File S1. Sub-networks 1 – 9 and Their Composite Outcomes
Sub-network 1 and its composite outcomes
The sub-network 1 includes 46 nodes and 969 edges (Figure S1). The score of cluster
density is 21.065, which indicates that sub-network 1 is the most densely connected because it
possesses the highest cluster density score among 9 sub-networks. In Figure S1, the dark red
nodes represent higher network density based on MCODE. Dark green edges represent very
small p-values. There are 31 nodes that represent up-regulated, eight down-regulated, and seven
differently regulated. Most gene lists (67.39%) involving up-regulated nodes are related to seven
biological themes and 25 treatments or conditions.
Table S1 shows composite outcomes. There are 46 gene lists and 256 most frequently
shared genes identified in this sub-network. They are regulated by 32 treatments or conditions
from 32 publications related to 11 biological themes involving development, metabolism,
disease, yield, function, genome analysis, immune, pathogen, mechanism, energy, virus, and
photosynthesis in Arabidopsis. The top 10 most frequently shared genes with their gene
descriptions were specifically listed corresponding to different gene lists, different biological
themes, and treatments or conditions. These genes are the most active in sub-network 1. For
example, gene AT4G14365 (“putative E3 ubiquitin-protein ligase XBAT34”) has the highest
frequency of 35, which indicates it is the most active gene because it is regulated simultaneously
under 35 gene lists in sub-network 1. In other words, the gene connects directly 35 gene lists.
Therefore, it is the strongest link in sub-network 1.
The most significant function of sub-network 1 is biological process in response to chitin
(i.e. the most enriched term in sub-network 1 is “response to chitin”) based on results of analysis
of DAVID (Table 1). This indicates sub-network 1 is specifically associated with the chitin
signaling pathway rather than by random chance. The other significant functions of sub-network
1 are responding to carbohydrate stimulus, organic substance, defense response, and bacterium
based on the analysis of DAVID with a cutoff of 1.60E-16 p-value. This suggests that subnetwork 1 involves multiple signaling pathways.
Figure S1. Sub-network 1 corresponding to cluster 1. Node = name of gene list. Node Color =
MCODE_Scores from small to large and corresponds to color from light green to dark red. Edge Color =
p-values from large to small and corresponds to color from grey to dark green. (Figure S1 is the same as
Figure 3).
Table S1. Results of sub-network 1 corresponding to cluster 1.
ID
Cluster 1: Gene.List
1
ZHANG_PST-DC3000-GH3.51D/WT_UP_474
Biological.
Theme
Treatment/Condition
G G G G G G G G G G
1* 2 3 4 5 6 7 8 9 10
Disease
Pst Dc3000 (Avrrpt2)-Infected Gh3.5-1D
2 VERT_BRZ-ARF2_DN_445
Function
Bin2 Kinase And Arf2
v
3 HOEWYK_SE_ROOT_DN_896
Function
Selenium (Se) Deficiency And Toxicity
v
v
4 VERT_ARF2-COL_UP_553
Function
Bin2 Kinase And Arf2
v
v
5 LEE_FLU_WT_UP_352
Function
Executer Protein-Conditional Flu Mutant
WAN_WT_CHITOOCTAOSE-TREA
6
Function
TED_WATER-TREATED_DIFF_890
7 LALOI_SINGLET-OXYGEN_UP_182 Mechanism
WAN_FLG22_ELF26_CHITOOCT
Disease
AOSE_COMMON_DIFF_453
RAMONELL_CRAB-SHELL-CHITIN9 TREATED_CHITO-OCTAMERDisease
TREATED_SEEDLING_UP_1000
8
10 BLASING_3H-MANNITOL_UP_207Metabolism
11 XIN_ABA-ROP10-1_UP_341
v
v
21 CHANDRAN_WT-T2_UP_973
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
Chito-Octamers And Hydrolyzed Chitin
Treatment; T-Dna Insertion Mutants
v
v
v
v
v
v
v
v
v
v
Treatment-Mannitol; Diurnal Cycle
v
v
v
Conditional Fluorescent (Flu) Mutant;
Dark-To-Light Shift
Pathogen And Mamp Treatments;
Cbp60G Mutant
v
Development Treatment-Necrosis-Ethylene
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
Development Conditional Fluorescent (Flu) Mutant--Dark v v v v v v v v v
v
Development Oberon1 and Oberon2 Mutation
v
v
Development Conditional Fluorescent (Flu) Mutant--Dark v v v v v v v v v
v
Immune
v
Myb30 Knockout Mutant
Development Oberon1 and Oberon2 Mutation
v
v
v
v
Development Iron Deprivation
v
Disease
v
v
v
v
v
v
v
v
v
v
Psad-1 (Photosystem I Subunit D-1)
v
v
v
23 CHANDRAN_ICS1-WT-T2_UP_870 Disease
Salicylic Acid (Sa) Mutant Ics1
v
Energy
Photosystem I Subunit D-1; Light
v
v
v
Immune
Dichloroisonicotinic Acid;
Dichloroanthranilic Acid
v
v
v
Energy
Photosystem I Subunit D-1; Light
v
v
v
Immune
Dichloroisonicotinic Acid;
Dichloroanthranilic Acid
v
v
v
27
v
v
Vitamin E1 (Vte1)_Vte2-Deficient Mutant
v
v
26
v
v
v
25
v
v
Salicylic Acid (Sa) Mutant Ics1
24
v
v
v
PESARESI_STN7-1MUTANT/COL- Photosyn22
0_DN_188
thesis
PESARESI_PSAD1-1MUTANT/
COL-0_DN_868
KNOTH_COL-0_48H-DCATREATMENT_UP_423
PESARESI_STN7-1PSAD11MUTANT/WS-2_UP_344
KNOTH_COL-0_48H-INATREATMENT_UP_482
v
v
Development Abscisic Acid (Aba); Rop10
14 SATTLER_VTE2/WT-3D_UP_160 Function
20
v
v
v
v
v
19
v
v
v
v
v
18
v
v
v
13 BAE_NEP1_30MIN_UP_458
17
v
v
v
v
16
v
v
v
v
RAFFAELE_EXP.1_2-4H_WT/T0TIMEPOINT_UP_246
THOMAS_OBE1-1-OBE2-2/WT_
UP_922
CAMP_FLU_DARK/LIGHT-SHIFT_
UP_1206
THOMAS_OBE1I-OBE2I/WT_
UP_973
CAMP_FLU_PARAQUAT20MM_
UP_1206
DINNENY_48HRS_FE-DEPRIVATI
ON_UP_759
v
v
Chitooctaose-Treated; Water
Treated; Atlysm Rlk1 Mutant
Rps2 And Ndr1 Mutant; Infection By A
12 SATO_COL-101C_COL-NDR1_101C-NDR1_NDR1-NDR1BLIND_UP_576
Disease
Pseudomonas Syringae Strain
15
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
Table S1. (Continued)
ID
Biological.
Theme
Cluster 1: Gene.List
Treatment/Condition
G G G G G G G G G G
1* 2 3 4 5 6 7 8 9 10
28 PESARESI_WS-2/COL-O_DN_830 Energy
Photosystem I Subunit D-1; Light
v
MARCHIVE_1W_PNP+P-WT+
29
P_UP_601
Polynucleotide Phosphorylase_
Phosphorus (P) Starvation
v
Metabolism
30
DUVAL_6H_2µMTA-TREATMENT
Function
_UP_255
31
MARCHIVE_1W_WT-P-WT+P_
UP_409
32 MITSUDA_35S-NST1_UP_202
Metabolism
Mechanism
Thaxtomin A (Ta)
v
Polynucleotide Phosphorylase_
Phosphorus (P) Starvation
Nac Secondary Wall Thickening
Promoting Factor1 (Nst1) And Nst2
33 MA_HYPOCOTYL_WL/D_UP_1706Development Developmental And Environmental Cues
34 DAY_OST_DIFF_2648
Yield
Comparisons Some Methods
KASSCHAU_RDR2-DCL3Genome
MUTANT_DIFF_497
Analysis
WANG_CBP60G-1_24H_INOCUL
36
Disease
ATION-PSM-ES4326_UP_299
Rna-Dependent Rna Polymerase (Rdr);
Dicer-Like (Dcl)-Mutants
Pathogen And Mamp Treatments;
Cbp60G Mutant
37 ROMERO_SOM2_DN_217
Virus
RUBIN_LBD38OX-N/WT-N_
38
DN_341
39 KURIHARA_AGO1-25_UP_943
35
SOZZANI_SHR_TIME-COURSE_
DIFF_2481
v v
v
v
v v
v
v
v
v
v v
v
v
v
v
v v
v
v
v v
v
v
v
v v
v
v
v
Tev_Tev-At-Infected; Som
v
v
v v
Metabolism
Nitrogen (N) And Nitrate (No3–)
v
v
v
Mechanism
Argonaute1 (Ago1) And Hyl1-2 Mutants
v
v
v v
Nitrogen (N) And Nitrate (No3–)
v
v
v v
v
v
v
v v
v
Development Shortroot (Shr) And Scarecrow (Scr)
Nitrogen (N) And Nitrate (No3–)
Development Shortroot (Shr) And Scarecrow (Scr)
44 HOEWYK_SE_ROOT_UP_555
Metabolism
MHAMDI_GR1_CAT2_CAT245
Function
GR1/COL0_DIFF_659
CHANDRAN_LEAF_PM-ALTERED
46
Disease
_5DPI_UP_671
11
v
v
Glutathione Reductase (Gr)
v
32
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v v
v
v
v
v
v
v
v
v
v
Selenium (Se) Deficiency And Toxicity
Salicylic Acid (Sa) Mutant Ics1
v
v
v
SOZZANI_SCR_TIME-COURSE_
43
DIFF_1904
46
v
v
42 RUBIN_WT-N/WT-FN_UP_1165 Metabolism
T
v
v v
v
40 RUBIN_WT-FN/WT-N_DN_1164 Metabolism
41
v
v
v
v
v v
v
v
v
v
v
v
v
v
v
v v
v
v
3 3 3 3 3 3 3 3 2 2
5 4 3 2 1 0 0 0 9 9
Most frequently shared genes (Freq>=16, total 256 genes)
AT4G14365 AT5G39670 AT3G50930 AT1G27730 AT4G39670 AT2G22500 AT5G26920 AT5G52760 AT1G19020 AT4G33050 AT5G27420
AT1G72900 AT2G18690 AT2G31880 AT2G38470 AT5G54490 AT3G61190 AT4G37370 AT2G40140 AT3G26830 AT3G28210 AT4G27280
AT5G47220 AT1G13340 AT1G28480 AT1G80840 AT2G46400 AT3G08720 AT3G52400 AT4G12720 AT4G23810 AT5G25930 AT5G52750
AT5G57220 AT5G59820 AT1G14370 AT1G26380 AT1G43910 AT2G28400 AT2G43570 AT3G55980 AT4G02330 AT4G31800 AT5G20230
AT1G24140 AT1G66880 AT3G01830 AT4G11280 AT4G23190 AT5G06320 AT5G18470 AT5G35735 AT1G18570 AT1G19180 AT2G24850
AT2G32210 AT2G35930 AT3G44720 AT3G52430 AT3G54150 AT4G01700 AT5G01540 AT5G04340 AT1G17420 AT1G68620 AT1G73800
AT1G74360 AT2G24600 AT2G26190 AT2G29460 AT2G32030 AT3G57450 AT4G08850 AT4G20830 AT4G24380 AT5G13190 AT5G13200
AT5G22250 AT5G42050 AT5G49520 AT1G10340 AT1G17380 AT1G19380 AT1G65500 AT1G72940 AT2G05940 AT2G17040 AT2G32190
AT3G01290 AT3G09020 AT3G10930 AT3G11820 AT3G25780 AT3G60420 AT4G18880 AT4G29780 AT4G36500 AT5G10695 AT5G41740
AT5G61600 AT5G67340 AT1G01560 AT1G14870 AT1G32920 AT1G50740 AT1G58420 AT1G65690 AT1G66090 AT1G72520 AT2G26560
Table S1. (Continued)
Most frequently shared genes (Freq>=16, total 256 genes) (cont'd)
AT2G30140 AT2G39650 AT2G40000 AT2G43510 AT2G43620 AT3G04640 AT3G12580 AT3G18830 AT3G19580 AT3G25610 AT3G45640
AT3G56710 AT4G02410 AT4G17500 AT4G24570 AT5G10380 AT5G47070 AT5G47910 AT5G52640 AT1G17745 AT1G23710 AT1G27770
AT1G30700 AT1G45145 AT1G51890 AT1G55450 AT1G57630 AT1G63720 AT1G69840 AT1G69930 AT1G73500 AT1G74440 AT1G75040
AT2G20145 AT2G23810 AT2G30550 AT2G33580 AT2G41100 AT2G41640 AT3G09940 AT3G11840 AT3G19010 AT3G23250 AT3G46620
AT3G47480 AT3G49530 AT3G50480 AT3G54420 AT4G11890 AT4G17230 AT4G35180 AT4G36010 AT4G36990 AT5G24660 AT5G38900
AT5G39050 AT5G45110 AT5G45340 AT5G50200 AT5G51190 AT5G66640 AT1G07000 AT1G13210 AT1G16670 AT1G26420 AT1G32940
AT1G35210 AT1G56060 AT1G67810 AT1G73805 AT2G17220 AT2G18660 AT2G18680 AT2G26530 AT2G30750 AT2G38870 AT2G39210
AT2G41380 AT3G18250 AT3G19970 AT3G44260 AT4G01250 AT4G02380 AT4G22710 AT4G23180 AT4G30280 AT4G39640 AT4G39830
AT5G19240 AT5G25260 AT5G25440 AT5G42380 AT5G47230 AT5G59550 AT5G61010 AT5G61900 AT5G65300 AT5G66070 AT1G02360
AT1G05340 AT1G05575 AT1G08050 AT1G08920 AT1G09070 AT1G20510 AT1G24150 AT1G51660 AT1G61800 AT1G62300 AT1G66160
AT1G72920 AT1G73540 AT1G80820 AT2G22880 AT2G27660 AT2G32140 AT2G33380 AT2G34930 AT2G36220 AT2G38860 AT2G44500
AT3G02800 AT3G09830 AT3G16720 AT3G16860 AT3G24500 AT3G25600 AT3G28340 AT3G48650 AT3G50900 AT3G50950 AT3G51660
AT3G56400 AT4G20860 AT4G21990 AT4G38540 AT4G39950 AT5G02490 AT5G12420 AT5G26030 AT5G46050 AT5G48850 AT5G57560
AT5G62150 AT5G64510 AT5G67450
*Note: G1 = AT4G14365 (putative E3 ubiquitin-protein ligase XBAT34).
G2 = AT5G39670 (putative calcium-binding protein CML45). G3 = AT3G50930 (cytochrome BC1
synthesis). G4 = AT1G27730 (zinc finger protein STZ/ZAT10).
G5 = AT4G39670 (glycolipid transfer protein). G6 = AT2G22500 (uncoupling protein 5). G7 =
AT5G26920 (Cam-binding protein 60-like G). G8 = AT5G52760 (copper transport family protein). G9 =
AT1G19020 (hypothetical protein). G10 = AT4G33050 (calmodulin-binding protein).
Sub-network 2 and its composite outcomes
Sub-network 2 is shown in Figure. S2 and Table S2. It includes 54 nodes (gene lists) and
168 most frequently shared genes, which are regulated under 38 different treatments or
conditions from 38 publications related to 10 biological themes. The score of cluster density is
9.907. There are 17 nodes to be up-regulated, 34 to be down-regulated, and three to be
differently regulated. Most gene lists (62.96%) involving down-regulated nodes are related to
nine biological themes and 23 treatments or conditions. Compared to sub-network 1, subnetwork 2 has a lower cluster density score with even more treatments or conditions. Nine
themes in sub-network 2 are common with sub-network 1: development, disease, function,
genome analysis, mechanism, metabolism, photosynthesis, virus, and yield. This indicates the
two sub-networks have relationships linked by same themes.
More interestingly, no genes is common between the 256 most frequently shared genes in
sub-network 1 and the 168 most frequently shared genes in sub-network 2. This indicates the two
sub-networks have relatively independent functions. The most significant function of sub-
network 2 is biological process of plastid thylakoid membrane based on results of DAVID (Table
1), suggesting that sub-network 2 is specifically associated with plastid thylakoid membrane, i.e.
the lipid bilayer membrane of any thylakoid within a plastid. The other significant functions of
sub-network 2 are response to chloroplast thylakoid membrane, thylakoid membrane, plastid
thylakoid, and chloroplast thylakoid based on DAVID with cut-off p-value of 6.8E-58. The 10
most frequently shared genes with their gene descriptions corresponding to gene lists, biological
themes, and treatments or conditions were specifically listed in Table 4. Gene AT4G27030 (fatty
acid desaturase A), for example, has the highest frequency of 20, indicating it is the most active
gene in sub-network 2.
Figure S2. Sub-network 2 corresponding to cluster 2. Node = name of gene list. Node Color =
MCODE_Scores from small to large and corresponds to color from light green to dark red. Edge Color =
p-values from large to small and corresponds to color from grey to dark green. (Figure S2 is the same as
Figure 4).
Table S2. Results of sub-network 2 corresponding to cluster 2.
ID
Cluster 2: Gene.List
Biological.
Theme
Treatment/Condition
G G G G G G G G G G
1* 2 3 4 5 6 7 8 9 10
1 NELSON_ABA_4H_UP_254
Yield
2 WELLMER_RATIOS-R3_UP_1021
Development Apetala1And Cauliflower Mutants
v
3 ROMERO_SOM3_DN_196
THOMAS_OBE1-1-OBE2-2/WT_
4
DN_593
CHANDRAN_LMD_PM-ALTERED_
5
DN_502
CHODAVARAPU_GT1000GENESST
6
ARTSTOPEXPRESSION_DIFF_74
RONEMUS_AGO1-9_21D_
7
1.5X_DN_140
8 LORRAIN_GO_PIF4PIF5_UP_68
Virus
v
9
10
11
12
13
14
Zmnf-Yb2; Drought
Tev_Tev-At-Infected; Som
Reproduction Mutations In Oberon1 And Oberon2
Disease
Laser Microdissected
Mechanism
Dna Methylation In Exon Definition
v
v
Mutations In Ago1; Or The DicerLike Mutants Dcl1 And Dcl3
Development PhytochromesMutant; Far-Red Light v
Genome
v
HORVATH_POPLAR_UP_2704
Mature Leaf And Shoot Apices
Analysis
Mutant Allele Of Ataf1; Blumeria
v
JENSEN_NONE/BGH-ATAF_DN_552Development
Graminis F. Sp. Hordei Inoculation
DEEKEN_AGROBACTERIUM_TUM
v
ORS/TUMOR-FREE-INFLORESCE
Disease
Agrobacterium Tumefaciens
NCE-STALK_DN_2629
ZHENG_AGL15_AGL15-AGL18/
Reproduction AGAMOUS-Like15 (AGL15)
COL-OR-COL/35S-AGL15_DN_244
NEMHAUSER_BL_IAA-AUXINIaa-Auxin-Treatment;
Development
TREATMENT_DN_296
Brassinosteroids
KURIHARA_AGO1-25_DN_260
Mechanism Argonaute1 And Hyl1-2 Mutants
v
Metabolism
16 SCHWAGER_VFB/WT_DN_220
Development Vier F-Box Proteine; Csn4 Mutant
v
v
v
v
v
v
v
v
Virus
15 BLASING_4H-LIGHT_DN_203
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
Treatment-Mannitol; Diurnal Cycle
17 KANNO_DMS4/DRD1_DN_1493 Development Defective In Meristem Silencing 4 Mutants
DEEKEN_AGROBACTERIUM-TUME
v v
18
Disease
Agrobacterium Tumefaciens
FACIENS_TUMORS_DN_2720
19 XIN_ABA-ROP10-1-WT_DN_222 Development Abscisic Acid (Aba); Rop10
Photosyn
Y276H Mutant Of Phytochrome B;
v v
20 HU_WT-RC15/WT-D_DN_889
thesis
Dark-Grown Phyaphyb; Red Light
Mutant Allele Of Ataf1; Blumeria
v
21 JENSEN_NONE/BGH-COL_DN_505 Development
Graminis F. Sp. Hordei Inoculation
FAUTEUX_SILICON_INFECTED-ERY
22
Function
Powdery Mildew-Stressed; Treated With Si
SIPHE-CICHORACEARUM_UP_91
Mutant Allele Of Ataf1; Blumeria
v
23 JENSEN_COL/ATAF-BGH_DN_678 Development
Graminis F. Sp. Hordei Inoculation
Photosyn
Y276H Mutant Of Phytochrome B;
v v
24 HU_YHB-D/WT-D_DN_1461
thesis
Dark-Grown Phyaphyb; Red Light
YANT_NUCLEAR_RP_UNAMBIG_
25
Development Apetala2 (Ap2) Mutant
DN_705
TIWARI_4X2_BOTH-PLATFORM_
26
Development Fertilized Fis1 Mutant
UP_300
27 BLASING_3H-NO3_DN_216
Metabolism Treatment-Mannitol; Diurnal Cycle
Genome
Rdr2-1 And Drm1Drm2Cmt3; Dna
v
28 KURIHARA_DDC_UP_226
Analysis
Methyltransferase Triple Mutant
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
Table S2. (Continued)
ID
Cluster 2: Gene.List
DIJK_DEHYDRATION-STRESS_
DN_523
30 KURIHARA_HYL1-2_DN_1169
MERIGOUT_CO(NH2)2_NH4NO3_
31
SHOOTT_DN_241
32 MA_HYPOCOTYL_WL/D_DN_1401
29
33 SCHAFFER_DARK_UP_584
34 MA_ROOT_WL/D_UP_1657
BONARDI_PHOTOSYNTHETIC_ST
35 N7-DEPENDENT_STN8MUTANT_DIFF_33
MIURA_W/G_PHOTOSYNTHESIS
36
_DN_31
37
Biological.
Theme
Genome
Analysis
Mechanism
Dehydration Stress
v
v
v
v
v
v
v
v
v
v
v
v
Stn7-Dependent; Stn8-Mutant;
Photosynthesis
Illumination Changes
v
Genome
Analysis
v
SHIN_COL-0(R)/COL-0(D)_PIFQ(D) Photosyn
/COL-0(D)_UP_174
thesis
54
G G G G G G G G G G
1* 2 3 4 5 6 7 8 9 10
v
Argonaute1 And Hyl1-2 Mutants
Shoot Between [Co(Nh2)2]Function
And [Nh4No3]
Development Developmental & Environmental Cues
Photosyn
Day/night cycling in
v
thesis
physiological ways
Development Developmental & Environmental Cues
38 LORRAIN_PIF4PIF5_UP_142
Development
TANG_BRM-5/ESSP3_LEAVES_
39
Mechanism
UP_542
40 USADEL_KIN10_UP_506
Mechanism
41 MA_COTYLEDON_WL/D_DN_1552 Development
KAUFMANN_WT/AG-MUTANT_
42
Mechanism
BOLTING_DN_1232
BAENA-GONZALEZ_KIN10_OSS_ Photosyn
43
UP_278
thesis
44 GONZALI_SUCROSE_DN_429
Development
Photosyn
45 HU_YHB-RC50/WT-D_DN_1429
thesis
Photosyn
46 BAENA-GONZALEZ_KIN10_UP_506
thesis
Photosyn
47 HU_WT-RC50/WT-D_DN_1182
thesis
HOU_RGA_DURING-FLOWER_
Genome
48
UP_413
Analysis
49 BLASING_3H-MANNITOL_DN_200 Metabolism
NEMHAUSER_BL_IAA-AUXIN50
Development
TREATMENT_UP_342
51 ALONSO_ETHYLENE_UP_628
Development
52 SCHMID_0-7D_COL_DN_231
Development
53 SCHMID_COL_DN_231
Development
54 XIN_ABA-WT_UP_262
Development
T
Treatment/Condition
10
Variegated2 Mutant; Light/Dark
Cycle At 22C; Copper Sufficient
Etiolated Pif3 Mutant;Light
v
v
v
v
Phytochromes Mutant; Far-Red Light v
v
v
v
v
Mutations Affecting Brahma (Brm)
v
v
v
v
v
v
v
v
Ag Mutant; Bolting
v
Gibberellin (Ga) Treatment
Treatment-Mannitol; Diurnal Cycle
Iaa-Auxin-Treatment;
Brassinosteroids
Ethylene Insertion Mutation
Photoperiod
Photoperiod
Abscisic Acid (Aba); Rop10
38
v
v
v
Akin10; Light/Dark Cycle
Developmental & Environmental Cues
Kin10 And Kin11;
Darkness, Sugar And Stress
Sucrose; Dark
Y276H Mutant Of Phytochrome B;
Dark-Grown Phyaphyb; Red Light
Kin10 And Kin11;
Darkness, Sugar And Stress
Y276H Mutant Of Phytochrome B;
Dark-Grown Phyaphyb; Red Light
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
2 1 1 1 1 1 1 1 1 1
0 8 8 8 8 7 7 7 7 7
Table S2. (Continued)
Most frequently shared genes (Freq>=12, total 168 genes)
AT4G27030 AT1G29660 AT2G21330 AT3G01500 AT4G37980 AT1G06680 AT1G54040 AT1G71030 AT3G16250 AT3G50820 AT5G48490
AT5G54270 AT1G15820 AT1G15980 AT1G25230 AT1G29395 AT2G43550 AT3G21870 AT3G54050 AT1G09340 AT1G13930 AT1G20440
AT1G21400 AT1G64500 AT2G01890 AT2G34430 AT2G39730 AT3G02730 AT3G48360 AT3G54890 AT3G63140 AT4G37610 AT5G02160
AT5G19120 AT1G03130 AT1G12250 AT1G18060 AT1G20020 AT1G42970 AT1G61520 AT1G72610 AT1G76080 AT1G76100 AT2G05540
AT2G13360 AT2G20670 AT2G21210 AT2G30600 AT2G34420 AT2G39470 AT2G43010 AT3G08940 AT3G46780 AT3G61260 AT3G62550
AT4G05180 AT4G17090 AT4G28660 AT4G33010 AT4G37800 AT5G17300 AT5G22920 AT5G62280 AT1G02640 AT1G08380 AT1G14280
AT1G22690 AT1G23740 AT1G52230 AT1G65490 AT1G70820 AT1G77490 AT1G78370 AT2G18700 AT2G33830 AT2G38210 AT2G43100
AT2G45170 AT2G46340 AT3G18890 AT3G21670 AT3G26740 AT3G27690 AT3G28220 AT3G45780 AT3G47340 AT4G04640 AT4G09010
AT4G09650 AT4G17460 AT4G22890 AT4G27260 AT4G28780 AT5G01015 AT5G11070 AT5G18670 AT5G35630 AT5G38990 AT5G49360
AT5G55620 AT1G07010 AT1G11850 AT1G12780 AT1G12900 AT1G14150 AT1G23205 AT1G28330 AT1G29910 AT1G29920 AT1G30380
AT1G31330 AT1G32220 AT1G37130 AT1G55480 AT1G64680 AT1G64720 AT1G68010 AT1G68570 AT1G69870 AT1G74730 AT1G78460
AT1G80440 AT2G03750 AT2G04039 AT2G17880 AT2G25200 AT2G26080 AT2G26740 AT2G30950 AT2G47930 AT3G05730 AT3G16140
AT3G28270 AT3G47470 AT3G48420 AT3G49160 AT3G55800 AT3G56940 AT3G61470 AT3G62410 AT4G02530 AT4G02770 AT4G12310
AT4G12800 AT4G12830 AT4G19170 AT4G21210 AT4G21280 AT4G28030 AT4G28750 AT4G33660 AT4G38840 AT4G39710 AT5G01530
AT5G04140 AT5G05690 AT5G07020 AT5G14740 AT5G15850 AT5G20250 AT5G24210 AT5G35170 AT5G43750 AT5G48300 AT5G58260
AT5G64040 AT5G64410 AT5G65010
*Note: G1 = AT4G27030 (fatty acid desaturase A). G2 = AT1G29660 (GDSL esterase/lipase). G3 =
AT2G21330 (fructose-bisphosphate aldolase, class I).
G4 = AT3G01500 (carbonic anhydrase 1). G5 = AT4G37980 (cinnamyl alcohol dehydrogenase 7). G6 =
AT1G06680 (oxygen-evolving enhancer protein 2-1).
G7 = AT1G54040 (epithiospecifier protein). G8 = AT1G71030 (myb proto-oncogene protein). G9 =
AT3G16250 (NDH-dependent cyclic electron flow 1). G10 = AT3G50820 (oxygen-evolving enhancer
protein 1-2).
Sub-network 3 and its composite outcomes
The sub-network 3 includes 33 nodes (gene lists) and 124 most frequently shared genes
(Figure S3 and Table S3). There are 28 nodes to be up-regulated, four to be down-regulated, and
one to be differently regulated. Most gene lists (84.85%) involving up-regulated nodes are
related to nine biological themes and 20 treatments or conditions. By contrast to sub-networks 1
and 2, sub-network 3 is smaller in size, has a lower cluster density score, and less treatments or
conditions for gene lists. Sub-network 3 are regulated by 25 treatments or conditions from 25
publications associated with 11 biological themes. Nine themes in sub-network 3 are common
with sub-network 1: development, disease, energy, function, immune, mechanism, metabolism,
photosynthesis, and virus. There are seven common themes (development, disease, function,
mechanism, metabolism, photosynthesis, and virus) between sub-networks 3 and 2. These
indicate sub-networks 3 and 1 or 2 have relationships linked by the same themes.
The 10 most frequently shared genes with their gene descriptions corresponding to each
gene list in sub-network 3 are specifically listed in Table 5. Gene AT2G18690 has the highest
frequency at 17, indicating it is the most active genes (the strongest link) in sub-network 3.
Furthermore, the most frequently shared genes in sub-network 3 have lower frequency, which
means they are less active than those in sub-networks 1 and 2. Interestingly, there is no common
gene between the 168 most frequently shared genes in sub-network 2 and the 124 most
frequently shared genes in sub-network 3. There are 72 genes of intersection between subnetworks 1 and 3. This indicates sub-networks 2 and 3 have relatively independent functions and
sub-networks 1 and 3 maybe are similar to functions. The most significant function of subnetwork 3 is biological process in response to chitin based on results of analysis of DAVID. This
indicates sub-network 3 is specifically associated with the chitin signaling pathway, which is the
same as sub-network 1 but is different from sub-networks 2 (Table 1).
Figure S3. Sub-network 3 corresponding to cluster 3. Node = name of gene list. Node Color =
MCODE_Scores from small to large and corresponds to color from light green to dark red. Edge Color =
p-values from large to small and corresponds to color from grey to dark green. Edge label = number of
overlapping genes between both nodes. (Figure S3 is the same as Figure 5).
Table S3. Results of sub-network 3 corresponding to cluster 3.
ID
1
Cluster 3: Gene.List
RAFFAELE_EXP.1_6H_WT/T0TIMEPOINT_UP_258
2 WAN_MUTANT_DIFF_316
3
RAFFAELE_EXP.1_90-105MN_WT/
T0-TIMEPOINT_UP_176
Biological.
Theme
Treatment/Condition
Immune
Myb30 Knockout Mutant
Function
Chitooctaose-Treated; Water
Treated; Atlysm Rlk1 Mutant
Immune
Myb30 Knockout Mutant
4 LEE_COLD-ICE1_UP_240
Development Cold
RAFFAELE_EXP.2_90-105MN_WT/
5
T0-TIMEPOINT_UP_217
Immune
6 LEE_COLD_UP_655
Development Cold
Myb30 Knockout Mutant
G G G G G G G G G G
1* 2 3 4 5 6 7 8 9 10
v
v
v
RAFFAELE_EXP.2_2-4H_WT/
T0-TIMEPOINT_UP_272
Immune
Myb30 Knockout Mutant
v
8
NEMHAUSER_IAA-AUXIN-TREATMEN_
UP_335
Metabolism
Iaa-Auxin-Treatment;
Brassinosteroids
v
9
RAFFAELE_EXP.1_2-4H_MYB30OX/WT
_UP_150
Immune
Myb30 Knockout Mutant
v
10
COVINGTON_AUXIN_NOT-RHYTHMIC
_UP_227
Development Phytohormone Auxin
v
11
RAFFAELE_EXP.2_90-105MN_
MYB30OX/WT_UP_231
Immune
Myb30 Knockout Mutant
v
Photosyn
thesis
Mutant Of Phytochrome; Dark
-Grown Phyaphyb-Red Light
Immune
Myb30 Knockout Mutant
RAFFAELE_EXP.2_2-4H_MYB30OX/
WT_UP_189
DINNENY_72HRS_FE-DEPRIVATION_
14
UP_528
13
Development Iron Deprivation
16 WALLEY_5MIN_WOUNDING_UP_162
Mechanism
Mechanical Wounding
17 BETHKE_35S-ERF104_UP_574
Function
Ethylene; Flg22 Peptide
18 MA_HYPOCOTYL_LIGHT_UP_867
Development Developmental & Environmental Cues
PESARESI_STN7-1PSAD1-1MUTANT
19
/CL-0_DN_842
Energy
20 MA_COTYLEDON_WL/D_UP_1557
Development Developmental & Environmental Cues
22 MARCHIVE_3H_PNP+P-WT+P_UP_550
Thaxtomin A (Ta)
Metabolism
Polynucleotide Phosphorylase_
Phosphorus (P) Starvation
23 KRINKE_UPON-SA-TREATMENT_UP_473 Pathogen
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
Salicylic Acid (Sa) Treatment
v
v
v
v
v
24
WANG_CBP60G-1_24H_INOCULATION
-PSM-ES4326_DN_272
Development Treatment With Actinomycin D
v
25
GREGORY_EIN5/ABH1-MUTATION_
UP_779
Loss Of Xrn4/Ein5, 5-3 Exoribon
Development uclease, Abh1/Cbp80; Mrna Cap
Binding Complex
v
26
ROMERO_TEV_TEV-AT-INFECTED_
DN_1321
Virus
Tev_Tev-At-Infected; Som
v
v
v
Photosystem I Subunit D-1; Light
Function
v
v
v
Development Heat Shock
DUVAL_6H_100NM-IXB-TREATMENT_
UP_272
v
v
15 SUGIO_AZC_UP_260
21
v
v
7
12 HU_YHB-D/WT-D_UP_1610
v
v
v
v
v
v
v
v
Table S3. (Continued)
ID
27
Biological.
Theme
Cluster 3: Gene.List
LEEA_WS-2_INOCULATION_TUMOR_
UP_874
Treatment/Condition
Disease
Agrobacterium
28 KURIHARA_HYL1-2_UP_2627
Mechanism
Argonaute1 And Hyl1-2 Mutants
29 LEGNAIOLI_TOC1-OX/WT_UP_245
Mechanism
Abscisic Acid; Circadian Clock;
Drought
30 RUBIN_LBD37OX-N/WT-N_DN_327
Metabolism
Nitrogen (N) And Nitrate (No3–)
KEMPEMA_SLWF-NYMPH-FEEDING_
31
UP_703
Pest
32 KNOTH_6D-INA-TREATMENT_UP_379
Immune
33 CHANDRAN_LMD_PM-ALTERED_UP_963 Disease
T
33
11
G G G G G G G G G G
1* 2 3 4 5 6 7 8 9 10
v
Silverleaf Whitefly-Nymph-Fee
ding; Phytoalexin-Deficient4 Mu
Dichloroisonicotinic Acid;
Dichloroanthranilic Acid
Laser Microdissected
25
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
1 1 1 1 1 1 1 1 1 1
7 7 7 6 6 6 6 6 6 5
Most frequently shared genes (Freq>=10, total 124 genes)
AT2G18690 AT2G46400 AT5G59820 AT1G19180 AT1G27730 AT2G22500 AT2G43570 AT3G18830 AT3G26830 AT1G43910 AT1G75040
AT2G24850 AT3G61190 AT5G35735 AT5G54490 AT2G37040 AT2G38860 AT3G04640 AT3G25780 AT4G24570 AT5G10380 AT5G38710
AT5G39670 AT1G61800 AT1G72520 AT1G80820 AT2G04400 AT2G26440 AT3G21230 AT3G50930 AT4G21850 AT4G21990 AT4G31500
AT4G36500 AT4G37370 AT4G39670 AT5G13490 AT5G57560 AT1G02360 AT1G09560 AT1G51890 AT1G78210 AT2G16900 AT2G43290
AT3G23250 AT3G46620 AT3G53260 AT3G55840 AT3G57450 AT4G23150 AT4G25900 AT4G30280 AT5G06320 AT5G20150 AT5G52760
AT5G59550 AT1G05340 AT1G14870 AT1G26380 AT1G68620 AT1G74020 AT1G76600 AT2G22860 AT2G30550 AT2G35930 AT2G38470
AT2G38530 AT2G40750 AT2G41380 AT2G43510 AT3G02840 AT3G15210 AT3G16860 AT3G28540 AT3G51450 AT3G52430 AT3G56880
AT4G25030 AT4G30190 AT4G31550 AT4G35320 AT5G10760 AT5G20230 AT5G22630 AT5G26220 AT5G37740 AT5G40760 AT5G48850
AT1G02450 AT1G04770 AT1G09080 AT1G13340 AT1G19250 AT1G19670 AT1G30700 AT1G32940 AT1G35140 AT1G55210 AT1G57630
AT1G62300 AT1G69930 AT1G74710 AT2G27660 AT2G32190 AT3G04070 AT3G18250 AT3G25610 AT3G25760 AT3G44260 AT3G44720
AT3G47480 AT3G47540 AT3G50900 AT3G52400 AT4G01250 AT4G08850 AT4G20110 AT4G27280 AT4G33050 AT4G34590 AT5G09440
AT5G18470 AT5G33290 AT5G60950
*Note: G1 = AT2G18690 (hypothetical protein). G2 = AT2G46400 (putative WRKY transcription factor
46). G3 = AT5G59820 (C2H2-type zinc finger protein).
G4 = AT1G19180 (protein TIFY 10A). G5 = AT1G27730 (zinc finger protein STZ/ZAT10). G6 =
AT2G22500 (uncoupling protein 5). G7 = AT2G43570
(chitinase class 4-like protein). G8 = AT3G18830 (Polyol transporter 5).
G9 = AT3G26830 (cytochrome P450 71B15). G10 = AT1G43910 (P-loop containing nucleoside
triphosphate hydrolase-like protein).
Sub-network 4 and its composite outcomes
The sub-network 4 corresponding to cluster 4/module 4 is shown in Figure S4 and Table S4.
It includes 48 gene lists and 155 most frequently shared genes that were regulated by 32
treatments or conditions related to 11 biological themes. The top 10 most frequently shared
genes were specifically listed. Gene AT1G74670 (“putative gibberellin-regulated protein”) has
the highest frequency of 18. It is the most active genes (the strongest links) in sub-network 4.
The most enriched term is “response to auxin stimulus” based on DAVID, which indicates subnetwork 4 is specifically associated with auxin stimulus signaling pathway rather than by random
chance.
Figure S4. The sub-network 4 correspoding to cluster 4. Node = name of gene list. Node Color =
MCODE_Scores from small to large and corresponds to color from light green to dark red. Edge Color =
p-values from large to small and corresponds to color from grey to dark green. Edge label = number of
overlapping genes between both nodes.
Table S4. Results of sub-network 4 corresponding to cluster 4.
ID
1
2
3
4
5
6
Cluster 4: Gene.List
MERIGOUT_CO(NH2)2_NH4NO3_
ROOT_UP_550
BABU_PPV-INFECTED-LEAF_17DINOCULATION_DN_1456
BLASING_4H-LIGHT_UP_212
MANDAOKAR_JASMONATE_2H_
STAMEN_DIFF_197
MANDAOKAR_JASMONATE_22H_
STAMEN_DIFF_809
HE_BR-EARLY3H_UP_223
7 HU_WT-RC15/WT-D_UP_769
8
KLEINE_GROWTH-LIGHT-3H-BLUELIGHT_UP_858
9 HU_WT-RC50/WT-D_UP_1003
10
11
12
13
14
15
16
17
18
19
20
21
22
23
MANDAOKAR_JASMONATE_8H_
STAMEN_DIFF_490
PAUWELS_NINJA/WT-TREATEDCORONATINE_UP_169
SUGIO_HEAT-SHOCK_DN_1734
KAUFMANN_WT/AG-MUTANT_
BOLTING_UP_1651
HU_DARK_35S-MIF1_SEEDLINGS_
UP_1866
DEEKEN_AGROBACTERIUM-TUME
FACIENS_TUMORS_UP_2401
KAUFMANN_WT/AG-MUTANT
-STAGE12_UP_1910
DEEKEN_AGROBACTERIUM_
TUMORS/TUMOR-FREE-INFLO
RESCENCE-STALK_UP_2299
KAUFMANN_WT/AG-MUTANTSTAGE12_DN_973
MA_ROOT_WL/D_DN_1453
LEIVAR_SSTF-C1_WT-R1-WTRC-PIFQ-D/WT-D_DN_340
KLEINE_GROWTH-LIGHT-3HPHOTON_WT_UP_992
GUTIERREZ_UNSTABLEATGUTS_DIFF_95
TIWARI_2X4_BOTH-PLATFORM_
DN_93
24 LEE_HY5_UP_152
LEGNAIOLI_ABA_TOC1-OX_
MISS-EXPRESSED_218
26 EHLTING_VENN_DN_2648
25
Biological.
Theme
Function
Shoot Between [Co(Nh2)2]
And [Nh4No3]
Virus
Plum Pox Virus Infection
Metabolism
Mannitol; Ddiurnal Cycle
Development
Photosyn
thesis
Genome
Analysis
Photosyn
thesis
Function
v
Y276H Mutant Of Phytochrome
B; Dark; Continuous Red Light
v
v
v
v
v
v
v
v
v
v
v
v
v
v
Novel Interactor Of Jaz (Ninja)
v
Ag-Mutant; Bolting
Development Mini Zinc Finger 1 (Mif1); Dark
v
Disease
Agrobacterium Tumefaciens
v
Mechanism
Ag Mutant; Bolting
v
Disease
Agrobacterium Tumefaciens
v
Mechanism
Ag Mutant; Bolting
Development
Photosyn
thesis
Genome
Analysis
Genome
Analysis
Developmental & Environmental Cues
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
Light-Dark etc.***
Phytochrome A etc**.
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
Circadian Clock Controlled
Development Fertilized Fis1 Mutant
Metabolism
v
v
v
v
Metabolism
v
v
v
Mechanism
Mechanism
v
v
v
v
Development Heat Shock
Photosyn
thesis
v
v
Brassinosteroid (Br); Early 3H
Y276H Mutant Of Phytochrome
B; Dark; Continuous Red Light
Phytochrome A etc**.
v
v
Development Jasmonate (A Inducer) Treatment
28 RUBIN_WT-FN/WT-N_UP_1125
30 RUBIN_WT-N/WTFN_DN_1124
v
Development Jasmonate (A Inducer) Treatment
Metabolism
CHANDRAN_LEAF_PM-ALTERED_
5DPI_DN_580
G G G G G G G G G G
1* 2 3 4 5 6 7 8 9 10
Development Jasmonate (A Inducer) Treatment
27 KAKIZAKI_PPI2-1-TAG_DN_607
29
Treatment/Condition
v
Long Hypocotyl5 (Hy5)
Abscisic Acid (Aba); Circadian Clock;
Drought
Feeding By Diamond Back Moth Larvae
Plastid Protein Import2 Mutant (Ppi2))
Nitrogen (N) And Nitrate (No3–);
Lateral Organ Boundary Domain
Disease
Laser Microdissected
Metabolism
Nitrogen (N) And Nitrate (No3–);
Lateral Organ Boundary Domain
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
Table S4 (Continued)
ID
31
32
33
34
35
36
37
38
39
40
41
Biological.
Theme
Cluster 4: Gene.List
LEEA_WS-2_INOCULATION_
TUMOR_DN_1201
BRANCO-PRICE_9HS_IP_UP_295
MARCHIVE_1W_PNP-P-PNP+P_
UP_174
RAFFAELE_EXP.1_6H_MYB30OX
/WT_UP_149
MARCHIVE_1W_PNP-P-WT-P_
UP_154
BEZHANI_BRM-101_UP_90
SCHWAGER_VFB/WT_UP_213
TIWARI_6X2_BOTH-PLATFORM_
UP_776
LEIVAR_SSTF-C4_WT-R1-WTRC-PIFQ-D/WT-D_UP_382
ZHANG_PST-DC3000-GH3.5-1D/
WT_DN_357
WELLMER_RATIOS-R1_DN_993
44
45
46
47
T
48
Agrobacterium
Energy
Cellular Oxygen Deprivation Treament
Immune
v
v
v
v
Myb30 Knockout Mutant
v
Development Developmental & Environmental Cues
Function
Brahma And Splayed Mutants
Development Vier F-Box Proteine; Csn4 Mutant
v
Development Fertilized Fis1 Mutant
Photosyn
thesis
Light-Dark etc.***
v
Pst Dc3000 (Avrrpt2)-Infected
Disease
Gh3.5-1D
Development Apetala1 And Cauliflower Mutants
Photosyn
Y276H Mutant Of Phytochrome B;
thesis
Dark; Continuous Red Light
MARCHIVE_3H_PNP+P-WT+P_
DN_472
WELLMER_RATIOS-R4_UP_858
ZENTELLA_DEX_VECTOR_DN_244
WELLMER_RATIOS-R5_UP_926
THOMAS_OBE1I-OBE2I/WT_
DN_314
48 KANNO_DMS4/DRD1_UP_2610
Disease
G G G G G G G G G G
1* 2 3 4 5 6 7 8 9 10
Development Developmental & Environmental Cues
42 HU_YHB-RC50/WT-D_UP_1299
43
Treatment/Condition
v
Reproduction Mutations In Oberon1 And Oberon2
Development
11
Defective In Meristem Silencing 4
Mutants
32
v
v
v
v
v
v
Development Developmental & Environmental Cues
Development Apetala1 And Cauliflower Mutants
Development Bioactive Gibberellins; Della
Development Apetala1 And Cauliflower Mutants
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
1 1 1 1 1 1 1 1 1 1
8 7 7 7 6 6 6 6 6 6
Most frequently shared genes (Freq>=11, total 155 genes)
AT1G74670 AT1G04240 AT1G69530 AT5G44680 AT2G21880 AT2G44740 AT3G45140 AT4G34760 AT4G38840 AT5G47240 AT1G29500
AT4G12730 AT4G38860 AT5G06870 AT1G04250 AT1G76100 AT2G17500 AT3G17790 AT3G44990 AT4G12980 AT4G18970 AT4G22570
AT4G36540 AT5G22920 AT5G47370 AT1G18730 AT1G29440 AT2G34620 AT2G40610 AT2G43550 AT3G06070 AT3G21670 AT3G23030
AT3G25760 AT3G45780 AT3G48460 AT3G50270 AT4G08950 AT4G17340 AT4G29700 AT4G37610 AT4G37800 AT5G02940 AT5G16030
AT5G25460 AT5G39860 AT5G48490 AT5G55620 AT5G62360 AT1G11545 AT1G23020 AT1G25230 AT1G26770 AT1G29460 AT1G49975
AT1G51400 AT2G06850 AT2G10940 AT2G14210 AT2G18300 AT2G22990 AT2G28950 AT2G29290 AT2G45470 AT3G01500 AT3G03840
AT3G15720 AT3G26740 AT3G29030 AT3G47340 AT4G00050 AT4G03400 AT4G09890 AT4G16370 AT4G17460 AT4G19170 AT4G20260
AT4G23600 AT4G27520 AT4G28780 AT4G30450 AT4G35060 AT4G39675 AT5G06530 AT5G15160 AT5G19140 AT5G20630 AT5G23750
AT5G23820 AT5G24150 AT5G41050 AT5G45950 AT5G46690 AT5G49450 AT5G58260 AT5G65730 AT1G01120 AT1G02340 AT1G02820
AT1G02850 AT1G06080 AT1G09390 AT1G12240 AT1G14150 AT1G14280 AT1G16850 AT1G19670 AT1G23390 AT1G29510 AT1G52400
AT1G62480 AT1G74010 AT1G75460 AT1G75900 AT1G76090 AT1G76590 AT1G76790 AT1G78970 AT2G05540 AT2G14900 AT2G20670
AT2G22980 AT2G29450 AT2G29670 AT2G33380 AT2G34810 AT2G39350 AT2G40460 AT2G43535 AT2G47000 AT3G02040 AT3G02550
AT3G05640 AT3G14560 AT3G15540 AT3G16520 AT3G22740 AT3G23410 AT3G27690 AT3G28340 AT3G51895 AT3G62550 AT4G14690
AT4G23820 AT4G27450 AT4G30650 AT5G01015 AT5G03760 AT5G12050 AT5G20250 AT5G22500 AT5G28020 AT5G49360 AT5G50915
AT5G62280
*Note: G1-G10 = AT1G74670, AT1G04240, AT1G69530, AT5G44680, AT2G21880, AT2G44740, AT3G45140,
AT4G34760, AT4G38840, and AT5G47240.
Sub-network 5 and its composite outcomes
The sub-network 5 corresponding to cluster 5/module 5 is shown in Figure S5 and Table S5.
It includes 34 nodes (gene lists) and 109 most frequently shared genes, which are regulated by 26
treatments or conditions related to 11 biological themes. The top 10 most frequently shared
genes are specifically listed corresponding to different gene lists, biological themes, and
treatments or conditions. They are the most active genes in sub-network 5. Gene AT1G29500
(“SAUR-like auxin-responsive protein”) has the highest frequency of 10, which means the gene
is the strongest link in sub-network 5. The most enriched term in sub-network 5 is cell wall based
on functional analysis of DAVID. This indicates sub-network 5 is specifically associated with
cell wall signaling pathway.
Figure S5. The sub-network 5 corresponding to Cluster 5. Node = name of gene list. Node Color =
MCODE_Scores from small to large and corresponds to color from light green to dark red. Edge Color =
p-values from large to small and corresponds to color from grey to dark green. Edge label = number of
overlapping genes between both nodes.
Table S5. Results of sub-network 5 corresponding to cluster 5.
ID
Cluster 5: Gene.List
Biological.
Theme
Treatment/Condition
1 ZHANG_GH3.5-1D/WT_DN_156
Disease
2 ROMERO_SOM1_DN_466
MARCHIVE_3H_PNP-P-WT-P_
3
DN_261
4 BLASING_3H-NO3_UP_198
Virus
Metabolism
Pst Dc3000 (Avrrpt2)-Infected Gh3.51D
Tev_Tev-At-Infected; Som
Polynucleotide Phosphorylase;
Phosphorus (P) Starvation
Treatment-Mannitol; Diurnal Cycle
5 VERT_ARF2-COL_DN_342
Function
Function
G G G G G G G G G G
1* 2 3 4 5 6 7 8 9 10
v
v
v
v
v
Bin2 Kinase And Arf2
v
Developmental & Environmental Cues
v
7 ZHANG_ROOT_DIFF_270
LONG_WT/PYE-1-MUTANT-UN
8
DER(+FE&-FE)_DIFF_661
Reproduction
Pickle (Pkl); Gibberellin (Ga)
Energy
Iron Deficiency; Popeye; Brutus
10
KLEINE_HY5-MUTANT/WT_GRO
WTH-LIGHT_UP_290
11 KIDD_GENOTYPE_DIFF_298
12 WELLMER_RATIOS-R2_UP_854
MU_ACID-SYNTHETIC-GENE_
LEC1-OXI_DN_268
KEMPEMA_SLWF-NYMPH14
FEEDING_DN_557
LEIVAR_SSTF-C1_WT-R1-WT15
RC-PIFQ-D/WT-D_UP_287
13
Genome AnalysisHigh Intensity White Light etc.**
Phytochrome And Flowering Time1
Disease
Mutant Infection F. Oxysporum
Mutants Apetala1, Apetala2,
Genome Analysis
Apetala3, Pistillata, And Agamous
Mechanism
Fatty Acid Biosynthesis
Pest
Silverleaf Whitefly; PhytoalexinDeficient4 Mutants
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
Photosynthesis Light-Dark etc.***
16 MA_COTYLEDON_LIGHT_UP_495 Development
17
Phytohormone Gibberellin (Ga); Gnc;
Gnl/Cga1
v
v
v
6 MA_HYPOCOTYL_LIGHT_DN_799 Development
9 RICHTER_GA1/COL-0II_DN_2112 Development
v
MERIGOUT_CO(NH2)2_NH4NO3
Function
_SHOOTT_UP_225
Developmental & Environmental Cues
v
v
Shoot Between [Co(Nh2)2]-[Nh4No3]
v
18 DEEKEN_BL_UP_41
Disease
Agrobacterium Tumefaciens
v
v
SHIN_PHOTOSYNTHETIC_COL
19
-0(R)/COL-0(D)_UP_39
Photosynthesis Etiolated Pif3 Mutant; Light
v
v
20 DEEKEN_RL_UP_33
Disease
Agrobacterium Tumefaciens
v
v
Photosynthesis Etiolated Pif3 Mutant; Light
v
v
v
v
v
v
21
SHIN_PHOTOSYNTHETIC_
PIFQ(D)/COL-0(D)_UP_37
22 DELESSERT_C24WP_DN_350
Function
Ataf2
DEEKEN_CATEGORIES_AGROBA
CTERIUM_TUMORS/TUMOR-FR
23
EE-INFLORESCENCE-STALK_
DN_1704
Disease
Agrobacterium Tumefaciens
24 SEHR_INTERNODE_UP_74
Development
Jasmonate Signalling; Cambium
Mechanism
Nac Secondary Wall Thickening
Promoting Factor1 (Nst1) And Nst2
MITSUDA_NST1-1-NST3-1/WT_
DN_464
PESARESI_PSAD1-1MUTANT/
26
COL-0_UP_775
25
27
Photosynthesis Photosystem I Subunit D-1; Light
ROMERO_TEV_TEV-AT-INFECTED
Disease
_UP_497
28 KAKIZAKI_PPI2-1-TAG_UP_833
MARCHIVE_3H_PNP-P-WT-P
_UP_349
TANG_BRM-5/ESSP3_LEAVES
30
_DN_501
29
Metabolism
Plastid Protein Import2 Mutant (Ppi2))
Function
Polynucleotide Phosphorylase;
Phosphorus (P) Starvation
Mechanism
Mutations Affecting Brahma (Brm)
31 WELLMER_RATIOS-R2_DN_799
32 VERT_BRZ-ARF2_UP_386
Function
Bin2 Kinase And Arf2
Development
Vier F-Box Proteine; Csn4 Mutant
Function
Brahma And Splayed Mutants
SCHWAGER_VFB-CSN4/WT_
DN_119
34 BEZHANI_BRM-101_DN_93
T
34
11
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
Tev_Tev-At-Infected; Som
Mutants Apetala1, Apetala2,
Genome Analysis
Apetala3, Pistillata, And Agamous
33
v
26
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
10 9 8 8 8 8 8 8 8
8
Table S5 (continued)
Most frequently shared genes (Freq>=6, total 109 genes)
AT1G29500 AT2G16060 AT1G08380 AT1G30380 AT1G33811 AT1G67865 AT1G72610 AT2G02130 AT2G21650 AT4G28750 AT5G10180
AT1G15820 AT1G29440 AT1G32450 AT1G44575 AT1G70890 AT1G75750 AT2G06850 AT3G01500 AT3G03270 AT3G21055 AT3G47470
AT3G51600 AT3G54890 AT4G01430 AT4G19420 AT4G22490 AT4G27450 AT4G30270 AT5G09220 AT5G20630 AT5G23010 AT5G48485
AT5G49360 AT5G54270 AT5G55620 AT5G56870 AT5G57785 AT1G02640 AT1G03130 AT1G03870 AT1G06830 AT1G12080 AT1G12780
AT1G19530 AT1G20020 AT1G20620 AT1G21460 AT1G22500 AT1G22690 AT1G25230 AT1G28330 AT1G44800 AT1G52190 AT1G52230
AT1G55810 AT1G56430 AT1G62510 AT1G67860 AT1G75500 AT1G76080 AT1G77690 AT1G78370 AT2G05540 AT2G20670 AT2G25450
AT2G33830 AT2G34430 AT2G37750 AT2G40100 AT2G41090 AT2G47930 AT3G03840 AT3G04720 AT3G15450 AT3G15630 AT3G17790
AT3G27690 AT3G48360 AT3G48740 AT3G50660 AT3G50820 AT3G62410 AT3G63140 AT3G63160 AT4G00050 AT4G05180 AT4G12470
AT4G26320 AT4G34760 AT4G36540 AT4G38690 AT4G38840 AT4G38860 AT5G01600 AT5G02540 AT5G13730 AT5G14740 AT5G14780
AT5G18600 AT5G20250 AT5G22860 AT5G22920 AT5G23020 AT5G23820 AT5G24420 AT5G62280 AT5G64040 AT5G65730
*Note: G1-G10 = AT1G29500, AT2G16060, AT1G08380, AT1G30380, AT1G33811, AT1G67865, AT1G72610,
AT2G02130, AT2G21650, and AT4G28750.
Sub-network 6 and its composite outcomes
The sub-network 6 corresponding to cluster 6/module 6 is shown in Figure S6 and Table S6.
It includes 9 nodes (gene lists) and 34 most frequently shared genes, which are regulated by 6
treatments or conditions from 6 publications related to 3 biological themes. The top 10 most
frequently shared genes are specifically listed corresponding to different gene lists, biological
themes, and treatments or conditions. Gene AT1G02790 (“polygalacturonase 4”) has the highest
frequency at 10. They are the most active genes (the strongest links) in sub-network 6.
The most enriched term in sub-network 6 is external encapsulating structure organization
based on functional analysis of DAVID. This indicates sub-network 6 is specifically associated
with external encapsulating structure organization signaling pathway.
Figure S6. The sub-network 6 corresponding to cluster 6. Node = name of gene list. Node Color =
MCODE_Scores from small to large and corresponds to color from light green to dark red. Edge Color =
p-values from large to small and corresponds to color from grey to dark green. Edge label = number of
overlapping genes between both nodes.
Table S6. Results of sub-network 6 corresponding to cluster 6.
ID
Biological.
Theme
Cluster 6: Gene.List
1 WELLMER_ORGAN_DIFF_942
Reproduction
2 QIN_SIV-PT/4HPT_DN_235
Development
Treatment/Condition
Mutants Apetala1, Apetala2,
Apetala3, Pistillata, And
Agamous
Dry Pollen, Pollen Grown In
Vitro, And Pollen
Germinated And Grown
G G G G G G G G G G
1* 2 3 4 5 6 7 8 9 10
v
v
v
v v
v
v
v
v
v
v
v v
v
v
3
ZHANG_STAMENS/POLLEN_DIF
Development
F_923
Pickle (Pkl) ; Gibberellin (Ga)
v
4
TIWARI_2X6_BOTHPLATFORM_UP_288
Development
Fertilized Fis1 Mutant
v
v
v
5
OKAMOTO_ONLY-ABA2MUTANT_DRY-SEED_DN_54
Development
Aba2 Mutant; Dry; Seeds
v
v
v
v
6
GREGORY_EIN5MUTATION_DN_32
Development
v
v
v
7
WELLMER_ORGAN_FLOWERCDNA_DIFF_248
v v
v
v
8
QIN_SIV-PT/DRYPOLLEN_DN_356
9 WANG_DURING-PTG_DN_686
T
9
Loss Of Xrn4/Ein5,
Exoribonuclease, Abh1/Cbp80,
Mrna Cap Binding Complex
Mutants Apetala1, Apetala2,
Genome AnalysisApetala3, Pistillata, And
Agamous
Dry Pollen, Pollen Grown In
Development Vitro, And Pollen
Germinated And Grown
Development
3
v
v
Treatment With Actinomycin D
6
v
v
v
v
v
v
v
v
v
v
v
v v
v
v v
v
v
v
v
v
v v
v
v v
v
10 9 8 8 8 8 8 8 8 8
Most frequently shared genes (Freq>=5, total 34 genes)
AT1G02790 AT1G54070 AT2G16730 AT2G26850 AT2G47050 AT3G07820 AT3G07850 AT3G28830 AT4G16745 AT1G13950 AT1G52680
AT1G55560 AT1G67290 AT1G79250 AT2G02140 AT2G18180 AT2G19010 AT2G25790 AT2G28640 AT2G33870 AT2G47040 AT3G17980
AT3G28780 AT3G28980 AT4G07960 AT4G13560 AT4G15980 AT4G17690 AT4G24630 AT4G25780 AT4G27110 AT4G33230 AT5G38760
AT5G62750
*Note: G1-G10 = AT1G02790, AT1G54070, AT2G16730, AT2G26850, AT2G47050, AT3G07820, AT3G07850,
AT3G28830, AT4G16745, and AT1G13950.
Sub-network 7 and its composite outcomes
The sub-network 7 corresponding to cluster 7/module 7 is shown in Figure S7 and Table S7.
It includes 15 nodes (gene lists) and produces 53 most frequently shared genes that were
regulated by 14 treatments or conditions from 14 publications related to 6 biological themes. The
top 10 most frequently shared genes corresponding to different gene lists, biological themes, and
treatments were specifically listed. Gene AT1G73260 (“kunitz trypsin inhibitor 1”) has the
highest frequency of 8. They are the most active genes (the strongest links) in sub-network 7.
The most enriched term in sub-network 7 is glycoside biosynthetic process based on functional
analysis of DAVID. This indicates sub-network 7 is specifically associated with glycoside
biosynthetic process signaling pathway.
Figure S7. The sub-network 7 corresponding to cluster 7. Node = name of gene list. Node Color =
MCODE_Scores from small to large and corresponds to color from light green to dark red. Edge Color =
p-values from large to small and corresponds to color from grey to dark green. Edge label = number of
overlapping genes between both nodes.
Table S7. Results of sub-network 7 corresponding to cluster 7.
ID
Biological.
Theme
Cluster 7: Gene.List
PESARESI_STN7-1PSAD11 1MUTANT/CL-0_UP_628
2
Photosynthesis
CHANG_AZA-DC+TSA_UP_74
Function
3 MA_ROOT_LIGHT_DN_391
4
Development
ALVES-FERREIRA_AP3ES_UP_1269
Development
Treatment/Condition
Psad-1 (Photosystem I Subunit D-1);
Light Quality Changes
Aza-Dc, Tsa, Or Simultaneous
Treatment With Both Chemicals
Developmental & Environmental Cues
Floral Mutants Apetala3,
Sporocyteless/Nozzle, Male Sterile1
Gibberellin (Ga); Gnc; Gnl/Cga1
5 RICHTER_GNL-OX/COL-0II_DN_2300 Development
PESARESI_STN7-1PSAD1Photosynthesis Photosystem I Subunit D-1; Light
6 1MUTANT/WS-2_DN_295
Plant Nuclear Factor Y (Nf-Y) B; ZmnfNELSON_35S-CBF4_DN_215
Yield
7
Yb2; Drought
MERIGOUT_CO(NH2)2_NH4NO3_RO
Function
Shoot Between [Co(Nh2)2]-[Nh4No3]
8 OT_DN_375
DEEKEN_CATEGORIES_AGROBACTERI
UM_TUMORS/TUMOR-FREEDisease
Agrobacterium Tumefaciens
9 INFLORESCENCE-STALK_UP_1652
10 MA_ROOT_LIGHT_UP_489
Development
Developmental & Environmental Cues
11 VERT_BRZ-COL_UP_472
Function
Bin2 Kinase And Arf2
12
13
RICHTER_GNC-OX/COL-0II_DN_971
Development
LI_NFYA5_DN_108
Function
HU_LIGHT_35S14 MIF1_SEEDLINGS_UP_219
USADEL_DIURNAL-CYCLE15 SUC_DN_42
T
15
Development
Mechanism
6
G G G G G G G G G G
1* 2 3 4 5 6 7 8 9 10
v
v
v v
v
v v
v
v
v
v
v
v
v
Akin10 And Four Bzip Transcription
Factors; Light/Dark Cycle
14
v
v
v v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v v
v
v
v
v
v
v
v
v
v
v
Phytohormone Gibberellin (Ga); Gnc;
v v v
Gnl/Cga1
drought stress in an abscisic acid (ABA)v v
dependent manner
Mini Zinc Finger 1; Dark
v
v
v
v
v
v
v
v
v
v
8 7 6 6 6 6 6 6 6 6
Most frequently shared genes (Freq>=5, total 53 genes)
AT1G73260 AT2G30600 AT1G19530 AT1G64660 AT2G18700 AT2G38530 AT3G16450 AT4G04830 AT4G11650 AT4G13770 AT4G27450
AT1G12080 AT1G12780 AT1G49500 AT1G54740 AT1G60140 AT1G62280 AT1G64590 AT1G66760 AT1G69490 AT1G73330 AT2G01520
AT2G06850 AT2G17880 AT2G19970 AT2G22970 AT2G25900 AT2G38400 AT3G15450 AT3G15950 AT3G16460 AT3G19710 AT3G25190
AT3G30775 AT3G45160 AT3G62950 AT4G14630 AT4G18510 AT4G19410 AT4G30140 AT4G35770 AT4G38470 AT5G07440 AT5G22920
AT5G23020 AT5G40450 AT5G48000 AT5G49360 AT5G49450 AT5G56870 AT5G57655 AT5G59080 AT5G63160
*Note: G1-G10 = AT1G73260, AT2G30600, AT1G19530, AT1G64660, AT2G18700, AT2G38530, AT3G16450,
AT4G04830, AT4G11650, and AT4G13770.
Sub-network 8 and its composite outcomes
The sub-network 8 corresponding to cluster 8/module 8 is shown in Figure S8 and Table S8.
It includes 6 gene lists and 66 most frequently shared genes, which were regulated by 5
treatments or conditions from 5 publications related to 5 biological themes. The top 10 most
frequently shared genes were specifically listed corresponding to different gene lists, biological
themes, and treatments or conditions. Gene AT1G56110 (“homolog of nucleolar protein
NOP56”) has the highest frequency of 6. They are the most active genes (the strongest links) in
sub-network 8. The most enriched term in sub-network 8 is membrane-enclosed lumen based on
functional analysis of DAVID. This indicates sub-network 8 is specifically associated with
membrane-enclosed lumen signaling pathway.
Figure S8. The sub-network 8 corresponding to cluster 8. Node = name of gene list. Node Color =
MCODE_Scores from small to large and corresponds to color from light green to dark red. Edge Color =
p-values from large to small and corresponds to color from grey to dark green. Edge label = number of
overlapping genes between both nodes.
Table S8. Results of sub-network 8 corresponding to cluster 8.
ID
Cluster 8: Gene.List
Biological.
Theme
Treatment/Condition
1 DAY_EP_DIFF_2567
TIWARI_6X2_BOTH2
PLATFORM_DN_921
BLASING_4H-CARBON3
FIXCATION_UP_201
BAENA-GONZALEZ_KIN10_OSS
4
_DN_321
5 DAY_ESS_DIFF_2607
Yield
6 GONZALI_SUCROSE_UP_368
Development Sucrose; Dark
T
6
Comparisons Some Methods
Reproduction Fertilized Fis1 Mutant
Metabolism
Photosynthesis
Yield
G G G G G G G G G G
1* 2 3 4 5 6 7 8 9 10
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
Treatment-Mannitol; Diurnal Cycle v v v v v v v
Kin10 And Kin11; Darkness,
Sugar And Stress Conditions
Comparisons Some Methods
5
5
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
v
6 6 6 5 5 5 5 5 5 5
Most frequently shared genes (Freq>=4, total 66 genes)
AT1G56110 AT3G05060 AT3G44750 AT1G07370 AT1G44900 AT1G55900 AT3G12270 AT3G20330 AT3G23940 AT3G55010 AT4G25340
AT4G25630 AT4G30800 AT5G05990 AT5G22650 AT5G46280 AT5G62440 AT1G03360 AT1G23280 AT1G27400 AT1G30960 AT1G31660
AT1G48570 AT1G48630 AT1G48920 AT1G52930 AT1G61570 AT1G64880 AT1G71850 AT1G72440 AT1G77510 AT1G77550 AT1G80270
AT1G80530 AT2G16440 AT2G19670 AT2G21790 AT2G32990 AT2G34260 AT2G40360 AT2G47610 AT3G02760 AT3G06680 AT3G10530
AT3G11964 AT3G13230 AT3G15460 AT3G18130 AT3G18600 AT3G23830 AT3G49240 AT3G55510 AT3G56070 AT3G57150 AT3G58650
AT4G20020 AT4G28450 AT4G31810 AT5G02590 AT5G20160 AT5G27330 AT5G50730 AT5G50740 AT5G55920 AT5G61770 AT5G64670
*Note: G1-G10 = AT1G56110, AT3G05060, AT3G44750, AT1G07370, AT1G44900, AT1G55900, AT3G12270,
AT3G20330, AT3G23940, and AT3G55010.
Sub-network 9 and its composite outcomes
The sub-network 9 including 13 gene lists corresponding to cluster 9/module 9 is shown in
Figure S9 and Table S9. It includes 23 most frequently shared genes, which were regulated by 12
treatments or conditions from 12 publications related to 7 biological themes. The top 10 most
frequently shared genes were specifically listed corresponding to different gene lists, biological
themes, and treatments or conditions. Gene AT1G01470 (“putative desiccation-related protein
LEA14”) has the highest frequency of 6. They are the most active genes (the strongest links) in
sub-network 9. The most enriched term in sub-network 9 is response to abiotic stimulus based on
functional analysis of DAVID. This indicates sub-network 9 is specifically associated with
response to abiotic stimulus signaling pathway.
Figure S9. The sub-network 9 corresponding to cluster 9. Node = name of gene list. Node Color =
MCODE_Scores from small to large and corresponds to color from light green to dark red. Edge Color =
p-values from large to small and corresponds to color from grey to dark green. Edge label = number of
overlapping genes between both nodes.
Table S9. Results of sub-network 9 corresponding to cluster 9.
ID
1
2
3
4
5
6
7
Cluster 9: Gene.List
DINNENY_STE-RADIAL_FEDEPRIVATION_UP_455
WANG_DURING-PTG_UP_804
VERT_BRZ-COL_DN_471
BRANCO-PRICE_2HS_IP_9HS_
IP_UP_160
YANT_NUCLEAR_RP_UNAMBIG_
UP_732
LEE_COLD-CONTINUALLY_UP_146
RAFFAELE_EXP.1_90-105MN_
MYB30OX/WT_UP_113
8 LEE_COLD-TRANSIENTLY_UP_74
ABERCROMBIE_GO_ARSENIC9
TREATED_DN_90
BLASING_4H-CARBON-FIXCATION
10
_DN_205
Biological.
Theme
Treatment/Condition
G G G G G G G G G G
1* 2 3 4 5 6 7 8 9 10
Development Iron Deprivation
v
Development Treatment With Actinomycin D
Function
Bin2 Kinase And Arf2
v
Energy
Cellular Oxygen Deprivation Treament
v
Development Apetala2 (Ap2) Mutant
v
v v
Development Cold
v
v
Immune
Myb30 Knockout Mutant
Development Cold
v
v v
v
v
v
v
v
v
v v
v
v v
v
v
v
v
v
v
v
v
v
v
Toxin
Arsenic-Treatment
Metabolism
Treatment-Mannitol; Diurnal Cycle
v
Development Aluminum (Al) Toxicity
Mechanism
Dehydration Stress Conditions
v
13 DELESSERT_C24WP_UP_414
Function
Wounded
v
7
v
v
v
v
DIJK_DEHYDRATION-STRESS_
12
UP_640
13
v
v
11 HOEKENGA_AFGC_AL_UP_232
T
v
12
v v
v
v
v
v
v
v v
v
v
v
v
v
6 6 6 6 6 6 5 5 5 5
Most frequently shared genes (Freq>=5, total 23 genes)
AT1G01470 AT2G22500 AT2G23810 AT5G05410 AT5G58070 AT5G59820 AT1G09070 AT1G19180 AT1G20440 AT1G25400
AT1G27730 AT1G54100 AT1G62570 AT2G23120 AT2G41100 AT3G22370 AT4G11280 AT4G24570 AT4G37370 AT5G17850
AT5G20230 AT5G42050 AT5G59310
*Note: G1-G10 = AT1G01470, AT2G22500, AT2G23810, AT5G05410, AT5G58070, AT5G59820, AT1G09070,
AT1G19180, AT1G20440, and AT1G25400.