Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.6.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.24286	0.477
27DAP/17DAP	1.16776	0.833
39DAP/27DAP	0.96782	0.719
41DAP/39DAP	1.17424	0.359
42DAP/41DAP	1.179	0.797
43DAP/42DAP	0.93583	0.863
47DAP/43DAP	1.16363	0.769
52DAP/47DAP	0.79529	0.498
57DAP/52DAP	0.95796	0.956

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8946	0.167
17DAP/reference	0.9622	0.503
27DAP/reference	1.03449	0.721
39DAP/reference	0.98897	0.841
41DAP/reference	0.92869	0.201
42DAP/reference	1.14486	0.003
43DAP/reference	1.2922	0.01
47DAP/reference	1.22945	0.028
52DAP/reference	1.13393	0.108
57DAP/reference	1.05974	0.259

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.30087	0.142
27DAP/17DAP	0.82858	0.259
39DAP/27DAP	1.22362	0.453
41DAP/39DAP	0.99359	0.997
42DAP/41DAP	1.14786	0.401
43DAP/42DAP	1.20662	0.382
47DAP/43DAP	0.98831	0.939
52DAP/47DAP	1.16198	0.669
57DAP/52DAP	1.3661	0.363
57DAP/7DAP	1.20272

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79385	0.146
17DAP/reference	1.36675	1
27DAP/reference	0.80308	0.171
39DAP/reference	0.98637	0.64
41DAP/reference	1.16929	0.701
42DAP/reference	1.05072	0.675
43DAP/reference	0.9353	0.145
47DAP/reference	1.95064	0.056
52DAP/reference	1.15204	0.459
57DAP/reference	1.12287	0.158

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90238	0.248
17DAP/reference	1.2897	0.046
27DAP/reference	1.1846	0.1
39DAP/reference	1.18939	0.05
41DAP/reference	1.40927	0.027
42DAP/reference	1.23206	0.022
43DAP/reference	1.07398	0.875
47DAP/reference	1.11937	0.058
52DAP/reference	1.20761	0.01
57DAP/reference	0.92019	0.156

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1885	0.659
17DAP/reference	1.07394	0.531
27DAP/reference	1.05307	0.487
39DAP/reference	1.061	1
41DAP/reference	1.23503	0.205
42DAP/reference	1.38236	0.032
43DAP/reference	1.42051	0.023
47DAP/reference	1.5716	0.053
52DAP/reference	0.89332	0.405
57DAP/reference	1.50869	0.021

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03297	0.966
26DAP/20DAP	1.15377	0.594
34DAP/26DAP	1.21689	1
51DAP/34DAP	1.26268	0.535
52DAP/51DAP	0.69266	0.151
53DAP/52DAP	1.20619	0.537
55DAP/53DAP	0.83657	0.5
57DAP/55DAP	0.91436	0.619
62DAP/57DAP	N/A	N/A
68DAP/62DAP	1.04192	0.971
68DAP/14DAP	1.06643	0.558

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.46719	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.85766	0.329
Mature Green Tomato/Ripe Tomato	0.67036	0.047
Immature Eggplant/Mature Eggplant	1.01251	1
Ripe Pepper/Ripe Tomato	0.45064	0.293
Mature Eggplant/Ripe Tomato	0.30704	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.89349	0.944
1-1-2/M82	0.94951	0.754
12-2/M82	1.1509
12-4/M82	0.85683	1
1-3/M82	2.5549
2-1-1/M82	0.75508	0.784
2-1/M82	1.22393
2-6/M82	0.9724	1
3-2/M82	0.8325
4-1-1/M82	0.95758
4-1/M82	1.33821
4-3-2/M82	0.82094	1
4-3/M82	0.89978	1
5-3/M82	1.05833	1
6-2/M82	1.77239
6-3/M82	1.07234	1
7-1/M82	1.23936
7-2/M82	N/A	N/A
9-3-2/M82	0.87184	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.84005	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.19054	0.362
IL12-4/WTpooled	1.16705	0.532
IL1-4/WTpooled	0.78958	0.457
WT/WTpooled	1.11592	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	1.15943	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.74829	0.474
DC3000/delta hrp 6h	1.14475	1
DC3000/delta hrp 12h	0.95769	1
DC3000/delta hrp 24h	0.99594	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.26022	0.087
DC3000 delta B/DC3000 delta AB	0.97756	0.873

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.82923	0.328
Exp 36h	0.73514	0.471
Exp 60h	0.73545	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99001	1
Var 0h	0.91463	1
Var 12h I row2-row1	1.00082	1
Var 12h NI row2-row1	1.11217	0.649
Var 36h I row2-row1	1.28364	0.298
Var 36h NI row2-row1	1.12987	1
Var 60h I row2-row1	0.93178	0.293
Var 60h NI row2-row1	0.93714	1
Time course 0hI-0hNI	0.99865	1
Time course 12hI-12hNI	0.9514	0.746
Time course 36hI-36hNI	0.94626	0.403
Time course 60hI-60hNI	0.71236	0.011

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)	1.01276	0.798
transgenic ySAMdc/azygous control (breaker)	0.76948	0.119
transgenic ySAMdc/azygous control (red)	0.95296	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00507	0.766

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.12078	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.5507	0.105
Manapal/WT (break)	1.23948	0.381
Manapal/WT (red)	0.96646	0.863