Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.2.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.45039	0.403
27DAP/17DAP	1.04146	0.92
39DAP/27DAP	1.57061	0.114
41DAP/39DAP	0.85766	0.455
42DAP/41DAP	1.42819	0.458
43DAP/42DAP	1.57001	0.724
47DAP/43DAP	0.57842	0.074
52DAP/47DAP	0.72402	0.241
57DAP/52DAP	0.90481	0.882

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75788	0.047
17DAP/reference	1.00122	0.957
27DAP/reference	1.10847	0.291
39DAP/reference	1.02776	1
41DAP/reference	1.09756	0.48
42DAP/reference	1.55009	0.001
43DAP/reference	1.26571	0.008
47DAP/reference	1.10722	0.114
52DAP/reference	0.73077	0.014
57DAP/reference	0.85897	0.054

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.08955	0.036
27DAP/17DAP	0.79967	0.121
39DAP/27DAP	1.06771	0.611
41DAP/39DAP	1.00786	1
42DAP/41DAP	0.9734	0.746
43DAP/42DAP	2.05941	0.013
47DAP/43DAP	1.06861	0.805
52DAP/47DAP	0.80447	0.192
57DAP/52DAP	0.70789	0.185
57DAP/7DAP	2.19808	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94376	0.402
17DAP/reference	0.79185	0.22
27DAP/reference	1.10593	0.804
39DAP/reference	1.25444	0.096
41DAP/reference	1.21713	0.141
42DAP/reference	1.40966	0.016
43DAP/reference	1.31349	0.226
47DAP/reference	2.4354	0.042
52DAP/reference	1.08949	0.139
57DAP/reference	1.24717	0.654

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.70158	0.011
17DAP/reference	1.08315	0.723
27DAP/reference	1.07653	0.847
39DAP/reference	1.46561	0.016
41DAP/reference	1.1029	0.491
42DAP/reference	1.5317	0.008
43DAP/reference	1.04136	0.681
47DAP/reference	1.62107	0.008
52DAP/reference	1.03301	0.596
57DAP/reference	1.0897	0.887

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24502	0.444
17DAP/reference	1.19627	0.563
27DAP/reference	1.19168	0.105
39DAP/reference	1.056	0.733
41DAP/reference	1.63561	0.054
42DAP/reference	2.05619	0.082
43DAP/reference	2.4156	0.079
47DAP/reference	1.47482	0.021
52DAP/reference	1.17504	0.928
57DAP/reference	1.6841	0.023

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99433	1
26DAP/20DAP	1.79837	0.099
34DAP/26DAP	1.07297	0.819
51DAP/34DAP	0.82127	0.119
52DAP/51DAP	0.86615	0.151
53DAP/52DAP	1.17393	0.25
55DAP/53DAP	0.81183	0.058
57DAP/55DAP	0.7327	0.066
62DAP/57DAP	0.77585	0.028
68DAP/62DAP	0.93937	0.769
68DAP/14DAP	0.83651	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.22036	0.172

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.99993	0.863
Mature Green Tomato/Ripe Tomato	1.91456	0.016
Immature Eggplant/Mature Eggplant	0.91813	0.448
Ripe Pepper/Ripe Tomato	2.33857	0.258
Mature Eggplant/Ripe Tomato	3.30992	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.93922
1-1-2/M82	2.22457
12-2/M82	1.07606
12-4/M82	1.34028	1
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	0.86606
3-2/M82	1.19524	0.717
4-1-1/M82	N/A	N/A
4-1/M82	0.87542
4-3-2/M82	1.89893	0.508
4-3/M82	1.24251
5-3/M82	0.92742	0.642
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.02657	1
7-2/M82	0.76902
9-3-2/M82	1.3589	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.91005	0.321
IL2-6/WTpooled	1.19086	0.659
IL7-5/WTpooled	0.72577	1
IL7-3/WTpooled	1.06117	1
IL12-4/WTpooled	0.8947	0.71
IL1-4/WTpooled	1.0377	1
WT/WTpooled	1.0693	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	0.96241	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00383	1
DC3000/delta hrp 6h	1.08295	1
DC3000/delta hrp 12h	1.15564	1
DC3000/delta hrp 24h	0.87339	0.17

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.08467	0.384
DC3000 delta B/DC3000 delta AB	1.08889	0.353

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.23918	1
Exp 36h	1.03097	1
Exp 60h	1.08366	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00551	1
Var 0h	1.05461	1
Var 12h I row2-row1	0.90698	0.39
Var 12h NI row2-row1	1.04792	1
Var 36h I row2-row1	1.19996	0.309
Var 36h NI row2-row1	1.01185	1
Var 60h I row2-row1	0.73529	0.832
Var 60h NI row2-row1	0.98587	1
Time course 0hI-0hNI	1.05945	0.833
Time course 12hI-12hNI	0.96321	0.776
Time course 36hI-36hNI	0.9431	0.317
Time course 60hI-60hNI	1.02002	1

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)	0.83698	0.362
transgenic ySAMdc/azygous control (breaker)	0.29564	0.119
transgenic ySAMdc/azygous control (red)	1.05101	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.21758	0.08

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.07499	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.19812	0.14
Manapal/WT (break)	0.91544	1
Manapal/WT (red)	1.27421	1