Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.3.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.59482	0.021
27DAP/17DAP	0.90169	0.783
39DAP/27DAP	2.01276	0.078
41DAP/39DAP	1.02221	0.939
42DAP/41DAP	0.84445	0.774
43DAP/42DAP	1.49271	0.728
47DAP/43DAP	0.67001	0.14
52DAP/47DAP	1.24993	0.608
57DAP/52DAP	0.71748	0.462

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83625	0.044
17DAP/reference	0.69351	0.008
27DAP/reference	0.85823	0.036
39DAP/reference	0.74737	0.01
41DAP/reference	0.65213	0.008
42DAP/reference	0.86445	0.004
43DAP/reference	1.01148	0.728
47DAP/reference	1.12849	0.025
52DAP/reference	1.1462	0.242
57DAP/reference	1.23129	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86132	0.336
27DAP/17DAP	1.43241	0.033
39DAP/27DAP	0.7573	0.046
41DAP/39DAP	0.84379	0.465
42DAP/41DAP	1.39395	0.008
43DAP/42DAP	1.20945	0.176
47DAP/43DAP	1.01347	0.95
52DAP/47DAP	0.7626	0.113
57DAP/52DAP	0.69155	0.047
57DAP/7DAP	1.36591	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.39535	0.058
17DAP/reference	1.24057	0.092
27DAP/reference	1.22514	0.107
39DAP/reference	1.35581	0.009
41DAP/reference	1.17578	0.593
42DAP/reference	1.15207	0.405
43DAP/reference	1.35699	0.007
47DAP/reference	1.2806	0.115
52DAP/reference	1.29525	0.062
57DAP/reference	1.08294	0.5

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89073	0.176
17DAP/reference	0.70805	0.01
27DAP/reference	0.8482	0.054
39DAP/reference	0.89175	0.129
41DAP/reference	0.9545	0.315
42DAP/reference	0.82648	0.067
43DAP/reference	0.71401	0.007
47DAP/reference	0.69179	0.01
52DAP/reference	0.80809	0.008
57DAP/reference	0.77272	0.013

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.3418	0.18
17DAP/reference	1.1278	0.824
27DAP/reference	1.20706	0.044
39DAP/reference	1.36783	0.052
41DAP/reference	1.36542	0.06
42DAP/reference	1.56844	0.01
43DAP/reference	2.03848	0.007
47DAP/reference	1.13568	0.239
52DAP/reference	1.72818	0.063
57DAP/reference	1.5511	0.019

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.111	0.966
26DAP/20DAP	2.07621	0.097
34DAP/26DAP	0.79906	0.159
51DAP/34DAP	1.41478	0.159
52DAP/51DAP	1.10012	0.588
53DAP/52DAP	0.63082	0.056
55DAP/53DAP	0.64563	0.043
57DAP/55DAP	0.9657	0.825
62DAP/57DAP	1.47635	0.034
68DAP/62DAP	1.39985	0.754
68DAP/14DAP	2.32752	0.027

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.67979	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.08576	0.058
Mature Green Tomato/Ripe Tomato	0.45157	0.03
Immature Eggplant/Mature Eggplant	1.55954	0.05
Ripe Pepper/Ripe Tomato	0.67906	0.224
Mature Eggplant/Ripe Tomato	0.42868	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.3463	0.574
1-1-2/M82	1.17095	1
12-2/M82	0.89631	0.955
12-4/M82	0.77217	0.33
1-3/M82	1.58277
2-1-1/M82	0.8254	0.784
2-1/M82	0.74671	0.322
2-6/M82	1.49728	0.329
3-2/M82	1.45063
4-1-1/M82	0.87162	1
4-1/M82	0.59283
4-3-2/M82	3.00046	0.246
4-3/M82	2.34162	0.268
5-3/M82	1.01374	1
6-2/M82	1.49088	0.253
6-3/M82	0.64124
7-1/M82	0.83721	0.803
7-2/M82	1.54866	0.324
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.41634	0.277
IL2-6/WTpooled	0.58259	0.383
IL7-5/WTpooled	1.09472	0.75
IL7-3/WTpooled	1.17426	0.362
IL12-4/WTpooled	1.14446	0.516
IL1-4/WTpooled	0.99635	1
WT/WTpooled	0.99001	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	0.91381	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9524	1
DC3000/delta hrp 6h	1.06609	1
DC3000/delta hrp 12h	0.909	1
DC3000/delta hrp 24h	2.08301	0.03

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.97442	0.955
DC3000 delta B/DC3000 delta AB	0.86904	0.129

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.22573	0.254
Exp 36h	1.02109	1
Exp 60h	1.07597	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01925	1
Var 0h	0.99529	1
Var 12h I row2-row1	0.76173	0.467
Var 12h NI row2-row1	1.27975	0.191
Var 36h I row2-row1	1.08929	0.908
Var 36h NI row2-row1	1.2683	0.482
Var 60h I row2-row1	0.89531	0.293
Var 60h NI row2-row1	1.06773	1
Time course 0hI-0hNI	0.99322	1
Time course 12hI-12hNI	0.96138	0.65
Time course 36hI-36hNI	1.05255	0.651
Time course 60hI-60hNI	0.37863	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)	1.21144	0.271
transgenic ySAMdc/azygous control (breaker)	0.64667	0.142
transgenic ySAMdc/azygous control (red)	1.18411	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97258	0.323

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.8768	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	6.33332	0.093
Manapal/WT (break)	1.91356	0.183
Manapal/WT (red)	2.59865	0.134