Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.11.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88754	0.456
27DAP/17DAP	1.21107	0.839
39DAP/27DAP	1.47923	0.476
41DAP/39DAP	1.66052	0.331
42DAP/41DAP	1.11566	0.941
43DAP/42DAP	0.97385	0.912
47DAP/43DAP	1.59352	0.235
52DAP/47DAP	1.12971	0.976
57DAP/52DAP	1.1189	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95399	0.455
17DAP/reference	1.19122	0.014
27DAP/reference	1.05755	0.623
39DAP/reference	1.08296	0.086
41DAP/reference	1.2075	0.015
42DAP/reference	0.86944	0.011
43DAP/reference	1.01355	1
47DAP/reference	0.93757	0.207
52DAP/reference	0.79351	0.091
57DAP/reference	0.75997	0.042

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86752	0.135
27DAP/17DAP	0.96124	0.878
39DAP/27DAP	1.44845	0.046
41DAP/39DAP	0.81009	0.015
42DAP/41DAP	0.90663	0.37
43DAP/42DAP	1.18351	0.25
47DAP/43DAP	1.08305	0.812
52DAP/47DAP	1.42422	0.183
57DAP/52DAP	1.24678	0.376
57DAP/7DAP	1.59304	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94762	0.27
17DAP/reference	1.2	0.07
27DAP/reference	1.02934	0.664
39DAP/reference	0.86998	0.109
41DAP/reference	0.94161	0.311
42DAP/reference	0.87482	0.117
43DAP/reference	1.1173	0.157
47DAP/reference	1.01793	1
52DAP/reference	0.85228	0.033
57DAP/reference	0.89451	0.083

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1888	0.315
17DAP/reference	0.99226	0.673
27DAP/reference	0.8293	0.108
39DAP/reference	0.79124	0.102
41DAP/reference	0.82853	0.089
42DAP/reference	0.822	0.108
43DAP/reference	1.15589	0.259
47DAP/reference	0.98129	0.527
52DAP/reference	0.93518	0.22
57DAP/reference	1.1757	0.135

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95512	0.29
17DAP/reference	0.99362	0.763
27DAP/reference	1.3353	0.023
39DAP/reference	1.2313	0.035
41DAP/reference	1.0154	1
42DAP/reference	0.91948	0.445
43DAP/reference	0.84673	0.171
47DAP/reference	1.01427	0.708
52DAP/reference	1.56928	0.172
57DAP/reference	0.62726	0.037

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97331	1
26DAP/20DAP	0.84999	0.228
34DAP/26DAP	1.10352	0.819
51DAP/34DAP	1.37491	0.081
52DAP/51DAP	1.07519	0.77
53DAP/52DAP	1.26836	0.552
55DAP/53DAP	1.11201	0.547
57DAP/55DAP	0.99657	0.875
62DAP/57DAP	1.0657	0.767
68DAP/62DAP	0.92347	0.722
68DAP/14DAP	0.77348	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.69353	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.43746	0.036
Immature Eggplant/Mature Eggplant	4.12685	0.05
Ripe Pepper/Ripe Tomato	0.14092	0.224
Mature Eggplant/Ripe Tomato	0.13054	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.49085	0.591
1-1-2/M82	1.27305	1
12-2/M82	0.97764	1
12-4/M82	1.36902	1
1-3/M82	1.09605
2-1-1/M82	1.2171	0.764
2-1/M82	1.82849
2-6/M82	0.6994	0.382
3-2/M82	1.57407	0.463
4-1-1/M82	0.82097	1
4-1/M82	1.50367
4-3-2/M82	0.69533	0.37
4-3/M82	1.47894	1
5-3/M82	1.1906	1
6-2/M82	0.89713	1
6-3/M82	0.90464	1
7-1/M82	0.84414
7-2/M82	0.89771	0.519
9-3-2/M82	0.79128	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.39048	0.277
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.3561	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.11101	1
WT/WTpooled	1.70942	0.999

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	0.98365	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99608	1
DC3000/delta hrp 6h	1.12259	1
DC3000/delta hrp 12h	1.1427	1
DC3000/delta hrp 24h	1.10048	0.422

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	1.67927

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.75917	0.693
Exp 60h	1.43177	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02868	1
Var 0h	0.51797	1
Var 12h I row2-row1	1.08069	0.473
Var 12h NI row2-row1	1.00289	1
Var 36h I row2-row1	0.979	1
Var 36h NI row2-row1	0.46948
Var 60h I row2-row1	0.84432
Var 60h NI row2-row1	1.08108	1
Time course 0hI-0hNI	1.06169	0.662
Time course 12hI-12hNI	1.146	0.373
Time course 36hI-36hNI	1.20114	0.015
Time course 60hI-60hNI	2.07795	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)	0.72126	0.246
transgenic ySAMdc/azygous control (breaker)	0.8394	0.49
transgenic ySAMdc/azygous control (red)	1.15776	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02488	0.334

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.1689	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.60215	1
Manapal/WT (break)	0.82511	0.333
Manapal/WT (red)	1.13446	0.164