Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.10.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.23925	0.414
27DAP/17DAP	0.96268	0.959
39DAP/27DAP	1.34275	0.35
41DAP/39DAP	0.98458	0.902
42DAP/41DAP	0.8802	0.774
43DAP/42DAP	0.96257	0.877
47DAP/43DAP	1.20147	0.584
52DAP/47DAP	1.1642	0.773
57DAP/52DAP	1.10084	0.96

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98036	0.589
17DAP/reference	1.08737
27DAP/reference	0.94687	0.359
39DAP/reference	0.86951	0.513
41DAP/reference	0.93148	0.114
42DAP/reference	1.00826	0.931
43DAP/reference	1.02326	0.705
47DAP/reference	0.98472	0.473
52DAP/reference	0.99955	1
57DAP/reference	0.97874	0.526

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08331	0.205
27DAP/17DAP	1.01442	0.957
39DAP/27DAP	0.94931	0.587
41DAP/39DAP	0.95068	0.875
42DAP/41DAP	1.11751	0.46
43DAP/42DAP	0.88859	0.073
47DAP/43DAP	1.01106	0.957
52DAP/47DAP	1.08606	0.681
57DAP/52DAP	1.01343	0.957
57DAP/7DAP	1.033	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08724	0.28
17DAP/reference	1.05856	0.102
27DAP/reference	1.15385	0.017
39DAP/reference	1.00802	0.865
41DAP/reference	1.04045	0.402
42DAP/reference	1.06177	0.1
43DAP/reference	1.05287	0.344
47DAP/reference	0.98519	0.671
52DAP/reference	1.06948	0.062
57DAP/reference	1.09802	0.026

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01902	0.732
17DAP/reference	1.06156	0.437
27DAP/reference	1.03965	0.692
39DAP/reference	0.93284	0.113
41DAP/reference	1.02128	1
42DAP/reference	1.06627	0.543
43DAP/reference	1.09726	0.056
47DAP/reference	0.97608	0.423
52DAP/reference	0.9879	0.469
57DAP/reference	0.93767	0.135

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06077	0.296
17DAP/reference	1.02208	0.784
27DAP/reference	1.14946	0.085
39DAP/reference	0.98659	0.755
41DAP/reference	1.05409	0.296
42DAP/reference	1.13416	0.138
43DAP/reference	1.06544	0.459
47DAP/reference	0.9477	0.286
52DAP/reference	1.01951	0.965
57DAP/reference	0.99684	0.828

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01128	1
26DAP/20DAP	1.09834	0.66
34DAP/26DAP	0.87974	0.237
51DAP/34DAP	0.92091	0.537
52DAP/51DAP	1.00008	1
53DAP/52DAP	0.97011	0.868
55DAP/53DAP	0.95638	0.761
57DAP/55DAP	0.929	0.694
62DAP/57DAP	0.89762	0.28
68DAP/62DAP	1.08367	0.515
68DAP/14DAP	1.13946	0.384

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.10162	0.045

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.54095	0.058
Mature Green Tomato/Ripe Tomato	0.94747	0.715
Immature Eggplant/Mature Eggplant	1.40236	0.062
Ripe Pepper/Ripe Tomato	0.58379	0.224
Mature Eggplant/Ripe Tomato	1.50301	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00496	1
1-1-2/M82	1.01323	1
12-2/M82	N/A	N/A
12-4/M82	1.01775	1
1-3/M82	1.0791	0.479
2-1-1/M82	1.12338	0.764
2-1/M82	0.85974
2-6/M82	0.93845	1
3-2/M82	1.08358	0.84
4-1-1/M82	1.02264	1
4-1/M82	0.9014	0.665
4-3-2/M82	1.15269
4-3/M82	1.0731	1
5-3/M82	0.98392	0.49
6-2/M82	1.02304	1
6-3/M82	1.02495	1
7-1/M82	0.82869
7-2/M82	0.89509	0.881
9-3-2/M82	0.69598	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.6726
IL7-3/WTpooled	1.6023
IL12-4/WTpooled	0.78055	1
IL1-4/WTpooled	1.26781	0.426
WT/WTpooled	1.14685	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	1.04941	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04154	0.823
DC3000/delta hrp 6h	0.9826	0.95
DC3000/delta hrp 12h	0.98199	1
DC3000/delta hrp 24h	0.94584	0.598

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.06959	0.052
DC3000 delta B/DC3000 delta AB	1.00835	0.748

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.79785	0.245
Exp 36h	1.2681	0.489
Exp 60h	1.34742	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97167	1
Var 0h	1.41731	0.239
Var 12h I row2-row1	1.30452	0.272
Var 12h NI row2-row1	0.99989	1
Var 36h I row2-row1	1.0559	1
Var 36h NI row2-row1	0.99304	0.852
Var 60h I row2-row1	1.00898	1
Var 60h NI row2-row1	0.97607	1
Time course 0hI-0hNI	1.00884	1
Time course 12hI-12hNI	1.04616	0.682
Time course 36hI-36hNI	1.13264	0.101
Time course 60hI-60hNI	1.18019	0.019

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)	0.94492	0.529
transgenic ySAMdc/azygous control (breaker)	0.81663	0.131
transgenic ySAMdc/azygous control (red)	0.90913	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01427	0.766

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.80944	0.228

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.80677	0.172
Manapal/WT (break)	1.02583	1
Manapal/WT (red)	1.33245	0.222