Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.2.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87704	0.975
27DAP/17DAP	1.51212	0.609
39DAP/27DAP	1.14942	0.713
41DAP/39DAP	0.96092	0.854
42DAP/41DAP	0.93825	1
43DAP/42DAP	0.94365	0.877
47DAP/43DAP	1.02826	0.943
52DAP/47DAP	0.86956	0.634
57DAP/52DAP	1.30981	0.826

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83241	0.194
17DAP/reference	0.99611	0.819
27DAP/reference	1.1057	0.771
39DAP/reference	1.1297	0.691
41DAP/reference	1.10919	0.158
42DAP/reference	0.95224	0.295
43DAP/reference	1.18985	0.233
47DAP/reference	0.95816	0.445
52DAP/reference	1.1138	0.354
57DAP/reference	1.00463	0.767

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.21539	0.252
27DAP/17DAP	1.13846	0.699
39DAP/27DAP	0.86965	0.093
41DAP/39DAP	1.32532	0.19
42DAP/41DAP	0.86851	0.083
43DAP/42DAP	0.89878	0.127
47DAP/43DAP	1.0763	0.765
52DAP/47DAP	0.92102	0.702
57DAP/52DAP	1.13803	0.523
57DAP/7DAP	1.23154

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.37288	0.024
17DAP/reference	1.42432	0.03
27DAP/reference	1.27096	0.06
39DAP/reference	1.22328	0.02
41DAP/reference	1.09074	0.232
42DAP/reference	1.09681	0.686
43DAP/reference	1.18701	0.041
47DAP/reference	0.98068	0.671
52DAP/reference	1.26302	0.076
57DAP/reference	1.21273	0.07

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19314	0.531
17DAP/reference	1.01559	0.747
27DAP/reference	1.10071	0.303
39DAP/reference	1.23714	0.355
41DAP/reference	0.91956	0.373
42DAP/reference	1.14014	0.951
43DAP/reference	0.85793	0.263
47DAP/reference	0.98874	0.59
52DAP/reference	1.12763	0.057
57DAP/reference	1.16209	0.345

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.57135	0.031
17DAP/reference	1.12166	0.572
27DAP/reference	1.01225	1
39DAP/reference	1.2793	0.038
41DAP/reference	0.96291	0.512
42DAP/reference	1.14025	0.47
43DAP/reference	1.30854	0.03
47DAP/reference	0.9249	0.315
52DAP/reference	1.57179	0.102
57DAP/reference	1.52802	0.401

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07095	0.966
26DAP/20DAP	1.19254	0.53
34DAP/26DAP	1.07785	1
51DAP/34DAP	0.96859	0.791
52DAP/51DAP	0.94249	1
53DAP/52DAP	1.31939	0.065
55DAP/53DAP	1.03897	0.989
57DAP/55DAP	1.06271	0.955
62DAP/57DAP	0.45508	0.002
68DAP/62DAP	1.14299	1
68DAP/14DAP	0.85473	1

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.96096	0.306

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.34696	0.073
Mature Green Tomato/Ripe Tomato	1.50388	0.058
Immature Eggplant/Mature Eggplant	1.7513
Ripe Pepper/Ripe Tomato	58.2845	0.256
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.95067
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.3742

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.07735	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.95687	0.418
IL12-4/WTpooled	1.02061	1
IL1-4/WTpooled	1.05594
WT/WTpooled	0.93707	1

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	0.92346	0.75

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06165	0.921
DC3000/delta hrp 6h	1.16327	1
DC3000/delta hrp 12h	1.02697	1
DC3000/delta hrp 24h	0.53661	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.60821
DC3000 delta B/DC3000 delta AB	3.07231

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.85233	0.328
Exp 36h	0.81048	0.539
Exp 60h	0.83956	0.522

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	1.09755	1
Var 0h	0.9309	1
Var 12h I row2-row1	0.89917	0.705
Var 12h NI row2-row1	1.11539	0.649
Var 36h I row2-row1	1.36106	0.742
Var 36h NI row2-row1	0.78964	0.584
Var 60h I row2-row1	0.88649	0.832
Var 60h NI row2-row1	0.77016	0.292
Time course 0hI-0hNI	1.03646	0.719
Time course 12hI-12hNI	0.97987	0.847
Time course 36hI-36hNI	1.10574	0.07
Time course 60hI-60hNI	1.70486	0.008

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	0.87596	0.291
transgenic ySAMdc/azygous control (breaker)	1.08288	1
transgenic ySAMdc/azygous control (red)	0.94449	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9389	0.099

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.24654	0.277

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.77133	0.09
Manapal/WT (break)	1.39451	0.123
Manapal/WT (red)	1.40791	0.222