Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.3.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.34439	0.017
27DAP/17DAP	0.61862	0.161
39DAP/27DAP	0.88727	0.537
41DAP/39DAP	1.64931	0.426
42DAP/41DAP	1.44766	0.595
43DAP/42DAP	1.10553	1
47DAP/43DAP	0.78209	0.429
52DAP/47DAP	1.37047	0.683
57DAP/52DAP	0.98954	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.62249	0.041
17DAP/reference	0.58134	0.009
27DAP/reference	0.69028	0.014
39DAP/reference	0.74502	0.146
41DAP/reference	1.12883	0.963
42DAP/reference	2.26199	0.006
43DAP/reference	1.30081	0.957
47DAP/reference	N/A	N/A
52DAP/reference	0.98659	0.636
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.4905	0.03
27DAP/17DAP	0.97628	0.878
39DAP/27DAP	1.06293	0.646
41DAP/39DAP	1.01705	0.896
42DAP/41DAP	1.06854	0.81
43DAP/42DAP	0.98574	0.875
47DAP/43DAP	1.03051	0.812
52DAP/47DAP	1.19538	0.46
57DAP/52DAP	1.18808	0.407
57DAP/7DAP	0.49573	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.95535	0.024
17DAP/reference	1.48888	0.011
27DAP/reference	1.12288	0.035
39DAP/reference	1.32377	0.01
41DAP/reference	1.20861	0.251
42DAP/reference	1.15938	0.059
43DAP/reference	0.93397	0.202
47DAP/reference	1.63924	0.318
52DAP/reference	0.83731	0.126
57DAP/reference	0.93658	0.183

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10598	0.582
17DAP/reference	0.66373	0.016
27DAP/reference	0.7349	0.093
39DAP/reference	0.69153	0.108
41DAP/reference	0.70815	0.068
42DAP/reference	0.87824	0.321
43DAP/reference	0.96946	0.552
47DAP/reference	0.91553	0.338
52DAP/reference	0.45433	0.003
57DAP/reference	0.59063	0.02

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.86814	0.025
17DAP/reference	1.01082	0.681
27DAP/reference	1.69689	0.02
39DAP/reference	1.27586	0.146
41DAP/reference	1.09026	0.306
42DAP/reference	1.15365	0.163
43DAP/reference	1.40017	0.349
47DAP/reference	1.1085	0.76
52DAP/reference	1.37039	0.09
57DAP/reference	1.40315	0.175

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1414	1
26DAP/20DAP	1.74243	0.109
34DAP/26DAP	0.66205	0.077
51DAP/34DAP	0.63334	0.065
52DAP/51DAP	1.4367	0.089
53DAP/52DAP	0.85872	0.122
55DAP/53DAP	0.97174	0.784
57DAP/55DAP	0.89892	0.568
62DAP/57DAP	0.93934	0.871
68DAP/62DAP	0.99783	0.863
68DAP/14DAP	0.5033	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.47841	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	5.50418	0.058
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	0.41296	0.057
Ripe Pepper/Ripe Tomato	0.34895	0.224
Mature Eggplant/Ripe Tomato	0.89502	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.17126	0.877
1-1-2/M82	1.08228	1
12-2/M82	1.07016	1
12-4/M82	1.00006	1
1-3/M82	2.94066	0.26
2-1-1/M82	0.8937	0.465
2-1/M82	0.99548	1
2-6/M82	0.95354
3-2/M82	N/A	N/A
4-1-1/M82	0.90996	1
4-1/M82	0.72327
4-3-2/M82	1.20624
4-3/M82	0.93581	1
5-3/M82	0.84794	0.364
6-2/M82	1.04309	1
6-3/M82	1.00542	1
7-1/M82	0.85416	0.476
7-2/M82	1.10659	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.9745	1
IL2-6/WTpooled	0.81998	0.473
IL7-5/WTpooled	1.01447	1
IL7-3/WTpooled	0.78867	0.31
IL12-4/WTpooled	0.65345	0.554
IL1-4/WTpooled	1.0476	1
WT/WTpooled	1.05401	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	1.43088	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92453	1
DC3000/delta hrp 6h	1.10839	1
DC3000/delta hrp 12h	0.97205	1
DC3000/delta hrp 24h	0.52174	0.043

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.37962	0.042
DC3000 delta B/DC3000 delta AB	1.42404	0.133

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.09897	1
Exp 36h	0.80009	0.504
Exp 60h	0.75599	0.32

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96734
Var 0h	1.06006	0.98
Var 12h I row2-row1	0.85038	0.39
Var 12h NI row2-row1	1.19352	0.649
Var 36h I row2-row1	1.20522	0.283
Var 36h NI row2-row1	0.88697	0.549
Var 60h I row2-row1	0.87302	0.582
Var 60h NI row2-row1	0.97038	1
Time course 0hI-0hNI	0.89732	0.262
Time course 12hI-12hNI	1.0029	1
Time course 36hI-36hNI	1.10696	0.316
Time course 60hI-60hNI	1.57224	0.025

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)	1.02555	0.931
transgenic ySAMdc/azygous control (breaker)	1.14922	1
transgenic ySAMdc/azygous control (red)	1.34081	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08233	0.687

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89868	1
Manapal/WT (break)	1.23947	0.14
Manapal/WT (red)	0.78438	0.216