Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.1.1.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0955	0.863
27DAP/17DAP	1.07355	0.872
39DAP/27DAP	0.83547	0.487
41DAP/39DAP	1.24717	0.342
42DAP/41DAP	1.01099	1
43DAP/42DAP	0.99665	0.937
47DAP/43DAP	1.16067	0.309
52DAP/47DAP	1.11069	0.819
57DAP/52DAP	0.93336	0.908

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.60176	0.03
17DAP/reference	0.46933	0.008
27DAP/reference	0.46067	0.013
39DAP/reference	0.3576	0.009
41DAP/reference	0.35045	0.009
42DAP/reference	0.48115	0.001
43DAP/reference	0.27543	0.012
47DAP/reference	0.41966	0.002
52DAP/reference	0.24243	0.013
57DAP/reference	0.32538	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97692	0.697
27DAP/17DAP	1.04761	0.872
39DAP/27DAP	1.07116	0.499
41DAP/39DAP	1.04953	0.748
42DAP/41DAP	1.03009	0.872
43DAP/42DAP	1.04382	0.446
47DAP/43DAP	1.05174	0.593
52DAP/47DAP	0.97507	0.868
57DAP/52DAP	0.98754	0.742
57DAP/7DAP	0.94585	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80415	0.07
17DAP/reference	0.65981	0.02
27DAP/reference	0.96688	0.494
39DAP/reference	0.74881	0.043
41DAP/reference	0.72461	0.127
42DAP/reference	1.0137	0.641
43DAP/reference	1.13573	0.344
47DAP/reference	0.7441	0.293
52DAP/reference	0.98084	0.523
57DAP/reference	0.90363	0.156

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.55484	0.022
17DAP/reference	0.72689	0.109
27DAP/reference	0.71358	0.134
39DAP/reference	0.36787	0.011
41DAP/reference	0.52947	0.01
42DAP/reference	0.39509	0.011
43DAP/reference	0.51208	0.012
47DAP/reference	0.2008	0.045
52DAP/reference	0.28912	0.004
57DAP/reference	0.23589	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98054	0.607
17DAP/reference	1.45958	0.602
27DAP/reference	0.9594	0.566
39DAP/reference	0.74202	0.035
41DAP/reference	1.09009	0.826
42DAP/reference	0.63717	0.059
43DAP/reference	0.6225	0.023
47DAP/reference	0.36656	0.005
52DAP/reference	0.58779	0.128
57DAP/reference	0.98325	0.553

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.53205	0.961
26DAP/20DAP	0.93185	1
34DAP/26DAP	1.0759	1
51DAP/34DAP	1.00309	1
52DAP/51DAP	0.96145	1
53DAP/52DAP	1.0803	0.413
55DAP/53DAP	0.95637	0.698
57DAP/55DAP	1.17644	0.559
62DAP/57DAP	0.97461	1
68DAP/62DAP	0.61805	0.429
68DAP/14DAP	0.5031	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.98111	0.422

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.70966	0.058
Mature Green Tomato/Ripe Tomato	0.90494	0.317
Immature Eggplant/Mature Eggplant	0.38614	0.047
Ripe Pepper/Ripe Tomato	3.97242	0.236
Mature Eggplant/Ripe Tomato	10.2846

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	0.85029
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	0.99045
4-3-2/M82	1.11653
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	0.84625
7-2/M82	N/A	N/A
9-3-2/M82	0.84139	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.95327	1
IL2-6/WTpooled	1.17161	0.46
IL7-5/WTpooled	1.22444
IL7-3/WTpooled	0.79771	0.31
IL12-4/WTpooled	0.86848	1
IL1-4/WTpooled	0.96339	1
WT/WTpooled	0.9878	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	1.02851	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.8942	1
DC3000/delta hrp 6h	0.9501	0.95
DC3000/delta hrp 12h	1.56143	1
DC3000/delta hrp 24h	0.35889	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.03883	0.408
DC3000 delta B/DC3000 delta AB	1.03336	0.614

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98586	1
Exp 36h	0.86258	0.661
Exp 60h	0.87696	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98973	1
Var 0h	0.70941	0.782
Var 12h I row2-row1	1.17567	0.187
Var 12h NI row2-row1	0.94662	0.906
Var 36h I row2-row1	1.00483	1
Var 36h NI row2-row1	0.95741	0.522
Var 60h I row2-row1	1.02862	1
Var 60h NI row2-row1	1.11278	0.904
Time course 0hI-0hNI	0.99574	1
Time course 12hI-12hNI	1.0158	0.82
Time course 36hI-36hNI	0.97795	0.468
Time course 60hI-60hNI	0.93973	0.319

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)	1.16256	0.654
transgenic ySAMdc/azygous control (breaker)	2.42998	0.162
transgenic ySAMdc/azygous control (red)	1.09785	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.44032	0.099

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.79626	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	18.9576	0.083
Manapal/WT (break)	6.65868	0.123
Manapal/WT (red)	2.00924	0.413