Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.19.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87994	0.278
27DAP/17DAP	0.84754	0.622
39DAP/27DAP	1.05878	1
41DAP/39DAP	0.78273	0.322
42DAP/41DAP	1.09584	0.92
43DAP/42DAP	1.03281	1
47DAP/43DAP	0.85595	0.522
52DAP/47DAP	1.06877	0.963
57DAP/52DAP	1.99168	0.758

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96123	0.589
17DAP/reference	0.96416	0.664
27DAP/reference	1.15413	0.771
39DAP/reference	1.13889	0.593
41DAP/reference	1.5685	0.203
42DAP/reference	0.95131	0.305
43DAP/reference	0.95258
47DAP/reference	1.07992	0.91
52DAP/reference	1.33649	0.302
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03623	0.947
27DAP/17DAP	1.07301	0.867
39DAP/27DAP	0.78349	0.066
41DAP/39DAP	1.18052	0.817
42DAP/41DAP	0.92229	0.511
43DAP/42DAP	0.97244	0.801
47DAP/43DAP	0.98194	0.911
52DAP/47DAP	0.87258	0.677
57DAP/52DAP	1.12443	0.632
57DAP/7DAP	0.93751	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08502	1
17DAP/reference	0.96993	0.447
27DAP/reference	0.90912	0.2
39DAP/reference	1.18667	0.511
41DAP/reference	1.10153	0.891
42DAP/reference	1.05656	1
43DAP/reference	0.91745	0.21
47DAP/reference	0.91538	0.504
52DAP/reference	0.87201	0.196
57DAP/reference	0.81598	0.057

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97122	0.77
17DAP/reference	1.28258	0.223
27DAP/reference	1.31358	0.082
39DAP/reference	1.03658	0.682
41DAP/reference	1.17863	0.406
42DAP/reference	1.21565	0.247
43DAP/reference	1.05964	0.817
47DAP/reference	1.03732	0.916
52DAP/reference	0.88846	0.171
57DAP/reference	0.88025	0.073

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00982	0.75
17DAP/reference	0.92598	0.499
27DAP/reference	0.86155	0.126
39DAP/reference	0.92272	0.199
41DAP/reference	1.09265	0.57
42DAP/reference	1.1786	0.5
43DAP/reference	1.12118	0.625
47DAP/reference	1.10866	0.48
52DAP/reference	0.92189	0.482
57DAP/reference	1.1445	0.371

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99211	1
26DAP/20DAP	1.05684	0.793
34DAP/26DAP	0.95085	0.917
51DAP/34DAP	1.02382	0.978
52DAP/51DAP	0.84611	1
53DAP/52DAP	1.15102	0.343
55DAP/53DAP	0.8915	0.389
57DAP/55DAP	1.41581	0.195
62DAP/57DAP	0.88124	0.466
68DAP/62DAP	0.83151	0.668
68DAP/14DAP	0.87767	0.063

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.79145	0.108

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.14918	0.113
Mature Green Tomato/Ripe Tomato	1.58638	0.034
Immature Eggplant/Mature Eggplant	1.26363	0.05
Ripe Pepper/Ripe Tomato	1.09386	1
Mature Eggplant/Ripe Tomato	1.56471	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.01681	1
12-2/M82	0.84955
12-4/M82	0.91223	0.33
1-3/M82	1.42584
2-1-1/M82	0.76262
2-1/M82	1.11107
2-6/M82	1.15314
3-2/M82	N/A	N/A
4-1-1/M82	1.55476
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.08548	1
5-3/M82	0.99366	1
6-2/M82	1.36573
6-3/M82	0.83315	0.916
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	1.0032	1
IL2-6/WTpooled	1.06528	1
IL7-5/WTpooled	1.34797	0.792
IL7-3/WTpooled	0.79444	0.418
IL12-4/WTpooled	0.99686	1
IL1-4/WTpooled	0.83622	0.415
WT/WTpooled	1.05311	0.911

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	0.98696	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0323	1
DC3000/delta hrp 6h	1.41698
DC3000/delta hrp 12h	0.82917	1
DC3000/delta hrp 24h	1.09113	0.467

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.66678	0.023
DC3000 delta B/DC3000 delta AB	0.70664	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02925	1
Exp 36h	1.02404	1
Exp 60h	1.29704	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.10529	1
Var 0h	0.95898	1
Var 12h I row2-row1	0.77753	0.338
Var 12h NI row2-row1	0.88551	0.546
Var 36h I row2-row1	1.08912	0.41
Var 36h NI row2-row1	1.03616	1
Var 60h I row2-row1	0.91403	0.582
Var 60h NI row2-row1	1.00269	1
Time course 0hI-0hNI	1.16612	0.574
Time course 12hI-12hNI	0.95082	0.698
Time course 36hI-36hNI	0.81359	0.026
Time course 60hI-60hNI	0.39523	0.005

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)	1.00673	0.931
transgenic ySAMdc/azygous control (breaker)	0.88605	0.49
transgenic ySAMdc/azygous control (red)	0.94518	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.77299	0.071

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.75128	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.07953	0.087
Manapal/WT (break)	1.17295	0.381
Manapal/WT (red)	1.01947	1