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Table 1 Generated gene co-expression networks and genes belonging to each network

From: Global transcriptome profiling reveals differential regulatory, metabolic and hormonal networks during somatic embryogenesis in Coffea arabica

Co-expression network

Genes belonging to the co-expression network

Transcription factor-related genes

Auxin-related genes

Secondary metabolism-related genes

Leaf

SERK1

Auxin Response Factor 9 (ARF9)

Small Auxin Up RNA 32 (SAUR32)

SAUR36

SAUR71

Auxin Binding Protein 19 (ABP19)

Phenylalanine Ammonia Lyase 1 (PAL1)

PAL2

PAL3

4-cinnamoyl CoA ligase 1 (4CL1)

4CL2

Chalcone Synthase (CHS)

Caffeine Synthase (DXMT)

Caffeoyl Shikimate Esterase (CSE)

Cinnamoyl - CoA Reductase 1 (CCR1) CCR2

Caffeic acid O-MethylTransferase (COMT1)

Dedifferentiation

SERK2

CLV3

AUX12

AUX15

AUX22

IAA4

IAA9

IAA13

IAA14

IAA28

IAA29

PIN-FORMED1 (PIN1)

PIN2

PIN3

SAUR72

Xanthosine Methyltransferase 1 (XMT1)

MXMT

CCR1

COMT1

Caffeoyl-CoA-O-MethylTransferase 1 (CCOMT1)

HydroxyCinnamoyl-CoA shikimate/quinate hydroxycinnamoyl Transferase (HCT)

Embryogenic callus

ABI3

BBM

WUS

WOX2

AGL15

LEC1

ARF4

ARF5

IAA33

TAA1

 

Redifferentiation

FUS3

ARF4

TAA1

YUCCA4

SAUR72

PIN1

CHS

XMT1

CSE

CCR1

COMT1

Hydroxycinnamoyl-CoA Quinate hydroxycinnamoyl Transferase (HQT) Cinnamyl-Alcohol Dehydrogenase (CAD)

  1. Auxin-related genes, transcription factor-related genes and secondary metabolism-related genes clustered in four types of expression profiles and co-expression networks were inferred. Four co-expression networks were obtained: Leaf, Dedifferentiation, Embryogenic callus, Redifferentiation