Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.17.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.70504	0.111
27DAP/17DAP	1.4559	0.746
39DAP/27DAP	1.31426	0.453
41DAP/39DAP	0.89852	0.574
42DAP/41DAP	0.97496	1
43DAP/42DAP	0.77265	0.801
47DAP/43DAP	1.06928	0.943
52DAP/47DAP	1.17892	0.786
57DAP/52DAP	1.11406	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84631	0.085
17DAP/reference	0.67521	0.008
27DAP/reference	0.9669	0.623
39DAP/reference	0.7171	0.016
41DAP/reference	0.65772	0.009
42DAP/reference	0.86664	0.052
43DAP/reference	0.81734	0.018
47DAP/reference	0.87303	0.098
52DAP/reference	1.26456	0.158
57DAP/reference	1.31833	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.27519	0.081
27DAP/17DAP	0.89517	0.782
39DAP/27DAP	0.93788	0.721
41DAP/39DAP	1.11239	0.719
42DAP/41DAP	0.83222	0.173
43DAP/42DAP	1.0626	0.664
47DAP/43DAP	1.13004	0.744
52DAP/47DAP	0.96121	0.898
57DAP/52DAP	0.89214	0.637
57DAP/7DAP	0.7787	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88631	0.361
17DAP/reference	1.03357	1
27DAP/reference	1.05416	0.974
39DAP/reference	1.02572	0.96
41DAP/reference	0.92427	0.375
42DAP/reference	1.01976	0.675
43DAP/reference	1.19189	0.256
47DAP/reference	1.04437	0.885
52DAP/reference	1.05708	1
57DAP/reference	1.08291	0.468

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81782	0.124
17DAP/reference	0.67305	0.004
27DAP/reference	0.90842	0.269
39DAP/reference	0.98022	0.509
41DAP/reference	1.01288	0.749
42DAP/reference	0.90329	0.15
43DAP/reference	0.83801	0.162
47DAP/reference	0.76478	0.013
52DAP/reference	0.83377	0.01
57DAP/reference	0.66388	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07512	1
17DAP/reference	0.9851	0.727
27DAP/reference	1.06971	0.298
39DAP/reference	1.09243	0.512
41DAP/reference	1.03382	0.916
42DAP/reference	1.14337	0.701
43DAP/reference	1.05925	0.867
47DAP/reference	0.79258	0.021
52DAP/reference	0.74723	0.18
57DAP/reference	1.6976	0.044

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10737	0.966
26DAP/20DAP	1.23196	0.689
34DAP/26DAP	0.76273
51DAP/34DAP	1.23036	0.654
52DAP/51DAP	1.28693	0.542
53DAP/52DAP	1.35095	0.458
55DAP/53DAP	1.17565	0.434
57DAP/55DAP	0.75107	0.202
62DAP/57DAP	1.0431	0.935
68DAP/62DAP	1.82739	0.653
68DAP/14DAP	2.58831	0.031

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.2561	0.306

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.00474	0.058
Mature Green Tomato/Ripe Tomato	1.4539	0.019
Immature Eggplant/Mature Eggplant	0.63663	0.062
Ripe Pepper/Ripe Tomato	2.3236	0.235
Mature Eggplant/Ripe Tomato	1.03784	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.98924	0.958
12-2/M82	1.04566
12-4/M82	0.92245
1-3/M82	N/A	N/A
2-1-1/M82	1.11467	0.236
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.89024
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	0.90373
5-3/M82	0.92075	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.88156
9-3-2/M82	0.97505	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.53894	0.277
IL2-6/WTpooled	1.08041	0.788
IL7-5/WTpooled	0.95892
IL7-3/WTpooled	0.94202	1
IL12-4/WTpooled	1.35757	0.516
IL1-4/WTpooled	0.939	0.834
WT/WTpooled	1.02852	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	0.99141	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02458	1
DC3000/delta hrp 6h	1.02653	0.95
DC3000/delta hrp 12h	0.96333	1
DC3000/delta hrp 24h	0.92345	0.543

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	2.03097

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04464	1
Exp 36h	0.73099	0.504
Exp 60h	0.64493	0.257

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97431	1
Var 0h	0.83482	0.933
Var 12h I row2-row1	0.97054	0.77
Var 12h NI row2-row1	1.15709	1
Var 36h I row2-row1	0.94285	1
Var 36h NI row2-row1	0.80054	0.61
Var 60h I row2-row1	0.95489	0.952
Var 60h NI row2-row1	0.82335	0.866
Time course 0hI-0hNI	0.89585	0.468
Time course 12hI-12hNI	1.00687	0.868
Time course 36hI-36hNI	1.04318	0.355
Time course 60hI-60hNI	1.44122	0.011

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)	0.89881	0.338
transgenic ySAMdc/azygous control (breaker)	1.11936	0.178
transgenic ySAMdc/azygous control (red)	0.94003	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.08046	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.30507	0.084
Manapal/WT (break)	1.272	0.183
Manapal/WT (red)	0.98259	0.863