Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.8.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.53218	0.062
27DAP/17DAP	1.02886	0.92
39DAP/27DAP	1.17833	0.956
41DAP/39DAP	0.87897	0.52
42DAP/41DAP	1.09561	0.954
43DAP/42DAP	0.92368	0.801
47DAP/43DAP	0.98975	0.92
52DAP/47DAP	1.61579	0.466
57DAP/52DAP	1.33336	0.908

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74676	0.052
17DAP/reference	0.82033	0.169
27DAP/reference	0.94543	0.406
39DAP/reference	0.94786	0.513
41DAP/reference	0.70542	0.085
42DAP/reference	0.88899	0.033
43DAP/reference	1.13822	0.033
47DAP/reference	1.00999	0.674
52DAP/reference	1.23993	0.176
57DAP/reference	1.17155	0.147

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.21772	0.057
27DAP/17DAP	0.99	0.919
39DAP/27DAP	0.77525	0.053
41DAP/39DAP	0.96647	0.934
42DAP/41DAP	0.89434	0.399
43DAP/42DAP	0.88159	0.101
47DAP/43DAP	1.29795	0.765
52DAP/47DAP	0.95352	0.884
57DAP/52DAP	1.04221	0.951
57DAP/7DAP	0.63226	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90555	0.146
17DAP/reference	1.09358	0.437
27DAP/reference	0.99564	0.698
39DAP/reference	0.81881	0.021
41DAP/reference	0.77288	0.06
42DAP/reference	0.7981	0.048
43DAP/reference	0.91371	0.166
47DAP/reference	0.92146	0.383
52DAP/reference	0.7059	0.026
57DAP/reference	0.97124	0.426

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.932	0.374
17DAP/reference	1.03564	0.756
27DAP/reference	0.82976	0.134
39DAP/reference	0.92353	0.183
41DAP/reference	0.90148	0.048
42DAP/reference	0.8588	0.067
43DAP/reference	0.90913	0.25
47DAP/reference	0.87593	0.06
52DAP/reference	1.03787	0.938
57DAP/reference	0.93836	0.338

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97096	0.526
17DAP/reference	0.94411	0.519
27DAP/reference	0.96474	0.566
39DAP/reference	0.92288	0.133
41DAP/reference	1.12147	0.439
42DAP/reference	0.97893	0.671
43DAP/reference	0.85231	0.137
47DAP/reference	0.96352	0.396
52DAP/reference	0.97384	0.663
57DAP/reference	1.00805	0.873

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.19226	0.966
26DAP/20DAP	1.27222	0.315
34DAP/26DAP	0.93339	0.811
51DAP/34DAP	0.96338	0.807
52DAP/51DAP	0.8361	0.151
53DAP/52DAP	0.88171	0.581
55DAP/53DAP	0.7986	0.024
57DAP/55DAP	0.98758	0.938
62DAP/57DAP	47.0886	0.767
68DAP/62DAP	1.02748	1
68DAP/14DAP	1.73376	0.384

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.98418	0.635

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.7867	0.077
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	1.63647

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.25229
1-1-2/M82	N/A	N/A
12-2/M82	0.76663
12-4/M82	1.10134	1
1-3/M82	N/A	N/A
2-1-1/M82	1.08172	1
2-1/M82	N/A	N/A
2-6/M82	1.17077
3-2/M82	0.93342
4-1-1/M82	N/A	N/A
4-1/M82	1.4068
4-3-2/M82	1.27495
4-3/M82	1.23418
5-3/M82	1.08527
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.71694
7-2/M82	N/A	N/A
9-3-2/M82	1.26866

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.85888
IL12-4/WTpooled	1.08661	0.557
IL1-4/WTpooled	1.19625	0.426
WT/WTpooled	0.57256

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	1.0683	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01293	0.921
DC3000/delta hrp 6h	1.14552	1
DC3000/delta hrp 12h	1.06514	1
DC3000/delta hrp 24h	1.04195	0.582

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.02887	0.598
DC3000 delta B/DC3000 delta AB	1.05563	0.646

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89053	1
Exp 36h	1.00393	1
Exp 60h	1.08575	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.06293	1
Var 0h	0.54328	1
Var 12h I row2-row1	1.1207	0.58
Var 12h NI row2-row1	0.77897	1
Var 36h I row2-row1	1.00534	1
Var 36h NI row2-row1	0.84057	0.478
Var 60h I row2-row1	2.29395	1
Var 60h NI row2-row1	0.97539	1
Time course 0hI-0hNI	0.9922	1
Time course 12hI-12hNI	0.94448	0.719
Time course 36hI-36hNI	1.05744	0.58
Time course 60hI-60hNI	0.87614	0.007

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)	0.86395	0.338
transgenic ySAMdc/azygous control (breaker)	0.95684	1
transgenic ySAMdc/azygous control (red)	1.08518	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97532	0.313

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.91653	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.02471	1
Manapal/WT (break)	0.94156	1
Manapal/WT (red)	0.88665	0.274