2555 Supplementary figure 1.1. Gene association network of ...10.1186/1752-0509-6-100/... · LHCB2:4 OHP PSAO PSAH2 PSAD2 SDR pyPdiK glyHyd fam3 KHC3H RAP2.7 AP2 P-glycerateK FLA9

SS2

IPK2a

GWD3

YGGT

WLIM1

sulfotrans

PGMP

AT-GTL1PIF4

pectinacetylest jmjC

LCB2

WLIM2a

SSADH1

HMGB3PlipaseA2

DPE1

a-AMY2

LACTAtIDD2

LCL1LIM

ATHB-2

HAP5BTOC1

glyHyd fam4

PglyK

AAE17

NMT3

hydP-rich glyco

HFR1

isocitrateDehydro

TGA3

AXR3

glyTfam20

GGT2

B-box

myb

LHY

glyHy17

B-box STH

CCA1

pectinesterase

COL2

IAA9CDF1

cytochromeC

GBSS

COL

ATHB-12

COL7

DNA-binding

bHLHFbiP

aldolase

SMO2

galSyntAtTLP7

PSI-Lglucosamine

ACP

PFK

AtTLP11PGR5

myb

GLK2

PIFI

BEL10

ISA1

ATMYB30

HAP2A

sc-acyl-CoAox

ATHB5

DGAT

fer-naDP(+)red

ISA3

ATPsyntI

SBE2-1

DPE2

GWD1/SEX1

ATFC008

SEX4/PTPKIS1

HMGB2

COL

6PgluconDehyd

AGLU-like4

KDSA

OBP4

WRKY13

dehydratase

LZF1

Dof

thioesterase

pectinacetylest

LACS6

PL/glyT

Zn-DHHC

kinase

lipase class3

SS1

HDG1

NDH-O

B-box

ADS2

MTLPD2

pyrDecarb

PRE1

zinc-binding

b-AMY3/CT-BMY

MBF1B

a-AMY3

glyDehyd COL1

myb

CDS1

HYH

a-gal

TF

PGM

DofPtidylserine decarb

BT3

B-box

IAA18

bHLHFBPase

pyrDehydroE1

OBF5

myb

PglyceroM pectinesterase

AP2

AMP-syntt-L GBF1

TRFL3

HKL1pyroP

TCP10 mito-substrate carrier

PsbQ

OR16pep

GNC

lipase class3

MYB51

Dof

SucP

ATERF6

petM

AtHB23

FA hyd

TPPA

IPS1

photosysII5kD

TF

PFK

ATIPK1

UNE10

ACG9

StP-c b-AMY9

StP-p

pectinacetylest

ADOF1

myb

acid Ptase

CZF1

gly-cleavSysH

ATHB6FA desat

ferChloroCP5

lipase

xyloglucan

DGD1

pectinase

VOZ2

carboK

C2H2

pfkB-kinase

PSAN

ACX2

xylKinase

DRE-binding

AtTLP6

FAD3

PIL6

COL5LHCB6

STO CDF3

LHCB3

SCL3

b-AMY6

2-oxogluDehydroE1

ARF17pyrK

AMP-binding

scarecrow

Pesterase

AGP17

LHCB2:4OHP

PSAO PSAH2

PSAD2

SDRpyPdiKglyHyd fam3

KHC3H RAP2.7

AP2

P-glycerateK

FLA9

PSAD1aldo/ketored

LHCB4.2

SSI2

RVE2bZIP

CAB

CAB4

pyrK

ZML1

GPRI1

din10

oxidoreductase

XTR3

malatedehydro

L-lactatedehyd

3-oxoacyl-syntII galSynt

Cox11hydP-rich

glyco

AtTLP2

BLH1

TCP

ARF8

PHR1

SLD1

BLH6

PPC1

zinc-binding expressed protein

RuBisCOact kinase

AGPasepyridineNuc carbHyd

IPS2

NF-YA4

CP12domain

alk-a-gal

B3

PHYB

PsbQ

enoyl-CoAhyd

"triosePiso,cyt" LACS8

BT4

MYB29EXGT-A3

AtIDD5

malateOxidored ISA2/DBE1

AL7

CKB3NF-YC12transketolase

SS4

ribose5PAT

ELF3COL9

kinase

galSyntLAG1

ACO

GDCSH

Page 1 of 1

27/4/2555file:///D:/JOBY2010/1480_GGM_MS-edit/Smith_R2.5_GeneNet1.0.1/Cytoscape/Smit...

Papapit_SBI

Text Box

Supplementary figure 1.1. Gene association network of 106 TF, 6 clock, and 173 metabolic genes. The network contains 277 nodes and 1,174 edges. The metabolic genes were selected from 11 functional categories (defined by MapMan and shown in Table 2 in the main article). These 11 functional groups are related to carbon metabolism in a broader view.

AtTLP2PRE1 mybTGA3 PHYBPIL6 COL5

WLIM2a

GBSSDPE1

CDF3COL STOCOL7

SBE2-1

CCA1

COL2

B-box

STH

StP-p StP-c

DPE2

a-AMY2

LIM

AtHB23

OBF5

SS1

PGMP TCP10

ATHB5

COL9AtTLP11 b-AMY6ISA2/DBE1 LCL1PIF4IAA9 GWD3

ARF8

GBF1

BLH6

bZIP

AtTLP6CDF1

C2H2 DNA-binding

TRFL3Dof

AtTLP7

DRE-binding RVE2

ATHB-2

BEL10

VOZ2

GLK2

WRKY13

PHR1

b-AMY3/CT-BMY

SCL3

IAA18

GPRI1

BLH1

RAP2.7bHLH

ATHB-12

ATMYB30

myb

B3

scarecrow

TCP

AP2ATERF6

TF

KHC3H

ATHB6 zinc-binding

B-box

AP2

MBF1B

SS4

AtIDD5

zinc-binding

GNC

ARF17

TOC1

AT-GTL1

TF

bHLH

myb

HDG1

BT4

HFR1

OBP4

Dof

AtIDD2

jmjCHAP2A

AGLU-like4 LZF1

mybADOF1

BT3ZML1Dof

AL7

MYB29HAP5B

NF-YA4

CKB3HMGB3

CZF1

HMGB2

NF-YC12

ATFC008ISA1

COLMYB51

Page 1 of 1

27/4/2555file:///D:/JOBY2010/1480_GGM_MS-edit/Smith_R2.5_GeneNet1.0.1/Cytoscape/st_1...

Papapit_SBI

Text Box

Supplementary figure 1.2. The intersection result of the networks constructed by starch genes (Figure 2 in the main article) and carbon-related genes (Supp. figure 1.1). This intersected network contains 177 nodes and 181 edges. All nodes in the starch network are in the carbon network and 68% of edges in the starch network were detected in the carbon network.

Clock

Node symbols

OPP

PS

Starch

TCATCA

TF

Cell wall

Fermentation

Gluconeogenesis

Glycolysis

Lipid

Major CHO

Minor CHO

Mitochrondrial electron transport electron transport

Documents

2555 Supplementary figure 1.1. Gene association network of ...10.1186/1752-0509-6-100/... · LHCB2:4 OHP PSAO PSAH2 PSAD2 SDR pyPdiK glyHyd fam3 KHC3H RAP2.7 AP2 P-glycerateK FLA9