Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.1.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	6.60335	0.016
27DAP/17DAP	1.06262	0.926
39DAP/27DAP	2.00936	0.073
41DAP/39DAP	0.65438	0.053
42DAP/41DAP	1.07974	1
43DAP/42DAP	1.00754	0.925
47DAP/43DAP	0.79022	0.386
52DAP/47DAP	0.38566	0.033
57DAP/52DAP	1.27097	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.73743	0.111
17DAP/reference	1.21646	0.457
27DAP/reference	2.20026	0.01
39DAP/reference	3.67059	0.012
41DAP/reference	2.57643	0.013
42DAP/reference	3.53358	0.001
43DAP/reference	1.88341	0.007
47DAP/reference	1.9461	0.001
52DAP/reference	0.84089	0.139
57DAP/reference	1.33793	0.014

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.13495	0.037
27DAP/17DAP	1.44227	0.031
39DAP/27DAP	0.99361	1
41DAP/39DAP	1.47613	0.914
42DAP/41DAP	0.82777	0.126
43DAP/42DAP	0.8717	0.143
47DAP/43DAP	0.75379	0.012
52DAP/47DAP	1.51117	0.074
57DAP/52DAP	0.71678	0.049
57DAP/7DAP	2.15003	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27872	0.166
17DAP/reference	1.65666	0.01
27DAP/reference	2.74762	0.006
39DAP/reference	3.28109	0.006
41DAP/reference	5.33663	0.006
42DAP/reference	4.72455	0.006
43DAP/reference	3.47692	0.006
47DAP/reference	2.54167	0.014
52DAP/reference	3.53489	0.007
57DAP/reference	3.0677	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.33491	0.006
17DAP/reference	1.26933	0.161
27DAP/reference	2.20481	0.06
39DAP/reference	3.50232	0.011
41DAP/reference	5.18432	0.004
42DAP/reference	3.16613	0.007
43DAP/reference	1.27001	0.489
47DAP/reference	4.93276	0.008
52DAP/reference	2.36375	0.006
57DAP/reference	2.06844	0.066

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.41242	0.026
17DAP/reference	1.09358	0.814
27DAP/reference	1.60365	0.033
39DAP/reference	3.22485	0.004
41DAP/reference	2.53829	0.006
42DAP/reference	3.428	0.006
43DAP/reference	3.49938	0.011
47DAP/reference	1.16592	0.388
52DAP/reference	0.8382	0.189
57DAP/reference	1.63216	0.113

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.11568	0.966
26DAP/20DAP	0.59983	0.223
34DAP/26DAP	0.82695	0.834
51DAP/34DAP	1.03301	0.96
52DAP/51DAP	1.18483	0.742
53DAP/52DAP	0.71699	0.245
55DAP/53DAP	0.74354	0.188
57DAP/55DAP	0.8957	0.619
62DAP/57DAP	0.83491	0.162
68DAP/62DAP	1.18413	0.336
68DAP/14DAP	0.88123	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	40.2435	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	4.65914	0.058
Mature Green Tomato/Ripe Tomato	1.46767	0.209
Immature Eggplant/Mature Eggplant	9.5298	0.05
Ripe Pepper/Ripe Tomato	0.12114	0.224
Mature Eggplant/Ripe Tomato	0.12924	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.80713	0.651
1-1-2/M82	1.39873	1
12-2/M82	0.97895	1
12-4/M82	1.3438	1
1-3/M82	0.35679
2-1-1/M82	0.84224	0.784
2-1/M82	0.91085	0.519
2-6/M82	1.0727	0.695
3-2/M82	1.01333	1
4-1-1/M82	0.93519	1
4-1/M82	0.70041
4-3-2/M82	0.78599
4-3/M82	0.91975	1
5-3/M82	1.0092	1
6-2/M82	0.70701	1
6-3/M82	0.96851	1
7-1/M82	1.11178	0.598
7-2/M82	1.06188	1
9-3-2/M82	1.10682	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.02244	1
IL2-6/WTpooled	1.85903
IL7-5/WTpooled	0.63469	1
IL7-3/WTpooled	0.87116
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.94289	0.415
WT/WTpooled	0.92581	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	1.12296	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04154	0.921
DC3000/delta hrp 6h	1.02656	1
DC3000/delta hrp 12h	1.06788	1
DC3000/delta hrp 24h	0.84382	0.069

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.00243	1
DC3000 delta B/DC3000 delta AB	1.8563

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88576	1
Exp 36h	0.665	0.471
Exp 60h	0.74747	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97716	1
Var 0h	1.13279	0.98
Var 12h I row2-row1	0.90215	0.627
Var 12h NI row2-row1	0.85502	0.713
Var 36h I row2-row1	1.23194	1
Var 36h NI row2-row1	0.82969	0.276
Var 60h I row2-row1	1.21528	0.543
Var 60h NI row2-row1	0.94968	1
Time course 0hI-0hNI	1.03485	1
Time course 12hI-12hNI	1.00524	0.892
Time course 36hI-36hNI	0.75211	0.023
Time course 60hI-60hNI	0.57697	0.009

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)	0.92061	0.391
transgenic ySAMdc/azygous control (breaker)	0.89614	0.49
transgenic ySAMdc/azygous control (red)	1.39638	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00955	0.687

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.02042	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.8627	1
Manapal/WT (break)	1.0899	0.183
Manapal/WT (red)	1.30279	0.222