Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.10.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92322	0.627
27DAP/17DAP	1.01543	1
39DAP/27DAP	1.01591	1
41DAP/39DAP	0.97783	0.897
42DAP/41DAP	0.81458	0.774
43DAP/42DAP	1.10683	0.957
47DAP/43DAP	1.04694	0.895
52DAP/47DAP	1.2678	0.615
57DAP/52DAP	0.92054	0.852

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78039	0.041
17DAP/reference	0.7251	0.008
27DAP/reference	0.92661	0.339
39DAP/reference	0.86527	0.078
41DAP/reference	0.70434	0.009
42DAP/reference	0.86698	0.02
43DAP/reference	0.88946	0.088
47DAP/reference	0.90097	0.137
52DAP/reference	1.13856	0.242
57DAP/reference	1.18912	0.012

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14115	0.515
27DAP/17DAP	1.1322	0.706
39DAP/27DAP	0.84012	0.161
41DAP/39DAP	1.083	0.417
42DAP/41DAP	1.01316	0.976
43DAP/42DAP	0.85882	0.034
47DAP/43DAP	0.90448	0.439
52DAP/47DAP	1.32467	0.377
57DAP/52DAP	1.37426	0.085
57DAP/7DAP	0.95513	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80722	0.077
17DAP/reference	0.84947	0.035
27DAP/reference	1.09321	0.371
39DAP/reference	0.78186	0.017
41DAP/reference	0.84669	0.021
42DAP/reference	0.93853	0.2
43DAP/reference	0.92441	0.21
47DAP/reference	0.85907	0.101
52DAP/reference	0.76431	0.013
57DAP/reference	0.79715	0.018

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.64417	0.011
17DAP/reference	0.67157	0.005
27DAP/reference	1.02776	1
39DAP/reference	1.07671	1
41DAP/reference	1.15911	0.335
42DAP/reference	1.08257	0.18
43DAP/reference	0.946	0.404
47DAP/reference	0.81206	0.056
52DAP/reference	0.88769	0.031
57DAP/reference	0.52391	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83783	0.035
17DAP/reference	0.99275	0.751
27DAP/reference	1.0032	0.843
39DAP/reference	0.89152	0.05
41DAP/reference	1.0738	0.637
42DAP/reference	1.13377	0.635
43DAP/reference	0.97977	0.484
47DAP/reference	0.9707	0.465
52DAP/reference	0.78197	0.096
57DAP/reference	1.83607	0.058

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.33736	0.966
26DAP/20DAP	1.09898	1
34DAP/26DAP	1.2243	1
51DAP/34DAP	0.71612	0.097
52DAP/51DAP	1.17925	0.439
53DAP/52DAP	0.80956	0.153
55DAP/53DAP	1.19603	0.444
57DAP/55DAP	0.85374	0.423
62DAP/57DAP	1.15104	0.021
68DAP/62DAP	2.16817	0.042
68DAP/14DAP	3.48904	0.022

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.71864	0.023

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.97599	0.71
Mature Green Tomato/Ripe Tomato	1.23948	0.185
Immature Eggplant/Mature Eggplant	1.0162	1
Ripe Pepper/Ripe Tomato	2.05665	1
Mature Eggplant/Ripe Tomato	2.24426	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.20311
1-1-2/M82	0.85194
12-2/M82	1.02848
12-4/M82	0.96385	1
1-3/M82	0.59955	0.378
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	1.32246	0.84
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	1.43759
5-3/M82	1.08306	1
6-2/M82	0.54457
6-3/M82	1.02558
7-1/M82	1.17586
7-2/M82	0.96779
9-3-2/M82	0.85693	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.99546	1
IL2-6/WTpooled	1.16263	0.441
IL7-5/WTpooled	0.60989
IL7-3/WTpooled	1.03691	1
IL12-4/WTpooled	0.9572	0.71
IL1-4/WTpooled	1.10446	1
WT/WTpooled	1.07732	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	0.88751	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99518	1
DC3000/delta hrp 6h	0.95059	0.95
DC3000/delta hrp 12h	0.8804	1
DC3000/delta hrp 24h	1.05803	0.633

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.08183	0.145
DC3000 delta B/DC3000 delta AB	1.15036	0.423

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96993	1
Exp 36h	1.02384	1
Exp 60h	0.94013	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9877	1
Var 0h	0.81133	1
Var 12h I row2-row1	0.88324	0.705
Var 12h NI row2-row1	1.01767	1
Var 36h I row2-row1	1.02797	1
Var 36h NI row2-row1	1.2233	1
Var 60h I row2-row1	0.91479	0.306
Var 60h NI row2-row1	0.93228	0.977
Time course 0hI-0hNI	0.97158	0.87
Time course 12hI-12hNI	1.00207	1
Time course 36hI-36hNI	1.07883	0.101
Time course 60hI-60hNI	0.7581	0.008

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)	1.10902	0.326
transgenic ySAMdc/azygous control (breaker)	1.34336	0.172
transgenic ySAMdc/azygous control (red)	1.04635	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.1021	0.105

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.93842	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.27618	0.087
Manapal/WT (break)	1.60208	0.13
Manapal/WT (red)	1.15928	1