Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.4.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8538	0.364
27DAP/17DAP	0.99777	1
39DAP/27DAP	0.81401	0.462
41DAP/39DAP	1.31261	0.423
42DAP/41DAP	1.37279	0.792
43DAP/42DAP	1.18693	0.785
47DAP/43DAP	1.0775	0.979
52DAP/47DAP	1.31116	0.456
57DAP/52DAP	1.04338	0.985

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82135	0.066
17DAP/reference	1.01762	0.606
27DAP/reference	1.01419	0.934
39DAP/reference	1.00735	0.842
41DAP/reference	1.03156	0.963
42DAP/reference	0.84506	0.005
43DAP/reference	0.99041	0.805
47DAP/reference	0.91563	0.083
52DAP/reference	0.82749	0.121
57DAP/reference	0.88687	0.101

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.76812	0.068
27DAP/17DAP	1.06379	0.761
39DAP/27DAP	0.9331	0.394
41DAP/39DAP	0.99482	1
42DAP/41DAP	1.00152	0.932
43DAP/42DAP	1.12964	0.176
47DAP/43DAP	1.06746	0.765
52DAP/47DAP	0.99043	0.93
57DAP/52DAP	1.02623	0.838
57DAP/7DAP	1.00812	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98698	0.613
17DAP/reference	0.91018	0.017
27DAP/reference	0.95865	0.325
39DAP/reference	0.98747	0.64
41DAP/reference	0.87106	0.082
42DAP/reference	0.98542	0.612
43DAP/reference	0.85509	0.105
47DAP/reference	0.88431	0.079
52DAP/reference	0.95195	0.332
57DAP/reference	0.9843	0.477

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05294	0.384
17DAP/reference	0.82961	0.046
27DAP/reference	0.92071	0.304
39DAP/reference	0.92156	0.314
41DAP/reference	0.80759	0.177
42DAP/reference	0.87108	0.189
43DAP/reference	0.94424	0.438
47DAP/reference	0.97441	0.473
52DAP/reference	0.90526	0.327
57DAP/reference	0.9597	0.519

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00507	1
17DAP/reference	0.88052	0.205
27DAP/reference	0.8057	0.036
39DAP/reference	0.87618	0.133
41DAP/reference	0.97233	0.56
42DAP/reference	0.77996	0.071
43DAP/reference	0.79258	0.088
47DAP/reference	0.94651	0.215
52DAP/reference	0.79	0.125
57DAP/reference	0.71276	0.067

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99196	1
26DAP/20DAP	1.08226	0.813
34DAP/26DAP	0.83964	0.399
51DAP/34DAP	0.98912	0.883
52DAP/51DAP	1.07544	0.742
53DAP/52DAP	1.09635	0.882
55DAP/53DAP	1.15234	0.131
57DAP/55DAP	1.01436	1
62DAP/57DAP	1.401	0.767
68DAP/62DAP	1.32826	0.549
68DAP/14DAP	1.19638	0.915

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.2596	0.184

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.21391
Mature Green Tomato/Ripe Tomato	1.05673	0.715
Immature Eggplant/Mature Eggplant	1.29824	0.061
Ripe Pepper/Ripe Tomato	0.9903	1
Mature Eggplant/Ripe Tomato	0.98872	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.18946	0.536
1-1-2/M82	0.82775	1
12-2/M82	0.85422
12-4/M82	1.01376	1
1-3/M82	0.59652
2-1-1/M82	1.11777
2-1/M82	N/A	N/A
2-6/M82	1.04021
3-2/M82	1.01834
4-1-1/M82	0.76841
4-1/M82	0.72315	0.737
4-3-2/M82	0.96911
4-3/M82	1.32047	0.268
5-3/M82	0.93231	0.447
6-2/M82	N/A	N/A
6-3/M82	0.94728	1
7-1/M82	1.20124
7-2/M82	1.02013	1
9-3-2/M82	1.05112	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.66242
IL2-6/WTpooled	1.35068	0.659
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.90308	1
IL1-4/WTpooled	0.77709
WT/WTpooled	0.91695	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	0.95901	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94705	1
DC3000/delta hrp 6h	1.08565	1
DC3000/delta hrp 12h	0.89784	1
DC3000/delta hrp 24h	0.99044	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.83528
DC3000 delta B/DC3000 delta AB	0.98916	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.81921	1
Exp 36h	1.14971	1
Exp 60h	1.07481	1

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	1.10643	0.421
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.06915	0.297
transgenic ySAMdc/azygous control (breaker)	1.07607	0.248
transgenic ySAMdc/azygous control (red)	0.92738	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00266	0.854

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.08417	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.08103	0.307
Manapal/WT (break)	0.99953	1
Manapal/WT (red)	0.84101	0.183