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Table 2 Gene expression and protein abundance. Genes/proteins involved in the significantly (P < 0.05) enriched pathways comparing the expression levels between slow (SG) to fast (FG) growing chickens (n = 5)

From: Alanine-specific appetite in slow growing chickens is associated with impaired glucose transport and TCA cycle

Measurement

Identification of genes and proteins

SG Chickens

FG Chickens

SE

P value

Normalized Gene Expressiona

DLAT

29.42

23.59

1.32

0.0152

PDHX

6.11

5.12

0.23

0.0213

OGDH

59.74

49.22

2.48

0.0222

LIAS

9.53

8.49

0.27

0.0385

PDHB

58.91

49.82

2.32

0.0402

Normalized Protein Abundance (× 106)b

CKMT1A

4.22

3.37

0.41

0.0000

CKM

1.51

0.94

0.14

0.0000

CKB

13.21

8.72

1.11

0.0000

CS

0.46

0.59

0.05

0.0000

YWHAE

0.27

0.34

0.04

0.0028

YWHAZ

0.97

1.11

0.12

0.0028

SDHB

1.12

0.78

0.10

0.0044

YWHAQ

0.10

0.13

0.02

0.0047

TPI1

2.47

1.78

0.19

0.0051

GOT1

1.21

0.86

0.10

0.0077

PRPS2

0.08

0.09

0.01

0.0084

ENO1

1.67

2.10

0.15

0.0126

PKM

1.65

2.05

0.20

0.0335

AGMAT

0.06

0.05

0.01

0.0350

SDHA

0.50

0.36

0.05

0.0373

  1. Abbreviations: AGMAT Agmatinase, CKB, M Creatine Kinase Brain, Muscle, CS Citrate synthase, DAP Differentially abundant proteins, DEG Differentially expressed genes, DLAT dihydrolipoamide S-acetyltransferase, ENO1 Enolase 1, GOT1 Glutamic-oxaloacetic transaminase 1, LIAS Lipoic acid synthetase, OGDH oxoglutarate (α-ketoglutarate) dehydrogenase, PDHB pyruvate dehydrogenase (lipoamide) beta, PDHX pyruvate dehydrogenase complex component, PKM Pyruvate Kinase, PRPS2 Phosphoribosyl pyrophosphate synthetase 2, SDHA, B Succinate dehydrogenase complex flavoprotein subunit A, B, SE standard error, TPI1 Triosephosphate isomerase 1, YWHAE, Q, Z Tyrosine 3-monooxygenase/ tryptophan 5-monooxygenase activation protein epsilon, theta, zeta
  2. aNormalized gene expression refers to FPKM (Fragments Per Kilobase of transcript per Million mapped reads) calculated using RNA-seq data in Limma. Baysian model with t-statistics moderated across genes were used to identify significant differences. RNA-seq data were based on 2 × 125 bp Paired-End Dual indexed reads and average of ~ 27 million sequence reads per sample
  3. bNormalized protein abundance refers to the peak area (intensity × retention time) of the proteins’ spectra. Peak areas were obtained using SWATH (Sequential Window Acquisition of All Theoretical Mass Spectra) analyses of LC-MS/MS data
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BMC Genomics

ISSN: 1471-2164

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