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Table 1 Descriptions and expression patterns of 17 differentially expressed genes that probably correlate with beak morphology

From: Evolution of beak morphology in the Ground Tit revealed by comparative transcriptomics

Pathways

Genes

Descriptions

TPM

NOISeq

RT-qPCR

P. humilis

P. major

Log2FC

P-adj

Log2FC

P

Wnt

WNT5A

Protein Wnt-5a

48.06

148.61

−1.63

0.00E+00

PRICKLE1

Prickle-like protein 1

14.86

55.20

−1.89

2.75E-06

−0.17

1.10E-01

WIF1*†

Wnt inhibitory factor 1

7.28

57.05

−2.97

8.87E-06

−3.28

5.30E-06

NFATC3

Nuclear factor of activated T-cells, cytoplasmic 3

8.98

39.30

−2.13

9.47E-05

FZD4

Frizzled-4

16.67

89.95

−2.43

1.54E-04

LEF1

Lymphoid enhancer-binding factor 1

60.50

143.01

−1.24

1.77E-04

FRZB*

Secreted frizzled-related protein 3

71.32

150.58

−1.08

3.47E-04

−3.23

4.12E-05

DAAM2

Disheveled-associated activator of morphogenesis 2

2.48

15.04

−2.60

3.47E-04

CCND1

G1/S-specific cyclin-D1

24.35

69.13

−1.51

4.18E-04

PRKACB

cAMP-dependent protein kinase catalytic subunit beta

34.22

73.42

−1.10

4.97E-04

MAPK/FGF

FGF17

Fibroblast growth factor 17

45.91

0.38

6.91

0.00E + 00

0.50

4.18E-01

FGF13*†

Fibroblast growth factor 13

11.33

3.71

1.61

4.21E-04

7.37

1.23E-08

STK3

Serine/threonine-protein kinase 38

11.70

40.72

−1.80

4.64E-04

OCD

NFATC1*

Nuclear factor of activated T-cells, cytoplasmic 1

5.82

39.32

−2.76

1.60E-08

−3.21

2.16E-05

ITGB3*†

Integrin beta-3

0.76

6.43

−3.08

8.57E-05

−5.49

1.21E-06

Notch

HES5

Transcription factor HES-5

117.76

17.23

2.77

3.11E-04

0.22

6.83E-01

Calcium

CACNA1G

Voltage-dependent T-type calcium channel subunit alpha-1G

4.28

14.60

−1.77

5.79E-04

  1. RNA-Seq analyzed expression patterns that were subsequently validated by RT-qPCR, in situ hybridization and functional experiments. The expression levels and patterns are shown with the results of NOISeq. Please see results of DESeq and edgeR in Additional file 2: Table S11. TPM (transcript per million) represents the expression level. Log2FC is the transformation of the fold change in expression levels. P-adj is the adjusted P-value using FDR, which is considered equivalent to 1 − qNOISeq in NOISeq. P in the last column is produced by student’s t-test for the relative expression of both species from RT-qPCR. Nine non-validated genes in RT-qPCR are filled with “--” in last two columns. Five confirmed genes by RT-qPCR are marked with “*”. “†” marks the three genes assayed by in situ hybridization. Two proved genes by functional experiments are bolded