Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.15.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88514	0.475
27DAP/17DAP	1.27155	0.799
39DAP/27DAP	2.91615	0.101
41DAP/39DAP	1.32374	0.742
42DAP/41DAP	0.784	0.397
43DAP/42DAP	0.72891	0.566
47DAP/43DAP	1.45886	0.459
52DAP/47DAP	0.98568	0.865
57DAP/52DAP	0.99049	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94308	0.362
17DAP/reference	0.77081	0.011
27DAP/reference	0.95059	0.497
39DAP/reference	0.79926	0.033
41DAP/reference	0.70049	0.008
42DAP/reference	0.93577	0.129
43DAP/reference	0.90488	0.061
47DAP/reference	0.95518	0.279
52DAP/reference	1.1924	0.32
57DAP/reference	1.40563	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.53882	0.047
27DAP/17DAP	1.48801	0.258
39DAP/27DAP	1.40649	0.174
41DAP/39DAP	1.508	0.065
42DAP/41DAP	1.02496	1
43DAP/42DAP	0.85736	0.189
47DAP/43DAP	1.23751	0.092
52DAP/47DAP	0.72733	0.093
57DAP/52DAP	1.04276	0.951
57DAP/7DAP	0.57918

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.66452	0.035
17DAP/reference	1.75271	0.006
27DAP/reference	1.7995	0.006
39DAP/reference	2.02486	0.005
41DAP/reference	1.71759	0.014
42DAP/reference	1.99863	0.007
43DAP/reference	2.02763	0.006
47DAP/reference	1.7684	0.037
52DAP/reference	1.89487	0.007
57DAP/reference	1.82743	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95361	0.487
17DAP/reference	0.74205	0.006
27DAP/reference	0.91051	0.22
39DAP/reference	1.05421	0.502
41DAP/reference	0.94093	0.322
42DAP/reference	0.83263	0.035
43DAP/reference	0.74441	0.013
47DAP/reference	0.89351	0.033
52DAP/reference	0.89031	0.016
57DAP/reference	0.7856	0.03

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.64026	0.026
17DAP/reference	1.02085	1
27DAP/reference	1.5877	0.041
39DAP/reference	1.60811	0.018
41DAP/reference	1.49982	0.025
42DAP/reference	1.52587	0.018
43DAP/reference	1.26562	0.426
47DAP/reference	0.89524	0.109
52DAP/reference	1.56201	0.132
57DAP/reference	1.62346	0.051

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03678	1
26DAP/20DAP	1.68528	0.099
34DAP/26DAP	0.95265	0.92
51DAP/34DAP	0.95797	0.737
52DAP/51DAP	0.88527	1
53DAP/52DAP	0.83881	0.301
55DAP/53DAP	1.02125	1
57DAP/55DAP	0.95312	0.823
62DAP/57DAP	1.10709	0.935
68DAP/62DAP	1.49694	0.151
68DAP/14DAP	1.86177	0.03

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.89403	0.016

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.50741	0.112
Mature Green Tomato/Ripe Tomato	0.47298	0.017
Immature Eggplant/Mature Eggplant	1.79778	0.05
Ripe Pepper/Ripe Tomato	1.00093	1
Mature Eggplant/Ripe Tomato	0.54259	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.81714	0.605
1-1-2/M82	1.13713	1
12-2/M82	0.87754	0.955
12-4/M82	1.09485	1
1-3/M82	1.65922	0.248
2-1-1/M82	1.00343	1
2-1/M82	0.97103	1
2-6/M82	1.05801
3-2/M82	1.08497
4-1-1/M82	1.03637	1
4-1/M82	0.62458
4-3-2/M82	1.33163	0.508
4-3/M82	0.80798	0.72
5-3/M82	1.23082	0.572
6-2/M82	N/A	N/A
6-3/M82	0.83654	0.982
7-1/M82	0.80088	1
7-2/M82	1.02947	1
9-3-2/M82	1.656

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.80945
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.59438
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.77089	0.834
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	1.39216	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09303	0.914
DC3000/delta hrp 6h	0.89171	0.95
DC3000/delta hrp 12h	0.97924	1
DC3000/delta hrp 24h	5.31841	0.027

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.75875	0.043
DC3000 delta B/DC3000 delta AB	1.43209	0.146

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07348	1
Exp 36h	1.4533	0.489
Exp 60h	1.14167	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01409	1
Var 0h	0.91501	1
Var 12h I row2-row1	1.19838	0.379
Var 12h NI row2-row1	1.08004	0.649
Var 36h I row2-row1	1.19411	0.298
Var 36h NI row2-row1	0.50692	0.61
Var 60h I row2-row1	0.8035	0.374
Var 60h NI row2-row1	0.73752	0.431
Time course 0hI-0hNI	1.10665	0.852
Time course 12hI-12hNI	2.11158	0.005
Time course 36hI-36hNI	3.18536	0.004
Time course 60hI-60hNI	12.2523	0.008

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)	0.95466	0.485
transgenic ySAMdc/azygous control (breaker)	1.00755	1
transgenic ySAMdc/azygous control (red)	0.94962	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08701	0.066

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95415	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.93833	1
Manapal/WT (break)	0.97276	1
Manapal/WT (red)	0.79987	0.274