Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.2.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89366	0.285
27DAP/17DAP	0.93255	0.877
39DAP/27DAP	1.15148	0.759
41DAP/39DAP	0.68555	0.111
42DAP/41DAP	1.17117	0.856
43DAP/42DAP	0.7896	0.551
47DAP/43DAP	1.03223	0.979
52DAP/47DAP	1.10545	0.943
57DAP/52DAP	0.94123	0.938

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30716	0.025
17DAP/reference	1.20123	0.193
27DAP/reference	1.17161	0.211
39DAP/reference	1.21742	0.214
41DAP/reference	1.14615	0.221
42DAP/reference	1.32456	0.001
43DAP/reference	1.20569	0.044
47DAP/reference	1.32425	0.001
52DAP/reference	1.10884	0.43
57DAP/reference	1.41287	0.01

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.26032	0.053
27DAP/17DAP	1.0434	0.905
39DAP/27DAP	0.96243	0.747
41DAP/39DAP	1.25577	0.727
42DAP/41DAP	0.98567	0.776
43DAP/42DAP	0.66803	0.022
47DAP/43DAP	1.08551	0.376
52DAP/47DAP	0.93191	0.575
57DAP/52DAP	0.9539	0.628
57DAP/7DAP	0.84156	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.48836	0.034
17DAP/reference	1.73974	0.006
27DAP/reference	1.69603	0.008
39DAP/reference	1.57765	0.005
41DAP/reference	1.53421	0.008
42DAP/reference	1.4616	0.024
43DAP/reference	1.17016	0.063
47DAP/reference	1.25623	0.044
52DAP/reference	1.97003	0.007
57DAP/reference	1.71518	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11742	0.443
17DAP/reference	1.29897	0.04
27DAP/reference	1.77694	0.013
39DAP/reference	1.46892	0.021
41DAP/reference	1.50207	0.006
42DAP/reference	1.5081	0.011
43DAP/reference	1.22405	0.304
47DAP/reference	1.48298	0.009
52DAP/reference	1.10511	0.181
57DAP/reference	1.02129	0.834

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.38993	0.026
17DAP/reference	1.02677	0.839
27DAP/reference	1.28588	0.059
39DAP/reference	1.34447	0.029
41DAP/reference	1.35244	0.008
42DAP/reference	1.23675	0.051
43DAP/reference	1.51523	0.019
47DAP/reference	1.07976	0.704
52DAP/reference	1.38348	0.074
57DAP/reference	1.79146	0.007

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94601	1
26DAP/20DAP	1.39216	0.285
34DAP/26DAP	0.80212	0.152
51DAP/34DAP	1.15611	0.207
52DAP/51DAP	0.84153	1
53DAP/52DAP	1.25844	0.121
55DAP/53DAP	0.9476	0.515
57DAP/55DAP	1.12699	0.793
62DAP/57DAP	1.04663	0.8
68DAP/62DAP	0.93818	0.769
68DAP/14DAP	0.92543	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.62743	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.2297	0.058
Mature Green Tomato/Ripe Tomato	1.27415	0.185
Immature Eggplant/Mature Eggplant	0.87694	0.092
Ripe Pepper/Ripe Tomato	0.96258	1
Mature Eggplant/Ripe Tomato	0.89497	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98939	1
1-1-2/M82	1.24227	1
12-2/M82	0.74398	0.678
12-4/M82	0.97636	0.619
1-3/M82	1.29652	0.479
2-1-1/M82	0.96493	1
2-1/M82	0.66776	0.322
2-6/M82	0.91329	1
3-2/M82	1.09273	0.967
4-1-1/M82	1.09652	1
4-1/M82	0.77766	1
4-3-2/M82	1.09863	0.508
4-3/M82	1.24637	0.268
5-3/M82	1.22701	1
6-2/M82	0.99445	1
6-3/M82	0.98004	1
7-1/M82	1.0252	1
7-2/M82	1.11846	0.385
9-3-2/M82	1.21674	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.91259
IL2-6/WTpooled	0.84633	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.3331	1
IL12-4/WTpooled	1.05809	1
IL1-4/WTpooled	1.01878
WT/WTpooled	1.03414	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	1.11176	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.10011	0.724
DC3000/delta hrp 6h	1.06304	1
DC3000/delta hrp 12h	0.96516	1
DC3000/delta hrp 24h	0.9862	0.978

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	1.24288	0.158

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94988	1
Exp 36h	1.15819	1
Exp 60h	1.07916	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99126	1
Var 0h	1.20158	0.325
Var 12h I row2-row1	1.06481	0.692
Var 12h NI row2-row1	1.11138	1
Var 36h I row2-row1	0.88337	1
Var 36h NI row2-row1	0.82463	0.549
Var 60h I row2-row1	0.95653	0.582
Var 60h NI row2-row1	0.80937	0.38
Time course 0hI-0hNI	0.83913	0.076
Time course 12hI-12hNI	1.0592	0.587
Time course 36hI-36hNI	1.29409	0.128
Time course 60hI-60hNI	1.4948	0.011

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)	0.97187	0.722
transgenic ySAMdc/azygous control (breaker)	1.15407	0.248
transgenic ySAMdc/azygous control (red)	1.03169	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.18965	0.061

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.74008	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.81803	1
Manapal/WT (break)	0.92645	1
Manapal/WT (red)	1.27214	0.142