Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.7.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.36622	0.561
27DAP/17DAP	1.08166	0.872
39DAP/27DAP	1.29288	0.511
41DAP/39DAP	0.83105	0.385
42DAP/41DAP	1.05289	0.994
43DAP/42DAP	0.98013	0.914
47DAP/43DAP	0.8564	0.546
52DAP/47DAP	1.06151	0.943
57DAP/52DAP	1.16611	0.44

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74885	0.033
17DAP/reference	0.56274	0.007
27DAP/reference	0.65774	0.012
39DAP/reference	0.65454	0.027
41DAP/reference	0.60456	0.021
42DAP/reference	0.6954	0.004
43DAP/reference	0.86521	0.17
47DAP/reference	0.6707	0.002
52DAP/reference	0.67874	0.069
57DAP/reference	0.90699	0.04

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11119	0.164
27DAP/17DAP	0.99314	0.969
39DAP/27DAP	1.05602	0.718
41DAP/39DAP	1.09817	0.727
42DAP/41DAP	1.00672	1
43DAP/42DAP	0.91304	0.256
47DAP/43DAP	1.02062	0.884
52DAP/47DAP	0.96291	0.857
57DAP/52DAP	0.91937	0.463
57DAP/7DAP	1.09586	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97849	0.55
17DAP/reference	0.92767	0.22
27DAP/reference	0.82628	0.062
39DAP/reference	0.7564	0.014
41DAP/reference	0.75291	0.047
42DAP/reference	0.73511	0.012
43DAP/reference	0.81147	0.059
47DAP/reference	0.67087	0.03
52DAP/reference	0.90209	0.163
57DAP/reference	0.87807	0.149

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.60406	0.011
17DAP/reference	0.64665	0.006
27DAP/reference	0.74641	0.038
39DAP/reference	0.63924	0.021
41DAP/reference	0.70955	0.042
42DAP/reference	0.71621	0.03
43DAP/reference	0.71991	0.062
47DAP/reference	0.7002	0.01
52DAP/reference	0.46416	0.004
57DAP/reference	0.65004	0.006

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23542	0.041
17DAP/reference	1.23344	0.675
27DAP/reference	1.02475	0.903
39DAP/reference	0.96002	0.464
41DAP/reference	1.04752	0.637
42DAP/reference	0.99781	0.816
43DAP/reference	0.82706	0.092
47DAP/reference	0.54309	0.005
52DAP/reference	0.76144	0.216
57DAP/reference	0.8483	0.167

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.78171	0.733
26DAP/20DAP	1.02613	1
34DAP/26DAP	0.95654	0.909
51DAP/34DAP	0.98218	0.835
52DAP/51DAP	1.08236	0.253
53DAP/52DAP	0.80833	0.311
55DAP/53DAP	1.02083	0.964
57DAP/55DAP	0.97159	0.859
62DAP/57DAP	1.10276	0.935
68DAP/62DAP	1.11249	0.747
68DAP/14DAP	0.52046	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.09379	0.285

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.25728	0.058
Mature Green Tomato/Ripe Tomato	1.35012	0.632
Immature Eggplant/Mature Eggplant	0.39623	0.062
Ripe Pepper/Ripe Tomato	6.893	0.244
Mature Eggplant/Ripe Tomato	3.31724	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.65044
1-1-2/M82	0.81925
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	1.16267
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.15243
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.5115	0.572
6-2/M82	2.93832
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.01197
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.96542	1
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	0.94842
WT/WTpooled	1.05022	0.957

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	0.99707	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94615	1
DC3000/delta hrp 6h	1.0258	1
DC3000/delta hrp 12h	0.66199	1
DC3000/delta hrp 24h	0.76685	0.04

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.98195	1
DC3000 delta B/DC3000 delta AB	1.03768	0.571

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.11073	1
Exp 36h	1.04314	1
Exp 60h	1.38891	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97323	1
Var 0h	1.05139	1
Var 12h I row2-row1	0.85815	0.338
Var 12h NI row2-row1	0.95069	0.713
Var 36h I row2-row1	1.03076	0.742
Var 36h NI row2-row1	1.04737	1
Var 60h I row2-row1	0.99554	1
Var 60h NI row2-row1	1.01895	1
Time course 0hI-0hNI	0.94336	0.606
Time course 12hI-12hNI	1.00684	0.868
Time course 36hI-36hNI	0.96847	0.411
Time course 60hI-60hNI	0.56457	0.006

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)	0.7798	0.324
transgenic ySAMdc/azygous control (breaker)	1.01888	1
transgenic ySAMdc/azygous control (red)	0.84456	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95558	0.12

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.49592	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.6797	0.093
Manapal/WT (break)	2.43917	0.381
Manapal/WT (red)	N/A	N/A