Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.7.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.33796	0.244
27DAP/17DAP	1.21164	0.781
39DAP/27DAP	1.00031	0.769
41DAP/39DAP	1.08271	0.649
42DAP/41DAP	1.08524	0.912
43DAP/42DAP	1.03894	1
47DAP/43DAP	1.48707	0.23
52DAP/47DAP	0.88222	0.673
57DAP/52DAP	1.23575	0.688

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85531	0.177
17DAP/reference	0.70861	0.017
27DAP/reference	0.95401	0.457
39DAP/reference	0.89875	0.37
41DAP/reference	0.79879	0.049
42DAP/reference	0.91224	0.163
43DAP/reference	0.90735	0.2
47DAP/reference	1.04494	0.72
52DAP/reference	1.37046	0.096
57DAP/reference	1.11201	0.147

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.46631	0.089
27DAP/17DAP	0.84775	0.537
39DAP/27DAP	0.63645	0.068
41DAP/39DAP	1.30431	1
42DAP/41DAP	1.49329	0.008
43DAP/42DAP	0.79024	0.143
47DAP/43DAP	0.88928	0.525
52DAP/47DAP	2.7056	0.048
57DAP/52DAP	2.76473	0.036
57DAP/7DAP	2.30602	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27576	0.058
17DAP/reference	1.57174	0.009
27DAP/reference	1.51621	0.007
39DAP/reference	1.57839	0.006
41DAP/reference	1.6356	0.013
42DAP/reference	1.64305	0.007
43DAP/reference	1.7599	0.006
47DAP/reference	1.20836	0.152
52DAP/reference	1.66691	0.007
57DAP/reference	1.54691	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.60843	0.022
17DAP/reference	0.57101	0.019
27DAP/reference	1.18632	0.715
39DAP/reference	1.80531	0.011
41DAP/reference	1.61095	0.269
42DAP/reference	1.36952	0.02
43DAP/reference	0.70091	0.053
47DAP/reference	0.73822	0.011
52DAP/reference	1.16544	0.208
57DAP/reference	0.57686	0.009

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2029	0.153
17DAP/reference	1.17082	0.865
27DAP/reference	1.56158	0.02
39DAP/reference	1.48771	0.014
41DAP/reference	1.48526	0.007
42DAP/reference	1.80812	0.027
43DAP/reference	1.50192	0.011
47DAP/reference	1.15519	1
52DAP/reference	1.2415	0.363
57DAP/reference	2.17476	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91829	1
26DAP/20DAP	6.28227	0.615
34DAP/26DAP	6.22609	1
51DAP/34DAP	3.65587	0.666
52DAP/51DAP	6.44338	0.033
53DAP/52DAP	0.61459	0.173
55DAP/53DAP	1.73526	0.382
57DAP/55DAP	0.2845	0.01
62DAP/57DAP	1.852	0.185
68DAP/62DAP	4.18937	0.23
68DAP/14DAP	5.44152	0.021

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.14778	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.84341
Mature Green Tomato/Ripe Tomato	0.74479	0.055
Immature Eggplant/Mature Eggplant	0.7477	0.144
Ripe Pepper/Ripe Tomato	0.45062	0.293
Mature Eggplant/Ripe Tomato	0.93375

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.97279
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
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	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.05028
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.7166	0.321
IL2-6/WTpooled	1.15554	0.395
IL7-5/WTpooled	1.19212	0.792
IL7-3/WTpooled	0.8622	0.418
IL12-4/WTpooled	1.0737	0.595
IL1-4/WTpooled	0.95971	0.834
WT/WTpooled	0.95086	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	1.2778	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.938	1
DC3000/delta hrp 6h	1.07959	1
DC3000/delta hrp 12h	1.21568	1
DC3000/delta hrp 24h	0.72705	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.01209	1
DC3000 delta B/DC3000 delta AB	0.95676	0.983

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	1.02231	1
Var 0h	0.96702	1
Var 12h I row2-row1	0.76113	0.565
Var 12h NI row2-row1	1.10881	1
Var 36h I row2-row1	1.25101	1
Var 36h NI row2-row1	1.81853	0.276
Var 60h I row2-row1	0.82442	0.582
Var 60h NI row2-row1	0.96051	1
Time course 0hI-0hNI	0.83032	0.276
Time course 12hI-12hNI	1.09306	1
Time course 36hI-36hNI	1.08735	0.504
Time course 60hI-60hNI	0.71732	0.081

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)	0.89941	0.295
transgenic ySAMdc/azygous control (breaker)	1.41261	0.248
transgenic ySAMdc/azygous control (red)	1.18475	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9382	0.058

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.17136	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.88136	1
Manapal/WT (break)	0.87761	1
Manapal/WT (red)	1.1971	0.222