Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.1.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99276	0.901
27DAP/17DAP	0.64968	0.08
39DAP/27DAP	1.03845	0.857
41DAP/39DAP	0.99725	0.909
42DAP/41DAP	1.06321	1
43DAP/42DAP	1.05674	1
47DAP/43DAP	1.27482	0.555
52DAP/47DAP	0.78609	0.6
57DAP/52DAP	1.26839	0.955

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05304	0.303
17DAP/reference	1.05999	0.092
27DAP/reference	0.9838	0.623
39DAP/reference	0.99386	0.885
41DAP/reference	1.01719	0.808
42DAP/reference	0.93023	0.091
43DAP/reference	1.04043	0.325
47DAP/reference	0.98332	0.445
52DAP/reference	0.82927	0.024
57DAP/reference	0.78132	0.016

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.55239	0.124
27DAP/17DAP	0.96997	0.887
39DAP/27DAP	0.71835	0.062
41DAP/39DAP	1.39584	0.087
42DAP/41DAP	0.75454	0.022
43DAP/42DAP	0.79096	0.137
47DAP/43DAP	1.07047	0.699
52DAP/47DAP	1.00186	0.947
57DAP/52DAP	0.95133	0.68
57DAP/7DAP	1.50516	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.63742	0.032
17DAP/reference	1.12704	0.269
27DAP/reference	0.81033	0.011
39DAP/reference	0.99021	0.64
41DAP/reference	0.89479	0.139
42DAP/reference	0.79571	0.017
43DAP/reference	0.65063	0.011
47DAP/reference	0.97728	0.671
52DAP/reference	0.5751	0.011
57DAP/reference	0.55586	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.28571	0.099
17DAP/reference	1.23125	0.011
27DAP/reference	1.02564	1
39DAP/reference	0.95706	0.348
41DAP/reference	0.88075	0.087
42DAP/reference	0.88849	0.067
43DAP/reference	1.068	0.874
47DAP/reference	0.9326	0.168
52DAP/reference	1.04517	0.789
57DAP/reference	1.08385	0.786

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20592	0.076
17DAP/reference	1.35077	0.233
27DAP/reference	0.9298	0.23
39DAP/reference	0.93704	0.271
41DAP/reference	0.76535	0.025
42DAP/reference	1.11935	0.347
43DAP/reference	0.88769	0.046
47DAP/reference	1.00427	0.754
52DAP/reference	0.80891	0.247
57DAP/reference	0.92757	0.387

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01933	1
26DAP/20DAP	1.49403	0.223
34DAP/26DAP	0.86322	0.653
51DAP/34DAP	1.27961	0.089
52DAP/51DAP	1.15001	0.467
53DAP/52DAP	1.12315	0.868
55DAP/53DAP	0.69668	0.024
57DAP/55DAP	0.73693	0.096
62DAP/57DAP	1.09878	0.393
68DAP/62DAP	0.91885	0.641
68DAP/14DAP	0.62657	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.8522	0.108

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.28547	0.058
Mature Green Tomato/Ripe Tomato	1.69917	0.019
Immature Eggplant/Mature Eggplant	1.19852	0.659
Ripe Pepper/Ripe Tomato	1.92649	0.258
Mature Eggplant/Ripe Tomato	6.15731	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.10166	0.877
1-1-2/M82	0.90466
12-2/M82	0.8277	0.678
12-4/M82	0.8493	0.358
1-3/M82	1.4977
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.92153	1
3-2/M82	0.97725	0.752
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	1.05993	1
5-3/M82	1.21557	0.572
6-2/M82	0.87127
6-3/M82	1.46891
7-1/M82	0.9712	1
7-2/M82	1.11436
9-3-2/M82	0.89721

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.87199
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.62359
IL7-3/WTpooled	0.91884	1
IL12-4/WTpooled	0.90592	1
IL1-4/WTpooled	2.23348	1
WT/WTpooled	0.79732	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	0.81004	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.12571	0.692
DC3000/delta hrp 6h	1.29131	0.631
DC3000/delta hrp 12h	0.89004	1
DC3000/delta hrp 24h	0.85127	0.069

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.91802	1
DC3000 delta B/DC3000 delta AB	0.91334	0.337

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96929	1
Exp 36h	1.04079	1
Exp 60h	1.05112	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.93279
Var 0h	1.02511	1
Var 12h I row2-row1	0.94102	0.705
Var 12h NI row2-row1	1.05731	1
Var 36h I row2-row1	0.91357	1
Var 36h NI row2-row1	1.12505	1
Var 60h I row2-row1	0.98392
Var 60h NI row2-row1	1.0401	1
Time course 0hI-0hNI	0.95328	0.729
Time course 12hI-12hNI	1.02746	0.785
Time course 36hI-36hNI	1.01064	1
Time course 60hI-60hNI	1.4093	0.673

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)	1.0267	0.331
transgenic ySAMdc/azygous control (breaker)	0.86898	0.251
transgenic ySAMdc/azygous control (red)	1.00084	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0275	0.247

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.18259	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.88067	1
Manapal/WT (break)	1.2177	0.381
Manapal/WT (red)	1.02717	1