Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.2.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.68909	0.042
27DAP/17DAP	1.01306	0.973
39DAP/27DAP	1.39132	0.183
41DAP/39DAP	0.96991	0.852
42DAP/41DAP	1.63229	0.219
43DAP/42DAP	0.92421	0.858
47DAP/43DAP	0.67125	0.106
52DAP/47DAP	1.00786	0.964
57DAP/52DAP	1.48252	0.561

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97128	0.526
17DAP/reference	0.80743	0.069
27DAP/reference	0.81133	0.078
39DAP/reference	0.88164	0.206
41DAP/reference	0.74031	0.065
42DAP/reference	1.08672	0.311
43DAP/reference	1.36	0.011
47DAP/reference	1.13056	0.081
52DAP/reference	1.36063	0.023
57DAP/reference	1.17253	0.141

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0739	0.662
27DAP/17DAP	1.30173	0.096
39DAP/27DAP	1.43665	0.062
41DAP/39DAP	0.90593	0.662
42DAP/41DAP	1.27528	0.011
43DAP/42DAP	1.37683	0.018
47DAP/43DAP	0.96999	0.855
52DAP/47DAP	0.9859	0.925
57DAP/52DAP	0.81919	0.082
57DAP/7DAP	1.27815	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08934	0.292
17DAP/reference	1.05031	0.477
27DAP/reference	1.0141	1
39DAP/reference	1.15957	0.141
41DAP/reference	1.22699	0.027
42DAP/reference	1.3864	0.021
43DAP/reference	1.51122	0.032
47DAP/reference	1.51109	0.016
52DAP/reference	1.24446	0.062
57DAP/reference	1.01086	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12558	0.741
17DAP/reference	0.91341	0.253
27DAP/reference	0.97293	0.483
39DAP/reference	0.91743	0.202
41DAP/reference	1.01125	1
42DAP/reference	1.123	0.254
43DAP/reference	1.01359	0.814
47DAP/reference	1.02948	0.916
52DAP/reference	0.81927	0.018
57DAP/reference	0.8752	0.194

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99829	0.699
17DAP/reference	0.89199	0.275
27DAP/reference	1.10493	0.088
39DAP/reference	1.08658	0.245
41DAP/reference	0.99382	0.754
42DAP/reference	1.41608	0.019
43DAP/reference	1.38642	0.01
47DAP/reference	1.03196	0.396
52DAP/reference	1.6611	0.058
57DAP/reference	1.17252	0.214

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02619	1
26DAP/20DAP	1.67602	0.102
34DAP/26DAP	0.98846	0.991
51DAP/34DAP	1.55622	0.036
52DAP/51DAP	0.94074	1
53DAP/52DAP	1.3704	0.882
55DAP/53DAP	1.02124	0.964
57DAP/55DAP	0.9751	0.828
62DAP/57DAP	0.65815	0.466
68DAP/62DAP	1.26643	0.206
68DAP/14DAP	1.84441	0.021

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	6.31395	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.90962	0.471
Mature Green Tomato/Ripe Tomato	0.63011	0.086
Immature Eggplant/Mature Eggplant	1.31278	0.096
Ripe Pepper/Ripe Tomato	0.69697	0.293
Mature Eggplant/Ripe Tomato	0.67372	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01602	1
1-1-2/M82	1.09313	1
12-2/M82	1.14095	1
12-4/M82	1.28367	1
1-3/M82	1.5999	1
2-1-1/M82	0.94648	0.784
2-1/M82	1.13483
2-6/M82	0.98858	1
3-2/M82	1.98238	0.463
4-1-1/M82	0.95308
4-1/M82	1.4878	1
4-3-2/M82	1.76878	0.284
4-3/M82	2.08746	0.268
5-3/M82	0.83075	0.642
6-2/M82	1.86414	0.253
6-3/M82	1.04474	1
7-1/M82	0.98277	1
7-2/M82	1.44496	0.318
9-3-2/M82	1.46482	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.80651	0.383
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.39405	0.362
IL12-4/WTpooled	0.93144	1
IL1-4/WTpooled	0.9526
WT/WTpooled	0.96013	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	1.16877	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.14365	0.758
DC3000/delta hrp 6h	0.92034	0.95
DC3000/delta hrp 12h	1.05559	1
DC3000/delta hrp 24h	2.04497	0.028

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.41971	0.05
DC3000 delta B/DC3000 delta AB	1.74902	0.061

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0733	1
Exp 36h	1.45457	0.489
Exp 60h	1.30564	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95153	1
Var 0h	0.91935	1
Var 12h I row2-row1	1.04042	0.736
Var 12h NI row2-row1	1.57454	0.266
Var 36h I row2-row1	1.10231	1
Var 36h NI row2-row1	0.9175	0.61
Var 60h I row2-row1	0.7072	0.285
Var 60h NI row2-row1	0.88754	0.572
Time course 0hI-0hNI	0.88509	0.188
Time course 12hI-12hNI	1.05898	0.65
Time course 36hI-36hNI	1.88419	0.005
Time course 60hI-60hNI	4.92198	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)	0.94696	0.529
transgenic ySAMdc/azygous control (breaker)	1.42862	0.166
transgenic ySAMdc/azygous control (red)	1.20457	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.13484	0.042

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.52092	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.96285	1
Manapal/WT (break)	0.92085	1
Manapal/WT (red)	0.7186	0.181