Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.13.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94859	0.713
27DAP/17DAP	1.0121	0.882
39DAP/27DAP	0.83266	0.482
41DAP/39DAP	1.84809	0.292
42DAP/41DAP	0.95878	1
43DAP/42DAP	0.94953	0.909
47DAP/43DAP	0.93106	0.729
52DAP/47DAP	1.50324	0.288
57DAP/52DAP	1.01151	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00189	0.844
17DAP/reference	0.96188	0.298
27DAP/reference	0.95938	0.114
39DAP/reference	0.99273	0.901
41DAP/reference	0.96686	0.201
42DAP/reference	0.9563	0.029
43DAP/reference	0.98882	0.745
47DAP/reference	0.91657	0.003
52DAP/reference	0.93053	0.189
57DAP/reference	0.90593	0.012

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02362	0.826
27DAP/17DAP	0.99413	0.943
39DAP/27DAP	1.05831	0.558
41DAP/39DAP	0.95936	0.91
42DAP/41DAP	1.02307	0.935
43DAP/42DAP	0.99032	0.928
47DAP/43DAP	0.98869	0.939
52DAP/47DAP	0.97775	0.901
57DAP/52DAP	0.97208	0.632
57DAP/7DAP	1.05447	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90929	0.062
17DAP/reference	0.99275	0.599
27DAP/reference	1.10711	0.073
39DAP/reference	0.96101	0.015
41DAP/reference	0.91126	0.015
42DAP/reference	1.0203	0.405
43DAP/reference	0.94864	0.105
47DAP/reference	0.92144	0.168
52DAP/reference	0.92051	0.046
57DAP/reference	0.94712	0.083

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01943	0.589
17DAP/reference	1.04601	0.658
27DAP/reference	0.95812	0.407
39DAP/reference	0.969	0.348
41DAP/reference	0.92156	0.091
42DAP/reference	0.9262	0.098
43DAP/reference	1.0993	0.23
47DAP/reference	0.93352	0.09
52DAP/reference	0.99099	0.576
57DAP/reference	1.05679	0.229

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02885	1
17DAP/reference	1.00528	1
27DAP/reference	1.01433	0.749
39DAP/reference	1.06439	0.235
41DAP/reference	0.90333	0.019
42DAP/reference	0.9392	0.361
43DAP/reference	0.9052	0.084
47DAP/reference	1.01314	1
52DAP/reference	1.0453	0.631
57DAP/reference	0.81413	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03722	0.966
26DAP/20DAP	0.9467	1
34DAP/26DAP	0.89581	0.399
51DAP/34DAP	0.92648	0.376
52DAP/51DAP	1.07856	0.349
53DAP/52DAP	0.95472	0.723
55DAP/53DAP	0.99159	0.886
57DAP/55DAP	0.97441	0.851
62DAP/57DAP	0.91269	0.466
68DAP/62DAP	0.87289	0.263
68DAP/14DAP	0.93724	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.98688	0.696

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.89476
Mature Green Tomato/Ripe Tomato	0.81647	0.119
Immature Eggplant/Mature Eggplant	1.05897	0.485
Ripe Pepper/Ripe Tomato	1.31048	1
Mature Eggplant/Ripe Tomato	1.58571

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03981	1
1-1-2/M82	0.9136	0.958
12-2/M82	0.96858	0.955
12-4/M82	0.96648
1-3/M82	0.94205	0.441
2-1-1/M82	0.94133
2-1/M82	1.93164
2-6/M82	0.95776	1
3-2/M82	0.98231	1
4-1-1/M82	0.95424	1
4-1/M82	1.00372	1
4-3-2/M82	0.78717	1
4-3/M82	0.91796
5-3/M82	0.94959	1
6-2/M82	1.04766	1
6-3/M82	1.02792	1
7-1/M82	1.02162	1
7-2/M82	0.92776	0.599
9-3-2/M82	0.79909	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.00831	1
IL2-6/WTpooled	0.88858	1
IL7-5/WTpooled	0.59157
IL7-3/WTpooled	1.24048	1
IL12-4/WTpooled	0.85209	0.71
IL1-4/WTpooled	0.89303	0.834
WT/WTpooled	1.00953	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	1.00154	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05513	0.921
DC3000/delta hrp 6h	1.0304	1
DC3000/delta hrp 12h	1.10332	1
DC3000/delta hrp 24h	0.99976	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.06843	0.229
DC3000 delta B/DC3000 delta AB	1.04558	0.503

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.13588	1
Exp 36h	0.91584	0.504
Exp 60h	1.06498	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99073	1
Var 0h	1.75658	1
Var 12h I row2-row1	1.11983	0.254
Var 12h NI row2-row1	0.97128	0.906
Var 36h I row2-row1	1.12492	1
Var 36h NI row2-row1	0.96304	0.791
Var 60h I row2-row1	1.20628	0.562
Var 60h NI row2-row1	1.0863	0.904
Time course 0hI-0hNI	1.06383	0.852
Time course 12hI-12hNI	1.03847	0.811
Time course 36hI-36hNI	0.94772	0.206
Time course 60hI-60hNI	1.07764	0.254

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)	1.03223	0.699
transgenic ySAMdc/azygous control (breaker)	1.07027	1
transgenic ySAMdc/azygous control (red)	0.96529	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04393	0.142

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.10117	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.0832	0.14
Manapal/WT (break)	0.91448	1
Manapal/WT (red)	0.61231	0.181