Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.1.16.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.20805	0.697
27DAP/17DAP	1.06404	0.902
39DAP/27DAP	0.91885	0.573
41DAP/39DAP	1.33477	0.289
42DAP/41DAP	1.15531	0.913
43DAP/42DAP	0.86317	0.729
47DAP/43DAP	1.16976	0.856
52DAP/47DAP	0.9916	0.875
57DAP/52DAP	1.03587	0.985

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98895	0.645
17DAP/reference	1.03233	0.427
27DAP/reference	0.98302	0.595
39DAP/reference	1.00592	0.857
41DAP/reference	1.04883	0.145
42DAP/reference	0.94312	0.034
43DAP/reference	0.96178	0.448
47DAP/reference	0.99845	0.72
52DAP/reference	0.89302	0.158
57DAP/reference	1.01174	0.927

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0268	0.881
27DAP/17DAP	0.99107	0.943
39DAP/27DAP	1.0893	0.46
41DAP/39DAP	0.97968	0.986
42DAP/41DAP	1.02642	0.961
43DAP/42DAP	1.02356	0.664
47DAP/43DAP	0.96228	0.805
52DAP/47DAP	1.11804	0.58
57DAP/52DAP	1.08007	0.732
57DAP/7DAP	0.96233	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75439	0.07
17DAP/reference	0.80655	0.019
27DAP/reference	0.82442	0.042
39DAP/reference	0.69434	0.146
41DAP/reference	0.81022	0.06
42DAP/reference	0.78438	0.021
43DAP/reference	0.79995	0.034
47DAP/reference	0.82043	0.168
52DAP/reference	0.90165	0.332
57DAP/reference	0.84708	0.02

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98794	0.77
17DAP/reference	0.96329	0.357
27DAP/reference	0.85434	0.037
39DAP/reference	0.9259	0.152
41DAP/reference	0.84073	0.091
42DAP/reference	0.98806	0.594
43DAP/reference	0.96181	0.438
47DAP/reference	0.94927	0.058
52DAP/reference	0.96334	0.259
57DAP/reference	0.93261	0.208

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85326	0.127
17DAP/reference	1.03678	0.977
27DAP/reference	0.78236	0.05
39DAP/reference	0.99406	0.643
41DAP/reference	0.8495	0.167
42DAP/reference	1.0111	0.816
43DAP/reference	1.03748	0.993
47DAP/reference	0.96211	0.409
52DAP/reference	0.97063	0.663
57DAP/reference	0.88053	0.042

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0449	0.966
26DAP/20DAP	0.97288	1
34DAP/26DAP	0.8761	0.343
51DAP/34DAP	1.18943	0.121
52DAP/51DAP	0.96187	1
53DAP/52DAP	0.91859	0.621
55DAP/53DAP	0.99389	0.876
57DAP/55DAP	0.89143	0.508
62DAP/57DAP	0.91592	0.466
68DAP/62DAP	1.08596	0.866
68DAP/14DAP	1.1822	0.179

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.56449	0.024

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.05606	0.666
Mature Green Tomato/Ripe Tomato	1.08623	0.898
Immature Eggplant/Mature Eggplant	1.11344	0.278
Ripe Pepper/Ripe Tomato	0.83955	1
Mature Eggplant/Ripe Tomato	1.05093	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.43762	0.742
1-1-2/M82	0.89647	1
12-2/M82	0.94619	0.955
12-4/M82	0.87267	0.298
1-3/M82	1.25769	0.479
2-1-1/M82	0.84152	0.92
2-1/M82	1.44052	0.345
2-6/M82	0.70038	0.501
3-2/M82	1.17025
4-1-1/M82	N/A	N/A
4-1/M82	0.68604	1
4-3-2/M82	0.62956	0.445
4-3/M82	0.85525	1
5-3/M82	1.37012	0.455
6-2/M82	1.06594	1
6-3/M82	0.93394	0.668
7-1/M82	N/A	N/A
7-2/M82	1.0198	1
9-3-2/M82	1.02423	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.01654	1
IL2-6/WTpooled	0.73053	0.383
IL7-5/WTpooled	0.87578	1
IL7-3/WTpooled	1.23098	1
IL12-4/WTpooled	1.04516	0.891
IL1-4/WTpooled	0.97012	1
WT/WTpooled	1.06678	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	0.86664	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06708	0.692
DC3000/delta hrp 6h	1.07518	0.95
DC3000/delta hrp 12h	1.01212	1
DC3000/delta hrp 24h	0.98341	0.945

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.16396	0.229
DC3000 delta B/DC3000 delta AB	1.12665	0.468

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88812	1
Exp 36h	1.25044	1
Exp 60h	0.98968	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9857	1
Var 0h	1.12495	1
Var 12h I row2-row1	1.24125	0.204
Var 12h NI row2-row1	1.09754	1
Var 36h I row2-row1	1.00354	1
Var 36h NI row2-row1	1.13661	1
Var 60h I row2-row1	0.9115	0.439
Var 60h NI row2-row1	1.05532	1
Time course 0hI-0hNI	0.85977	0.11
Time course 12hI-12hNI	1.0997	0.536
Time course 36hI-36hNI	1.03945	0.355
Time course 60hI-60hNI	1.03597	0.673

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)	1.00104	1
transgenic ySAMdc/azygous control (breaker)	1.21917	0.178
transgenic ySAMdc/azygous control (red)	1.03077	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95129	0.051

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.06539	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89242	1
Manapal/WT (break)	0.8234	0.333
Manapal/WT (red)	0.87563	0.315