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Table 3 Top 20 canonical pathways for QTL identified for all traits, and for co-localized QTL

From: Quantitative trait loci identified for blood chemistry components of an advanced intercross line of chickens under heat stress

Pathways for all identified QTL

Pathway

P-value

Ratio:

Genes in pathway that were identified in current study

1D-myo-inositol Hexakisphosphate Biosynthesis II (Mammalian)

1.93E-03

4/19

INPP5E,IPMK,SEC16A,PMPCA

AMPK Signaling

2.15E-03

13/178

CHRNA5,MTOR,STRADA,AK8,INSR,CHRNA3,PPM1J,CHRNB4,PIK3R2,ADRA2A,TSC1,FOXO1,ADRA1A

Angiopoietin Signaling

1.22E-03

6/66

NRAS,PIK3R2,BIRC5,CASP9,IKBKAP,FOXO1

Calcium Signaling

1.51E-02

11/178

CALR,CHRNA5,MYL4,CHRNB4,CAMK4,CHRNA3,CAMK1G,MEF2D,TPM1,RAP1A,MEF2A

Cardiac Hypertrophy Signaling

5.80E-03

14/223

MTOR,MYL4,CAMK4,RHOC,IGF1R,NRAS,PIK3R2,RHOT1,ADRA2A,MEF2D,MAP3K3,CACNA1D,MEF2A,ADRA1A

D-myo-inositol (1,3,4)-trisphosphate Biosynthesis

1.93E-03

4/19

INPP5E,IPMK,SEC16A,PMPCA

D-myo-inositol (1,4,5)-trisphosphate Degradation

1.44E-02

3/18

INPP5E,SEC16A,PMPCA

Dopamine Degradation

8.29E-03

4/28

ALDH1A1,ALDH1A3,MAOB,ALDH4A1

ERK5 Signaling

2.28E-03

7/63

MAP2K5,NRAS,NTRK1,MEF2D,NGF,MAP3K3,MEF2A

Ethanol Degradation IV

4.02E-03

4/23

ALDH1A1,TYRP1,ALDH1A3,ALDH4A1

Glioblastoma Multiforme Signaling

1.03E-02

10/146

WNT2B,IGF1R,NRAS,MTOR,PIK3R2,WNT5A,RHOC,RHOT1,TSC1, FOXO1

Glioma Signaling

7.71E-03

8/98

ABL1,TGFA,IGF1R,NRAS,MTOR,PIK3R2,CAMK4,CAMK1G

Histamine Degradation

1.22E-02

3/17

ALDH1A1,ALDH1A3,ALDH4A1

Human Embryonic Stem Cell Pluripotency

1.85E-03

11/134

WNT2B,PIK3R2,WNT5A,SMAD3,SMAD6,NTRK1,TCF7L2,BMP2,NGF,FOXO1,NOG

Non-Small Cell Lung Cancer Signaling

1.13E-02

6/65

ABL1,TGFA,NRAS,PIK3R2,CASP9,RXRA

Nur77 Signaling in T Lymphocytes

1.26E-03

7/57

MAP2K5,SIN3B,CASP9,RXRA,CAMK4,MEF2D,MAP3K3

Putrescine Degradation III

2.84E-03

4/21

ALDH1A1,ALDH1A3,MAOB,ALDH4A1

Superpathway of D-myo-inositol (1,4,5)-trisphosphate Metabolism

4.71E-03

4/24

INPP5E,IPMK,SEC16A,PMPCA

Thyroid Cancer Signaling

9.69E-04

6/40

NRAS,RET,RXRA,NTRK1,TCF7L2,NGF

Tryptophan Degradation X (Mammalian, via Tryptamine)

4.02E-03

4/23

ALDH1A1,ALDH1A3,MAOB,ALDH4A1

Pathways identified for co-localized QTL

Pathway

P-value

Ratio:

Genes in pathway that were identified in current study

2-oxobutanoate Degradation I

4.22E-02

1/5

MCEE

AMPK Signaling

4.42E-03

6/178

CHRNA5,PPM1J,CHRNB4,INSR,CHRNA3,ADRA1A

Calcium Signaling

1.55E-04

8/178

CALR,CHRNA5,CHRNB4,CHRNA3,CAMK1G,TPM1,RAP1A,MEF2A

Cardiac Hypertrophy Signaling

4.35E-02

5/223

IGF1R,NRAS,RHOC,MEF2A,ADRA1A

CDK5 Signaling

4.94E-02

3/105

NRAS,PPM1J,NGF

Cholecystokinin/Gastrin-mediated Signaling

4.95E-02

3/245

NRAS,RHOC,MEF2A

CTLA4 Signaling in Cytotoxic T Lymphocytes

4.01E-02

3/88

PPM1J,PTPN22,AP1M1

ERK5 Signaling

1.69E-02

3/63

NRAS,NGF,MEF2A

Germ Cell-Sertoli Cell Junction Signaling

4.93E-02

4/160

NRAS,TJP1,RHOC,RAB8B

Glioblastoma Multiforme Signaling

3.73E-02

4/146

WNT2B,IGF1R,NRAS,RHOC

Glioma Signaling

1.01E-02

4/98

TGFA,IGF1R,NRAS,CAMK1G

Integrin Signaling

3.33E-02

5/207

NRAS,TSPAN2,RHOC,TLN2,RAP1A

Methylmalonyl Pathway

3.39E-02

1/4

MCEE

mTOR Signaling

2.28E-02

5/187

NRAS,PPM1J,INSR,RHOC,RPS15

NF-κB Signaling

1.65E-02

5/172

TGFA,IGF1R,NRAS,INSR,NGF

PTEN Signaling

1.89E-02

4/118

IGF1R,NRAS,INSR,MAGI3

Renal Cell Carcinoma Signaling

2.32E-02

3/71

TGFA,NRAS,RAP1A

STAT3 Pathway

2.49E-02

3/73

IGF1R,NRAS,INSR

TCA Cycle II (Eukaryotic)

1.65E-02

2/23

IDH3A,ACO1

Thyroid Cancer Signaling

4.62E-02

2/40

NRAS,NGF

  1. All characterized genes within significant QTL regions were used as input in Ingenuity Pathway Analysis (IPA) software. The Top 20 significant (P ≤ 0.05) pathways are listed. The results are displayed for pathways identified when using all QTL regions (61 total QTL) which resulted in 682 (999 total) annotated genes used for pathway analysis. The bottom section of the table displays the pathways identified when using only the co-localized QTL regions (7 total co-localized QTL regions) which resulted in 185 (226 total) annotated genes used for pathway analysis. The pathways are the top canonical pathways identified by IPA and are listed in alphabetical order. The ratio refers to the number of genes that were identified in the current study compared to the total number of genes that are in the pathway according to IPA