Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-2.1.3.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.79995	0.324
27DAP/17DAP	0.85722	0.641
39DAP/27DAP	1.90565	0.165
41DAP/39DAP	0.90343	0.597
42DAP/41DAP	0.95687	1
43DAP/42DAP	1.23956	0.793
47DAP/43DAP	0.59664	0.099
52DAP/47DAP	1.60004	0.313
57DAP/52DAP	2.04714	0.82

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76485	0.054
17DAP/reference	0.48771	0.007
27DAP/reference	0.73441	0.011
39DAP/reference	0.70055	0.011
41DAP/reference	0.50787	0.049
42DAP/reference	0.96537	0.384
43DAP/reference	0.85687	N/A
47DAP/reference	1.29041	0.13
52DAP/reference	2.51361	0.01
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10194	0.708
27DAP/17DAP	1.1035	0.798
39DAP/27DAP	1.07229	0.854
41DAP/39DAP	1.01491	0.895
42DAP/41DAP	0.93938	0.607
43DAP/42DAP	0.9565	0.751
47DAP/43DAP	1.01602	1
52DAP/47DAP	1.74166	0.091
57DAP/52DAP	1.89125	0.05
57DAP/7DAP	1.15981	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.56904	0.032
17DAP/reference	1.30649	0.045
27DAP/reference	1.19649	0.664
39DAP/reference	1.47469	0.01
41DAP/reference	1.42242	0.046
42DAP/reference	1.41821	0.016
43DAP/reference	1.34562	0.066
47DAP/reference	1.5753	0.024
52DAP/reference	1.64703	0.007
57DAP/reference	1.557	0.017

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.72569	0.016
17DAP/reference	0.48075	0.004
27DAP/reference	0.7953	0.15
39DAP/reference	0.74258	0.01
41DAP/reference	0.8324	0.13
42DAP/reference	0.84973	0.067
43DAP/reference	0.66707	0.032
47DAP/reference	0.84638	0.071
52DAP/reference	0.52398	0.003
57DAP/reference	0.58178	0.006

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.75887	0.134
17DAP/reference	0.80365	0.243
27DAP/reference	1.25896	0.467
39DAP/reference	1.22833	0.466
41DAP/reference	1.37977	0.011
42DAP/reference	1.19162	0.556
43DAP/reference	1.13921	0.58
47DAP/reference	0.87108	0.199
52DAP/reference	1.42463	0.072
57DAP/reference	2.00724	0.005

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.13485	0.966
26DAP/20DAP	1.73327	0.111
34DAP/26DAP	1.26035	1
51DAP/34DAP	1.80614	0.177
52DAP/51DAP	1.29422	0.367
53DAP/52DAP	1.29111	0.095
55DAP/53DAP	1.14954	0.319
57DAP/55DAP	0.976	0.757
62DAP/57DAP	0.44422	0.001
68DAP/62DAP	1.24814	0.142
68DAP/14DAP	2.4903	0.022

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.66174	0.054

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.68135	0.192
Mature Green Tomato/Ripe Tomato	0.49741	0.079
Immature Eggplant/Mature Eggplant	1.37569	0.058
Ripe Pepper/Ripe Tomato	1.16331	1
Mature Eggplant/Ripe Tomato	0.9186	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.7654	N/A
1-1-2/M82	1.20369	N/A
12-2/M82	1.35639	1
12-4/M82	0.91288	0.619
1-3/M82	2.53785	0.248
2-1-1/M82	1.11063	N/A
2-1/M82	0.81036	N/A
2-6/M82	0.67579	0.501
3-2/M82	1.14985	0.967
4-1-1/M82	0.82186	1
4-1/M82	1.07993	N/A
4-3-2/M82	0.68968	0.698
4-3/M82	1.09848	1
5-3/M82	0.91158	1
6-2/M82	1.08451	1
6-3/M82	0.76095	1
7-1/M82	0.88531	1
7-2/M82	1.05262	1
9-3-2/M82	0.78576	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.706	0.243
IL2-6/WTpooled	1.15357	0.427
IL7-5/WTpooled	1.37177	0.792
IL7-3/WTpooled	0.91645	0.418
IL12-4/WTpooled	0.97773	1
IL1-4/WTpooled	1.03387	1
WT/WTpooled	0.9248	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	0.87715	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97474	1
DC3000/delta hrp 6h	0.77223	0.95
DC3000/delta hrp 12h	0.84738	1
DC3000/delta hrp 24h	0.73247	0.038

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.02339	1
DC3000 delta B/DC3000 delta AB	1.06569	0.503

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98798	1
Exp 36h	1.45889	1
Exp 60h	1.53869	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98694	1
Var 0h	0.96617	1
Var 12h I row2-row1	1.18793	0.544
Var 12h NI row2-row1	1.06606	1
Var 36h I row2-row1	0.99567	1
Var 36h NI row2-row1	1.22024	0.482
Var 60h I row2-row1	0.82402	0.439
Var 60h NI row2-row1	1.05932	1
Time course 0hI-0hNI	1.00593	1
Time course 12hI-12hNI	0.96758	0.776
Time course 36hI-36hNI	0.98963	0.654
Time course 60hI-60hNI	1.50143	0.673

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)	0.9906	0.862
transgenic ySAMdc/azygous control (breaker)	0.62927	0.131
transgenic ySAMdc/azygous control (red)	0.95867	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.13975	0.334

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.94723	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.01068	1
Manapal/WT (break)	0.91909	1
Manapal/WT (red)	0.8178	0.199