporter retromere complex[66]

SLC38A2

Q5F468

89

Sodium-coupled neutral amino acid transporter 2 (SNAT2)

19.3 ± 7.9

49.1 ± 9.5

−2.54

−4.8

<0.00001

cell volume regulation, response to osmotic stress or amino acid depletion [67]

  1. Annotated transcripts significantly up- or down-regulated 12 h after injection of bacterial lipopolysaccharides (LPS). Whole blood mRNA expression of injected female greenfinches was compared with a set of saline injected individuals using Baggerley's test [52]. Only Uniprot-SwissProt annotated transcripts with absolute fold-change >2, RPKM >8, identity >50% and e-values under 1E-20 are shown. Positive fold-change represents higher expression levels in the LPS-injected birds. RPKM values both for LPS and saline injected birds are given with ± SD. Functions related to the immune response and other related processes are reported for the transcripts. If a direct link could not be established, functions from proteins of the same family (according to Uniprot) were attributed to the annotated transcripts (marked in italics). Evidence from avian studies is marked in bold.
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BMC Genomics

ISSN: 1471-2164

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