Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.6.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.2932	0.452
27DAP/17DAP	1.0761	0.877
39DAP/27DAP	0.79796	0.421
41DAP/39DAP	1.21797	0.238
42DAP/41DAP	0.97528	1
43DAP/42DAP	1.07338	1
47DAP/43DAP	1.30047	0.429
52DAP/47DAP	0.89736	0.695
57DAP/52DAP	1.10891	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.52573	0.02
17DAP/reference	1.22794	0.143
27DAP/reference	0.92143	0.059
39DAP/reference	0.87365	0.029
41DAP/reference	0.89869	0.201
42DAP/reference	0.82348	0.003
43DAP/reference	0.94689	0.464
47DAP/reference	0.7215	0.001
52DAP/reference	0.78984	0.102
57DAP/reference	0.75395	0.054

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91665	0.299
27DAP/17DAP	0.96408	0.878
39DAP/27DAP	1.07941	0.603
41DAP/39DAP	1.05961	0.921
42DAP/41DAP	1.04196	0.879
43DAP/42DAP	1.14209	0.324
47DAP/43DAP	1.02693	0.95
52DAP/47DAP	1.14014	0.593
57DAP/52DAP	0.91675	0.391
57DAP/7DAP	1.08476	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.43038	0.069
17DAP/reference	1.46138	0.059
27DAP/reference	1.22005	0.246
39DAP/reference	1.10825	0.486
41DAP/reference	1.33878	0.121
42DAP/reference	1.1602	0.534
43DAP/reference	1.07686	0.672
47DAP/reference	1.45499	0.056
52DAP/reference	1.21508	0.183
57DAP/reference	1.17361	0.076

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.49795	0.06
17DAP/reference	2.09776	0.008
27DAP/reference	1.94083	0.017
39DAP/reference	1.50935	0.013
41DAP/reference	1.58737	0.014
42DAP/reference	1.40187	0.032
43DAP/reference	0.9774	0.569
47DAP/reference	1.21024	0.029
52DAP/reference	1.47213	0.006
57DAP/reference	0.90785	0.226

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10162	0.338
17DAP/reference	1.24589	0.427
27DAP/reference	1.3401	0.143
39DAP/reference	1.13289	0.296
41DAP/reference	1.02052	1
42DAP/reference	0.95675	0.552
43DAP/reference	0.94742	0.432
47DAP/reference	0.62831	0.005
52DAP/reference	0.84312	0.289
57DAP/reference	0.50073	0.018

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95279	0.733
26DAP/20DAP	0.82892	0.512
34DAP/26DAP	1.06552	1
51DAP/34DAP	1.08857	0.637
52DAP/51DAP	1.0335	0.965
53DAP/52DAP	0.98505	0.917
55DAP/53DAP	1.12427	0.527
57DAP/55DAP	1.06163	0.841
62DAP/57DAP	1.25704	0.678
68DAP/62DAP	1.0216	0.962
68DAP/14DAP	1.25595	0.594

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.9724	0.547

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.84423	0.058
Mature Green Tomato/Ripe Tomato	0.9227	0.522
Immature Eggplant/Mature Eggplant	0.68357	0.067
Ripe Pepper/Ripe Tomato	0.95412	1
Mature Eggplant/Ripe Tomato	5.42499	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03038	1
1-1-2/M82	1.02129	1
12-2/M82	1.74674
12-4/M82	0.63134
1-3/M82	0.82561	0.378
2-1-1/M82	1.03506	1
2-1/M82	N/A	N/A
2-6/M82	1.04286	1
3-2/M82	N/A	N/A
4-1-1/M82	0.73866	1
4-1/M82	0.90881	1
4-3-2/M82	0.78636	0.698
4-3/M82	0.76749
5-3/M82	0.91928	1
6-2/M82	0.79415
6-3/M82	1.1517
7-1/M82	0.84957
7-2/M82	1.00072	1
9-3-2/M82	0.87571	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.15664	0.46
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.09376	1
IL12-4/WTpooled	0.57062	0.566
IL1-4/WTpooled	1.04966	1
WT/WTpooled	0.8875	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	1.23467	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01237	0.921
DC3000/delta hrp 6h	0.89808	0.95
DC3000/delta hrp 12h	0.88882	1
DC3000/delta hrp 24h	1.06099	0.655

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	1.12641	0.586

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.84824	1
Exp 36h	1.37859	1
Exp 60h	0.83407	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9533	1
Var 0h	0.88801	0.933
Var 12h I row2-row1	1.04907	0.58
Var 12h NI row2-row1	0.79639	0.394
Var 36h I row2-row1	0.84929	0.805
Var 36h NI row2-row1	1.0891	1
Var 60h I row2-row1	1.35217	0.562
Var 60h NI row2-row1	1.30207	0.904
Time course 0hI-0hNI	1.02496	0.852
Time course 12hI-12hNI	1.03954	0.743
Time course 36hI-36hNI	0.9332	0.134
Time course 60hI-60hNI	0.9808	0.646

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)	1.04854	0.863
transgenic ySAMdc/azygous control (breaker)	0.29356	0.118
transgenic ySAMdc/azygous control (red)	1.26906	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04963	0.334

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.43118	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.19202	0.307
Manapal/WT (break)	1.41457	0.381
Manapal/WT (red)	1.32127	1