Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.18.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85226	0.413
27DAP/17DAP	0.90567	0.787
39DAP/27DAP	0.85522	0.544
41DAP/39DAP	1.50316	0.553
42DAP/41DAP	0.67172	0.774
43DAP/42DAP	0.95669	0.91
47DAP/43DAP	1.43441	0.293
52DAP/47DAP	1.44199	0.758
57DAP/52DAP	1.92956	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92749	0.194
17DAP/reference	1.00054	0.957
27DAP/reference	1.11616	0.132
39DAP/reference	1.05793	0.098
41DAP/reference	1.15788	0.043
42DAP/reference	0.97077	0.225
43DAP/reference	1.05364	0.569
47DAP/reference	1.09338	0.295
52DAP/reference	1.0013	0.636
57DAP/reference	1.00265	0.845

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91411	0.47
27DAP/17DAP	0.83941	0.241
39DAP/27DAP	1.03345	0.824
41DAP/39DAP	0.98812	1
42DAP/41DAP	0.82251	0.138
43DAP/42DAP	1.36931	0.066
47DAP/43DAP	1.04812	0.889
52DAP/47DAP	1.88579	0.145
57DAP/52DAP	2.60323	0.048
57DAP/7DAP	1.55299	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.35564	0.06
17DAP/reference	1.80409	0.007
27DAP/reference	1.63908	0.007
39DAP/reference	1.95606	0.006
41DAP/reference	1.9206	0.013
42DAP/reference	2.38717	0.007
43DAP/reference	2.67629	0.006
47DAP/reference	1.46968	0.2
52DAP/reference	1.64952	0.01
57DAP/reference	1.98183	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95	0.487
17DAP/reference	0.92216	0.208
27DAP/reference	0.84699	0.188
39DAP/reference	0.85819	0.085
41DAP/reference	0.84758	0.112
42DAP/reference	0.83736	0.089
43DAP/reference	0.85085	0.152
47DAP/reference	0.87715	0.168
52DAP/reference	0.86528	0.007
57DAP/reference	0.89272	0.03

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.33287	0.055
17DAP/reference	1.25413	0.443
27DAP/reference	1.95483	0.02
39DAP/reference	1.79195	0.012
41DAP/reference	1.63161	0.019
42DAP/reference	1.25306	0.356
43DAP/reference	1.2227	0.49
47DAP/reference	1.01655	0.847
52DAP/reference	1.51699	0.167
57DAP/reference	1.19276	0.604

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07866	0.966
26DAP/20DAP	1.4729	0.449
34DAP/26DAP	1.35464	0.819
51DAP/34DAP	1.13591	0.949
52DAP/51DAP	1.1627	0.606
53DAP/52DAP	0.81387	0.316
55DAP/53DAP	0.68185	0.181
57DAP/55DAP	1.05542	0.643
62DAP/57DAP	1.23774	0.445
68DAP/62DAP	0.94429	0.747
68DAP/14DAP	0.75783	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.08233	0.908

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.05289	1
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	1.51268	0.05
Ripe Pepper/Ripe Tomato	0.55049	0.224
Mature Eggplant/Ripe Tomato	0.68031	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00844	1
1-1-2/M82	0.97675	1
12-2/M82	1.43267	1
12-4/M82	1.1544
1-3/M82	0.86915	0.501
2-1-1/M82	0.97966	0.683
2-1/M82	N/A	N/A
2-6/M82	0.98677	1
3-2/M82	0.95973
4-1-1/M82	1.21946	1
4-1/M82	1.37459
4-3-2/M82	N/A	N/A
4-3/M82	1.0419	1
5-3/M82	0.8019	1
6-2/M82	1.41447	1
6-3/M82	0.95463	1
7-1/M82	0.708
7-2/M82	1.04162	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	1.22515	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05428	0.921
DC3000/delta hrp 6h	0.9407	0.95
DC3000/delta hrp 12h	0.94687	1
DC3000/delta hrp 24h	1.13192	0.243

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.93947	0.044
DC3000 delta B/DC3000 delta AB	1.369	0.103

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96182	1
Exp 36h	1.14738	1
Exp 60h	1.02541	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00788	1
Var 0h	0.84536	0.933
Var 12h I row2-row1	1.40711	0.296
Var 12h NI row2-row1	0.75406	0.627
Var 36h I row2-row1	0.78649	0.575
Var 36h NI row2-row1	0.9499	0.791
Var 60h I row2-row1	0.89228	0.832
Var 60h NI row2-row1	1.13919	0.904
Time course 0hI-0hNI	0.8401	0.09
Time course 12hI-12hNI	1.21058	0.015
Time course 36hI-36hNI	1.27281	0.19
Time course 60hI-60hNI	1.27322	0.033

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)	0.94371	0.289
transgenic ySAMdc/azygous control (breaker)	0.80674	0.173
transgenic ySAMdc/azygous control (red)	1.00353	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00034	1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.00654	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.84561	1
Manapal/WT (break)	0.87585	1
Manapal/WT (red)	0.5706	0.181