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Table 1 A Priori-Defined Gene Networks.

From: Identification of QTLs controlling gene expression networks defined a priori

Abbreviationa

Network Biological Description

# Genesb

# Cis QTLc

Referenced

BD

Genes down regulated by Botrytis

6

0

Unpublished (Kliebenstein)

BU

Genes up regulated by Botrytis

10

0

Unpublished (Kliebenstein)

CM

Camalexin biosynthetic pathway

7

1

[55]

CL

Genes involved in Photosynthesis

27

1

ABRC

FV

Flavonoid biosynthetic pathway

15

1

[19, 56]

FVTFe

Transcription Factors for FV

6

3

[57]

GS

Glucosinolate biosynthetic pathway

20

6

[18, 19]

LG

Lignin Production

43

11

[58] and this work

LGB

Lignin Production

9

1

[58] and this work

MT

Methionine biosynthetic pathway

5

0

ABRC and this work

MTB

Methionine biosynthetic pathway

5

1

ABRC and this work

PH

Phenylalanine biosynthetic pathway

11

5

ABRC

SN

Sinapate biosynthetic pathway

3

0

[59]

TP

Tryptophan biosynthetic pathway

9

2

[60]

WC

Wound-inducible genes controlled by COI1

7

1

[33] Net. C

WNM

Wound-inducible genes, no MeJA

4

0

[33] Net. G

WNC

Wound-inducible genes, not controlled by COI1

8

1

[33] Net. D

IC

Insect-inducible genes controlled by COI1

14

1

[33] Net. A

INC

Insect-inducible genes, not controlled by COI1

13

0

[33] Net. B

ND

SA-inducible genes controlled by NPR1

7

0

[34]

NS

SA-inducible secretory genes controlled by NPR1

16

3

[34]

  1. aAbbreviation for each gene network used in our study.
  2. b Genes shows the number of gene members in a given network.
  3. c Cis QTL is the number of the genes within the network that contain a cis eQTL controlling > 50% of the phenotypic variation per gene.
  4. d Reference indicates the reference source for the genes included in the network. Genes are listed in Additional file 1. ABRC refers to the use of functional network assignments as provided by the Arabidopsis Biological Resource Center [37]. The abbreviations Net. A, B, C, D and G refer to the network description provided by Reymond et al. (2004).
  5. e FVTF is not defined here as a network per se; this is a group of transcription factors that are known to affect the FV gene network. See Materials & Methods.