Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.14.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9716	0.779
27DAP/17DAP	0.70344	0.252
39DAP/27DAP	1.06784	1
41DAP/39DAP	1.06884	0.806
42DAP/41DAP	0.87577	1
43DAP/42DAP	1.31223	0.954
47DAP/43DAP	0.90621	0.671
52DAP/47DAP	1.2728	0.758
57DAP/52DAP	0.83789	0.85

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93786	0.336
17DAP/reference	1.02763	0.631
27DAP/reference	0.95923	0.514
39DAP/reference	0.89963	0.174
41DAP/reference	0.87114	0.065
42DAP/reference	0.89065	0.013
43DAP/reference	0.96196	0.394
47DAP/reference	0.98244	0.473
52DAP/reference	1.09247	0.141
57DAP/reference	1.00452	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94208	0.56
27DAP/17DAP	1.14045	0.694
39DAP/27DAP	0.93128	0.54
41DAP/39DAP	1.37835	0.197
42DAP/41DAP	0.8995	0.42
43DAP/42DAP	0.89216	0.383
47DAP/43DAP	1.17014	0.339
52DAP/47DAP	0.89537	0.433
57DAP/52DAP	1.0338	0.941
57DAP/7DAP	0.62896

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83044	0.104
17DAP/reference	1.03444	0.754
27DAP/reference	1.1897	0.301
39DAP/reference	0.95705	0.411
41DAP/reference	1.00535	1
42DAP/reference	1.04839	1
43DAP/reference	0.97324	0.48
47DAP/reference	0.95328	0.383
52DAP/reference	0.85053	0.09
57DAP/reference	0.91275	0.24

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06703	0.732
17DAP/reference	0.92912	0.307
27DAP/reference	0.98335	0.554
39DAP/reference	1.06849	0.725
41DAP/reference	0.97807	0.459
42DAP/reference	0.85509	0.01
43DAP/reference	1.0989	0.582
47DAP/reference	0.87096	0.044
52DAP/reference	0.96905	0.469
57DAP/reference	1.00918	0.98

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08315	0.505
17DAP/reference	0.97688	0.658
27DAP/reference	0.92895	0.076
39DAP/reference	1.01824	0.792
41DAP/reference	0.98509	0.682
42DAP/reference	0.98119	0.671
43DAP/reference	0.83506	0.098
47DAP/reference	0.9204	0.249
52DAP/reference	1.22009	0.443
57DAP/reference	0.98304	0.602

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09367	1
26DAP/20DAP	1.23241	0.524
34DAP/26DAP	0.88799	0.795
51DAP/34DAP	0.86237	0.109
52DAP/51DAP	1.26197	0.467
53DAP/52DAP	0.83158	0.207
55DAP/53DAP	1.27231	0.938
57DAP/55DAP	0.90752	0.731
62DAP/57DAP	1.1342	0.257
68DAP/62DAP	0.92742	0.747
68DAP/14DAP	1.65023	0.211

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.73293	0.043

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.72715
Mature Green Tomato/Ripe Tomato	0.76359
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.46402
Mature Eggplant/Ripe Tomato	0.87961	1

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	0.99128
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	N/A	N/A
4-3-2/M82	N/A	N/A
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	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.45474	0.277
IL2-6/WTpooled	0.58204	0.348
IL7-5/WTpooled	1.21616	0.792
IL7-3/WTpooled	1.52003	1
IL12-4/WTpooled	1.14909	0.646
IL1-4/WTpooled	0.95469	1
WT/WTpooled	1.07834	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	0.99576	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08275	0.921
DC3000/delta hrp 6h	0.90109	0.95
DC3000/delta hrp 12h	1.01718	1
DC3000/delta hrp 24h	1.44876	0.085

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.08798
DC3000 delta B/DC3000 delta AB	1.12065	0.528

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.13972	1
Exp 36h	1.45285	0.693
Exp 60h	1.26174	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	1.11335	1
Var 0h	1.88963	0.936
Var 12h I row2-row1	1.08381	0.406
Var 12h NI row2-row1	1.33657	0.649
Var 36h I row2-row1	0.97329	1
Var 36h NI row2-row1	0.8959	0.706
Var 60h I row2-row1	0.72528	0.374
Var 60h NI row2-row1	0.8836	0.69
Time course 0hI-0hNI	1.08495	0.662
Time course 12hI-12hNI	1.36788	0.006
Time course 36hI-36hNI	2.10438	0.004
Time course 60hI-60hNI	2.00816	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)	1.03117	0.748
transgenic ySAMdc/azygous control (breaker)	0.52903	0.119
transgenic ySAMdc/azygous control (red)	0.93442	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01103	0.656

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.71985	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.7904	0.172
Manapal/WT (break)	0.97693	1
Manapal/WT (red)	0.78991	0.181