Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.19.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.32738	0.403
27DAP/17DAP	0.65348	0.049
39DAP/27DAP	1.17786	0.755
41DAP/39DAP	1.80806	0.239
42DAP/41DAP	1.32311	0.514
43DAP/42DAP	1.84502	0.077
47DAP/43DAP	1.83026	0.223
52DAP/47DAP	1.81561	0.236
57DAP/52DAP	0.98383	0.952

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89482	0.489
17DAP/reference	1.15099	0.412
27DAP/reference	1.19309	0.394
39DAP/reference	1.4274	0.013
41DAP/reference	1.22829	0.041
42DAP/reference	1.31219	0.338
43DAP/reference	1.60738
47DAP/reference	1.32925	0.575
52DAP/reference	2.02699	0.008
57DAP/reference	1.66842	0.405

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.33214	0.055
27DAP/17DAP	1.21858	0.362
39DAP/27DAP	1.83625	0.04
41DAP/39DAP	0.43201	0.015
42DAP/41DAP	4.34362	0.001
43DAP/42DAP	3.96698	0.013
47DAP/43DAP	1.00365	0.983
52DAP/47DAP	1.26736	0.524
57DAP/52DAP	1.10654	0.851
57DAP/7DAP	6.39978	0.207

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.59045	0.077
17DAP/reference	0.55448	0.016
27DAP/reference	0.69989	0.011
39DAP/reference	1.19708	0.018
41DAP/reference	0.75974	0.107
42DAP/reference	0.79042	0.144
43DAP/reference	1.08878	0.665
47DAP/reference	1.76257	0.077
52DAP/reference	0.67013	0.03
57DAP/reference	0.40943	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.72649	0.222
17DAP/reference	0.9596	0.51
27DAP/reference	0.90941	0.34
39DAP/reference	0.97496	0.569
41DAP/reference	0.95897	0.403
42DAP/reference	1.18088	0.129
43DAP/reference	0.96288	0.516
47DAP/reference	1.41608	0.043
52DAP/reference	1.0566	0.761
57DAP/reference	1.08823	0.724

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.56467	0.05
17DAP/reference	0.83662	0.305
27DAP/reference	0.57864	0.036
39DAP/reference	0.80324	0.063
41DAP/reference	0.73345	0.035
42DAP/reference	2.46327	0.007
43DAP/reference	2.49029	0.007
47DAP/reference	1.35779	0.179
52DAP/reference	1.62421	0.081
57DAP/reference	1.2408	0.56

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.89223	1
26DAP/20DAP	0.7006	0.244
34DAP/26DAP	1.19625	1
51DAP/34DAP	4.16264	0.021
52DAP/51DAP	0.77703	0.151
53DAP/52DAP	6.34255	0.019
55DAP/53DAP	1.01223	0.951
57DAP/55DAP	0.90953	0.433
62DAP/57DAP	0.4897	0.007
68DAP/62DAP	0.85826	0.7
68DAP/14DAP	1.54098	0.018

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.13287	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.24162	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.13959	1
Mature Eggplant/Ripe Tomato	0.18842	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9453	0.944
1-1-2/M82	1.18152	1
12-2/M82	0.98919	1
12-4/M82	1.09933	1
1-3/M82	0.78122	0.501
2-1-1/M82	0.84597	0.683
2-1/M82	0.97941	1
2-6/M82	0.98362	1
3-2/M82	0.08889	0.428
4-1-1/M82	0.88437	0.668
4-1/M82	1.51243	0.853
4-3-2/M82	0.97209	1
4-3/M82	0.94312	1
5-3/M82	0.93608	1
6-2/M82	0.97321	1
6-3/M82	0.99047	1
7-1/M82	0.95878	0.408
7-2/M82	0.93666	0.57
9-3-2/M82	1.17023	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.82311
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.30954
IL1-4/WTpooled	1.04754
WT/WTpooled	0.95731	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	1.85099	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.21282	0.774
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.61201	1
DC3000/delta hrp 24h	0.74095	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.77362	0.027
DC3000 delta B/DC3000 delta AB	0.92964	0.456

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.10821	1
Var 0h	0.55432	0.258
Var 12h I row2-row1	1.19446	0.348
Var 12h NI row2-row1	1.084	0.649
Var 36h I row2-row1	1.29172	0.601
Var 36h NI row2-row1	1.09191	1
Var 60h I row2-row1	0.68193	0.293
Var 60h NI row2-row1	1.07672	0.904
Time course 0hI-0hNI	1.13849	0.246
Time course 12hI-12hNI	0.95445	0.569
Time course 36hI-36hNI	1.07812	0.513
Time course 60hI-60hNI	2.19147	0.008

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	0.72969	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.19235	0.194

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.15844	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	1.01314	1