Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.12.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14257	0.863
27DAP/17DAP	0.98622	0.982
39DAP/27DAP	0.78613	0.376
41DAP/39DAP	1.08888	0.806
42DAP/41DAP	1.04087	0.999
43DAP/42DAP	1.11905	1
47DAP/43DAP	1.00844	1
52DAP/47DAP	1.03578	0.982
57DAP/52DAP	1.18599	0.948

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.68445	0.007
17DAP/reference	1.3101	0.055
27DAP/reference	0.95555	0.484
39DAP/reference	1.31114	0.077
41DAP/reference	1.14729	0.073
42DAP/reference	1.91732	0.001
43DAP/reference	1.94688	0.007
47DAP/reference	1.75806	0.001
52DAP/reference	1.18825	0.023
57DAP/reference	1.21626	0.041

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06581	0.858
27DAP/17DAP	0.93958	0.614
39DAP/27DAP	0.91648	0.388
41DAP/39DAP	1.1292	0.682
42DAP/41DAP	1.09972	0.926
43DAP/42DAP	1.24819	0.212
47DAP/43DAP	0.90882	0.195
52DAP/47DAP	0.94519	0.726
57DAP/52DAP	1.01854	0.921
57DAP/7DAP	0.60981	0.181

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96416	0.495
17DAP/reference	0.83573	0.082
27DAP/reference	0.91961	0.062
39DAP/reference	0.72683	0.023
41DAP/reference	0.81941	0.082
42DAP/reference	0.74438	0.022
43DAP/reference	0.71125	0.015
47DAP/reference	0.99723	0.671
52DAP/reference	0.70119	0.033
57DAP/reference	0.7059	0.011

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.95001	0.035
17DAP/reference	2.0442	0.007
27DAP/reference	1.98104	0.012
39DAP/reference	1.36281	0.039
41DAP/reference	1.04143	0.749
42DAP/reference	1.75421	0.008
43DAP/reference	1.49889	0.014
47DAP/reference	1.6383	0.008
52DAP/reference	0.97414	0.469
57DAP/reference	1.45907	0.021

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16937	0.793
17DAP/reference	1.23906	0.496
27DAP/reference	0.90478	0.302
39DAP/reference	0.92241	0.299
41DAP/reference	0.94007	0.459
42DAP/reference	1.21907	0.49
43DAP/reference	1.71529	0.895
47DAP/reference	1.83198	0.01
52DAP/reference	1.15591	0.89
57DAP/reference	1.21315	0.604

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.32395	0.966
26DAP/20DAP	1.63873	0.099
34DAP/26DAP	1.25193	1
51DAP/34DAP	1.25648	0.039
52DAP/51DAP	0.74657	1
53DAP/52DAP	1.2484	0.284
55DAP/53DAP	0.8216	0.159
57DAP/55DAP	1.30443	0.274
62DAP/57DAP	1.12055	0.833
68DAP/62DAP	1.59012	0.088
68DAP/14DAP	2.57048	0.044

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.87049	0.422

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.63811	0.155
Mature Green Tomato/Ripe Tomato	0.81341	0.347
Immature Eggplant/Mature Eggplant	1.45244	0.05
Ripe Pepper/Ripe Tomato	3.40307	0.256
Mature Eggplant/Ripe Tomato	0.97093	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.23193	0.972
12-2/M82	N/A	N/A
12-4/M82	1.45139	0.611
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	1.34201	0.717
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.23258	1
4-3/M82	N/A	N/A
5-3/M82	1.22953	0.572
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.01771
7-2/M82	0.96005
9-3-2/M82	1.25865

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.99904	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	2.98197	0.792
IL7-3/WTpooled	1.16002
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.11212	1
WT/WTpooled	1.12782

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96456	1
DC3000/delta hrp 6h	1.02135	1
DC3000/delta hrp 12h	1.00159	1
DC3000/delta hrp 24h	1.11977	0.567

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.10158	1
DC3000 delta B/DC3000 delta AB	0.8138	0.288

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94565	1
Exp 36h	0.90819	0.749
Exp 60h	0.929	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96934	1
Var 0h	0.56299	1
Var 12h I row2-row1	0.944	0.565
Var 12h NI row2-row1	1.04261	1
Var 36h I row2-row1	0.80092	1
Var 36h NI row2-row1	1.00899	1
Var 60h I row2-row1	0.84737	0.582
Var 60h NI row2-row1	0.91681	0.69
Time course 0hI-0hNI	0.97896	0.93
Time course 12hI-12hNI	1.04565	0.633
Time course 36hI-36hNI	1.02102	0.874
Time course 60hI-60hNI	0.83586	0.047

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)	1.18006	0.3
transgenic ySAMdc/azygous control (breaker)	1.69696	0.162
transgenic ySAMdc/azygous control (red)	1.18787	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96443	0.128

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.21862	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.47962	0.086
Manapal/WT (break)	1.20434	0.183
Manapal/WT (red)	1.25817	1