Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.20.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19707	0.63
27DAP/17DAP	1.00178	0.994
39DAP/27DAP	0.85723	0.564
41DAP/39DAP	1.33053	0.516
42DAP/41DAP	0.93734	1
43DAP/42DAP	0.86828	0.775
47DAP/43DAP	1.18511	0.647
52DAP/47DAP	0.90897	0.712
57DAP/52DAP	1.2127	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19435	0.065
17DAP/reference	1.05971	0.248
27DAP/reference	1.00674	0.953
39DAP/reference	0.98063	0.554
41DAP/reference	1.05195	0.421
42DAP/reference	1.05852	0.089
43DAP/reference	1.0018	1
47DAP/reference	1.05935	0.11
52DAP/reference	1.12005	0.186
57DAP/reference	1.00623	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06206	1
27DAP/17DAP	0.99548	0.943
39DAP/27DAP	1.07064	0.685
41DAP/39DAP	1.09129	0.861
42DAP/41DAP	1.07002	0.783
43DAP/42DAP	0.99307	0.991
47DAP/43DAP	1.02004	0.857
52DAP/47DAP	0.94169	0.797
57DAP/52DAP	0.98444	0.789
57DAP/7DAP	0.8491	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.53333	0.065
17DAP/reference	1.67893	0.007
27DAP/reference	1.34082	0.301
39DAP/reference	1.79141	0.006
41DAP/reference	1.40824	0.02
42DAP/reference	1.50871	0.059
43DAP/reference	1.94031	0.007
47DAP/reference	1.29184	0.161
52DAP/reference	1.60051	0.008
57DAP/reference	1.75253	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04258	0.308
17DAP/reference	1.11374	0.074
27DAP/reference	1.03808	0.648
39DAP/reference	0.9989	0.702
41DAP/reference	1.03827	0.831
42DAP/reference	1.02275	1
43DAP/reference	0.88123	0.229
47DAP/reference	1.01703	0.89
52DAP/reference	1.0953	0.156
57DAP/reference	0.99699	0.834

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.38331	0.045
17DAP/reference	1.15797	0.306
27DAP/reference	1.8424	0.02
39DAP/reference	1.5399	0.018
41DAP/reference	1.61211	0.038
42DAP/reference	1.26442	0.138
43DAP/reference	1.25654	0.168
47DAP/reference	0.92904	0.153
52DAP/reference	1.78464	0.108
57DAP/reference	1.06975	0.842

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98985	1
26DAP/20DAP	0.90029	0.512
34DAP/26DAP	0.96789	0.944
51DAP/34DAP	1.04074	0.775
52DAP/51DAP	1.19423	0.089
53DAP/52DAP	1.33538	0.221
55DAP/53DAP	1.05412	0.79
57DAP/55DAP	1.54075	0.841
62DAP/57DAP	1.28411	0.723
68DAP/62DAP	0.95324	0.747
68DAP/14DAP	0.98867	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.88868	0.285

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.35509	0.058
Mature Green Tomato/Ripe Tomato	0.48659	0.017
Immature Eggplant/Mature Eggplant	0.66784	0.074
Ripe Pepper/Ripe Tomato	1.05053	1
Mature Eggplant/Ripe Tomato	4.99713

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.10487	0.877
1-1-2/M82	0.98963	1
12-2/M82	1.11294	1
12-4/M82	1.05149	1
1-3/M82	0.83649	0.378
2-1-1/M82	1.14179	0.689
2-1/M82	1.20037	0.335
2-6/M82	1.0533	1
3-2/M82	1.10192
4-1-1/M82	0.91939	1
4-1/M82	0.87863
4-3-2/M82	0.68785
4-3/M82	1.1126	1
5-3/M82	0.89805	0.642
6-2/M82	1.06395	1
6-3/M82	1.06637	1
7-1/M82	1.00929	1
7-2/M82	1.15271	0.324
9-3-2/M82	1.07815

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	N/A	N/A
IL7-3/WTpooled	1.10518
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	1.54497	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07295	0.894
DC3000/delta hrp 6h	1.22689	1
DC3000/delta hrp 12h	1.02195	1
DC3000/delta hrp 24h	1.05435	0.553

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.25587	0.313
DC3000 delta B/DC3000 delta AB	1.07291	0.403

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.86395	1
Exp 36h	0.88138	0.699
Exp 60h	0.82049	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9513	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.09555	0.296
Var 12h NI row2-row1	0.80222	0.82
Var 36h I row2-row1	0.93662	1
Var 36h NI row2-row1	1.1693	1
Var 60h I row2-row1	1.05957	1
Var 60h NI row2-row1	1.43839	0.904
Time course 0hI-0hNI	1.16386	0.852
Time course 12hI-12hNI	1.02429	1
Time course 36hI-36hNI	0.91281	0.323
Time course 60hI-60hNI	1.25959	0.137

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)	0.90772	0.362
transgenic ySAMdc/azygous control (breaker)	0.73375	0.131
transgenic ySAMdc/azygous control (red)	0.96283	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9687	0.07

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.63377	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.33025	0.14
Manapal/WT (break)	1.01813	1
Manapal/WT (red)	1.28826	1