Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.3.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94745	0.689
27DAP/17DAP	1.18153	0.833
39DAP/27DAP	0.84994	0.512
41DAP/39DAP	1.23309	0.426
42DAP/41DAP	0.89493	1
43DAP/42DAP	0.99743	0.937
47DAP/43DAP	1.15827	0.455
52DAP/47DAP	0.89944	0.688
57DAP/52DAP	0.99239	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11765	0.544
17DAP/reference	0.93166	0.567
27DAP/reference	1.04995	0.435
39DAP/reference	0.96809	0.75
41DAP/reference	1.08257	0.552
42DAP/reference	0.94496	0.287
43DAP/reference	0.62339	0.163
47DAP/reference	0.98244	0.568
52DAP/reference	1.03563	0.73
57DAP/reference	0.83025

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94939	0.277
27DAP/17DAP	1.04737	0.78
39DAP/27DAP	1.0298	0.654
41DAP/39DAP	1.05617	0.79
42DAP/41DAP	0.99054	0.865
43DAP/42DAP	1.06754	0.134
47DAP/43DAP	0.98263	0.857
52DAP/47DAP	1.0479	0.8
57DAP/52DAP	0.91379	0.39
57DAP/7DAP	0.98944	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16263	0.17
17DAP/reference	1.15891	0.092
27DAP/reference	0.93125	0.283
39DAP/reference	1.49957	0.016
41DAP/reference	1.26325	0.136
42DAP/reference	1.30859	0.021
43DAP/reference	1.13428	0.2
47DAP/reference	1.00929	1
52DAP/reference	1.03812	0.732
57DAP/reference	1.18649	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06288	0.524
17DAP/reference	0.88052	0.08
27DAP/reference	1.07726	0.576
39DAP/reference	0.92742	0.348
41DAP/reference	0.88963	0.212
42DAP/reference	1.03734	0.863
43DAP/reference	1.12018	0.466
47DAP/reference	1.04967	0.332
52DAP/reference	0.97774	0.407
57DAP/reference	1.01437	0.724

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.88278	0.025
17DAP/reference	0.94073	0.381
27DAP/reference	1.21273	0.033
39DAP/reference	1.07245	0.235
41DAP/reference	0.95782	0.417
42DAP/reference	4.73469	0.017
43DAP/reference	1.95618	0.375
47DAP/reference	1.07312	0.443
52DAP/reference	3.06912	0.094
57DAP/reference	1.29348	1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02077	0.966
26DAP/20DAP	0.97325	1
34DAP/26DAP	1.01811	1
51DAP/34DAP	1.06199	0.458
52DAP/51DAP	0.93914	1
53DAP/52DAP	0.95604	0.776
55DAP/53DAP	1.00816	0.951
57DAP/55DAP	1.21322	0.682
62DAP/57DAP	0.84902	0.088
68DAP/62DAP	0.96318	0.7
68DAP/14DAP	1.0705	0.785

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.97011	0.443

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.05565	0.666
Mature Green Tomato/Ripe Tomato	0.97039	0.66
Immature Eggplant/Mature Eggplant	1.02038	0.58
Ripe Pepper/Ripe Tomato	1.29649	1
Mature Eggplant/Ripe Tomato	1.33411	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97607	0.961
1-1-2/M82	0.9551	0.958
12-2/M82	0.94223	0.955
12-4/M82	0.95006	1
1-3/M82	0.99422	1
2-1-1/M82	0.96571	0.465
2-1/M82	1.57954
2-6/M82	0.99285	1
3-2/M82	0.93848
4-1-1/M82	1.09286	1
4-1/M82	0.91461	0.665
4-3-2/M82	0.92061	1
4-3/M82	0.93299	0.72
5-3/M82	1.0031	1
6-2/M82	1.32297	1
6-3/M82	1.0139	1
7-1/M82	1.15411
7-2/M82	1.03949	0.318
9-3-2/M82	0.86688	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.21477	1
IL2-6/WTpooled	0.98523	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.10698	1
IL12-4/WTpooled	1.22482	0.737
IL1-4/WTpooled	0.99654	1
WT/WTpooled	0.97398	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	1.01496	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99761	1
DC3000/delta hrp 6h	0.95764	0.95
DC3000/delta hrp 12h	0.99803	1
DC3000/delta hrp 24h	1.09224	0.356

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.93756	0.46
DC3000 delta B/DC3000 delta AB	1.07996	0.415

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98961	1
Exp 36h	0.88969	0.749
Exp 60h	1.07955	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96175	1
Var 0h	0.58581	1
Var 12h I row2-row1	0.89394	0.705
Var 12h NI row2-row1	0.91346	0.713
Var 36h I row2-row1	1.0938	0.908
Var 36h NI row2-row1	1.31375	1
Var 60h I row2-row1	0.98397	0.374
Var 60h NI row2-row1	0.99948	1
Time course 0hI-0hNI	0.99412	1
Time course 12hI-12hNI	0.96007	0.716
Time course 36hI-36hNI	1.005	0.857
Time course 60hI-60hNI	0.60385	0.007

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)	0.96029	0.391
transgenic ySAMdc/azygous control (breaker)	1.35225	0.248
transgenic ySAMdc/azygous control (red)	1.37636	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00196	0.854

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.96459	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.758	1
Manapal/WT (break)	0.91699	1
Manapal/WT (red)	0.91709	0.36