Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.9.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0834	0.863
27DAP/17DAP	1.33594	0.688
39DAP/27DAP	1.38744	0.176
41DAP/39DAP	0.93743	0.646
42DAP/41DAP	1.46822	0.481
43DAP/42DAP	0.98417	0.925
47DAP/43DAP	1.01371	0.904
52DAP/47DAP	1.10714	0.913
57DAP/52DAP	0.87204	0.684

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88985	0.188
17DAP/reference	1.03729	0.384
27DAP/reference	1.05431	0.15
39DAP/reference	0.95981	0.513
41DAP/reference	1.07973	0.145
42DAP/reference	0.93593	0.139
43DAP/reference	0.99978	0.904
47DAP/reference	0.96797	0.322
52DAP/reference	0.85404	0.223
57DAP/reference	1.04986	0.901

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03358	0.63
27DAP/17DAP	0.93706	0.195
39DAP/27DAP	1.13955	0.41
41DAP/39DAP	0.87339	0.321
42DAP/41DAP	1.02066	0.947
43DAP/42DAP	1.05108	0.079
47DAP/43DAP	1.02939	0.865
52DAP/47DAP	1.09199	0.779
57DAP/52DAP	1.03548	0.8
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97431	0.402
17DAP/reference	0.93611	0.018
27DAP/reference	0.87424	0.011
39DAP/reference	0.97925	0.264
41DAP/reference	0.93531	0.062
42DAP/reference	1.00554	1
43DAP/reference	1.04303	0.432
47DAP/reference	1.20039	0.104
52DAP/reference	0.9924	0.621
57DAP/reference	1.02034	0.536

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99479	0.884
17DAP/reference	0.96972	0.499
27DAP/reference	1.41196	0.437
39DAP/reference	1.19472	0.061
41DAP/reference	1.01199	0.718
42DAP/reference	0.9321	0.289
43DAP/reference	1.03127	0.845
47DAP/reference	0.90811	0.068
52DAP/reference	0.9535	0.327
57DAP/reference	0.9078	0.063

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96822	0.311
17DAP/reference	0.94937	0.165
27DAP/reference	0.92435	0.065
39DAP/reference	0.97093	0.133
41DAP/reference	0.95287	0.293
42DAP/reference	0.99262	0.671
43DAP/reference	0.99968	0.894
47DAP/reference	1.05328	0.294
52DAP/reference	0.99503	0.871
57DAP/reference	1.09404	0.801

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02528	0.966
26DAP/20DAP	0.99812	1
34DAP/26DAP	0.90326	0.322
51DAP/34DAP	1.05136	0.637
52DAP/51DAP	0.98496	1
53DAP/52DAP	1.08743	0.688
55DAP/53DAP	1.00405	0.994
57DAP/55DAP	1.08769	0.87
62DAP/57DAP	1.08536	0.8
68DAP/62DAP	0.97366	0.834
68DAP/14DAP	1.03364	0.958

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.68378	0.017

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.84062	0.301
Mature Green Tomato/Ripe Tomato	0.92323	0.287
Immature Eggplant/Mature Eggplant	1.52475	0.05
Ripe Pepper/Ripe Tomato	0.96883	1
Mature Eggplant/Ripe Tomato	0.70041	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.14252	0.574
1-1-2/M82	1.15382	1
12-2/M82	1.13908	1
12-4/M82	1.19663	1
1-3/M82	1.18309	0.479
2-1-1/M82	1.08513	0.375
2-1/M82	0.74845	0.345
2-6/M82	1.05545	0.695
3-2/M82	1.09359	0.967
4-1-1/M82	1.13094	1
4-1/M82	1.57058	0.429
4-3-2/M82	1.18242	0.508
4-3/M82	1.16735	1
5-3/M82	0.88955	0.642
6-2/M82	1.20168	1
6-3/M82	1.04611	1
7-1/M82	0.8623	0.476
7-2/M82	1.42332	0.291
9-3-2/M82	1.47824	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.37391
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	0.92023	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94212	1
DC3000/delta hrp 6h	1.01449	1
DC3000/delta hrp 12h	1.07241	1
DC3000/delta hrp 24h	1.05818	0.62

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.07699	0.057
DC3000 delta B/DC3000 delta AB	1.13173	0.284

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.06696	1
Exp 36h	1.11577	0.693
Exp 60h	1.01871	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97957	1
Var 0h	0.57916	1
Var 12h I row2-row1	1.16331	0.348
Var 12h NI row2-row1	1.01678	1
Var 36h I row2-row1	0.98776	1
Var 36h NI row2-row1	0.84993	0.478
Var 60h I row2-row1	1.25351	0.562
Var 60h NI row2-row1	1.1229	0.904
Time course 0hI-0hNI	1.10478	0.719
Time course 12hI-12hNI	1.04737	0.738
Time course 36hI-36hNI	1.04126	0.316
Time course 60hI-60hNI	1.35325	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)	1.05404	0.748
transgenic ySAMdc/azygous control (breaker)	0.94156	0.49
transgenic ySAMdc/azygous control (red)	1.0969	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.13029	0.092

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.72834	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.91777	1
Manapal/WT (break)	1.07719	1
Manapal/WT (red)	1.00021	1