Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.18.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93706	0.543
27DAP/17DAP	1.09455	0.849
39DAP/27DAP	0.85892	0.474
41DAP/39DAP	1.50964	0.38
42DAP/41DAP	0.96256	1
43DAP/42DAP	0.95118	0.705
47DAP/43DAP	1.01653	0.965
52DAP/47DAP	1.03217	0.96
57DAP/52DAP	1.03846	0.972

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1031	0.081
17DAP/reference	0.98707	0.597
27DAP/reference	1.0303	0.365
39DAP/reference	1.01864	0.639
41DAP/reference	1.05063	0.287
42DAP/reference	1.0365	0.08
43DAP/reference	1.04743	0.425
47DAP/reference	1.02303	0.575
52DAP/reference	1.01318	0.73
57DAP/reference	0.95854	0.156

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00087	1
27DAP/17DAP	0.9615	0.748
39DAP/27DAP	1.05186	0.558
41DAP/39DAP	1.11396	0.224
42DAP/41DAP	1.01781	0.886
43DAP/42DAP	0.98632	0.831
47DAP/43DAP	1.02639	0.857
52DAP/47DAP	1.08348	0.718
57DAP/52DAP	1.03288	0.856
57DAP/7DAP	1.05053	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93869	0.27
17DAP/reference	0.94603	0.124
27DAP/reference	0.86385	0.011
39DAP/reference	0.95621	0.025
41DAP/reference	1.00829	1
42DAP/reference	0.95726	0.144
43DAP/reference	1.01456	1
47DAP/reference	0.93217	0.101
52DAP/reference	1.03349	0.459
57DAP/reference	0.98682	0.569

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95938	0.374
17DAP/reference	0.98556	0.594
27DAP/reference	0.98128	0.467
39DAP/reference	1.0204	0.935
41DAP/reference	0.98534	0.505
42DAP/reference	1.03607	0.715
43DAP/reference	0.99087	0.736
47DAP/reference	1.07851	0.061
52DAP/reference	1.02396	0.343
57DAP/reference	1.00389	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93052	0.038
17DAP/reference	0.96755	0.381
27DAP/reference	0.91873	0.069
39DAP/reference	0.92308	0.092
41DAP/reference	0.95058	0.167
42DAP/reference	0.83439	0.016
43DAP/reference	0.95694	0.165
47DAP/reference	1.0278	0.68
52DAP/reference	0.86767	0.2
57DAP/reference	0.82686	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0421	0.945
26DAP/20DAP	0.97161	1
34DAP/26DAP	1.02754	1
51DAP/34DAP	0.98019	0.77
52DAP/51DAP	1.06209	0.446
53DAP/52DAP	0.92576	0.562
55DAP/53DAP	1.09251	0.693
57DAP/55DAP	1.02401	0.955
62DAP/57DAP	1	1
68DAP/62DAP	1.23215	0.278
68DAP/14DAP	1.11453	0.295

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.00571	0.908

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.03412
Mature Green Tomato/Ripe Tomato	1.06634	0.881
Immature Eggplant/Mature Eggplant	1.36995	0.142
Ripe Pepper/Ripe Tomato	2.09316	1
Mature Eggplant/Ripe Tomato	3.16744	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.09201	0.877
1-1-2/M82	0.92786	1
12-2/M82	0.96141	0.955
12-4/M82	1.01189	1
1-3/M82	1.05443	1
2-1-1/M82	1.15509	0.764
2-1/M82	1.36595
2-6/M82	0.96064	1
3-2/M82	0.8645	1
4-1-1/M82	1.09089	1
4-1/M82	0.96165	1
4-3-2/M82	0.95692	1
4-3/M82	1.10036	1
5-3/M82	1.01218	1
6-2/M82	1.10412	1
6-3/M82	0.99737	1
7-1/M82	0.98504	1
7-2/M82	1.15533	1
9-3-2/M82	0.74056

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.46111	0.419
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.65355	0.294
IL12-4/WTpooled	1.19836	0.695
IL1-4/WTpooled	1.10044
WT/WTpooled	1.10944	0.89

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	1.20248

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97058	1
DC3000/delta hrp 6h	1.17775	1
DC3000/delta hrp 12h	0.95372	1
DC3000/delta hrp 24h	1.03293	0.655

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.98029	1
DC3000 delta B/DC3000 delta AB	1.06868	0.437

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99827	1
Var 0h	1.43639	0.225
Var 12h I row2-row1	1.05923	0.506
Var 12h NI row2-row1	1.03086	1
Var 36h I row2-row1	0.80765	0.805
Var 36h NI row2-row1	1.14868	1
Var 60h I row2-row1	1.1793	1
Var 60h NI row2-row1	0.91113	0.572
Time course 0hI-0hNI	1.03139	1
Time course 12hI-12hNI	0.99503	1
Time course 36hI-36hNI	0.87808	0.119
Time course 60hI-60hNI	1.14721	0.137

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)	1.0383	1
transgenic ySAMdc/azygous control (breaker)	1.41888	1
transgenic ySAMdc/azygous control (red)	1.30108	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00943	0.556

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.79206	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.08482	1
Manapal/WT (break)	0.97624	1
Manapal/WT (red)	0.84308	0.424