Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.15.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9384	0.627
27DAP/17DAP	1.0462	0.92
39DAP/27DAP	0.86293	0.512
41DAP/39DAP	1.02546	1
42DAP/41DAP	1.2478	0.751
43DAP/42DAP	1.16052	0.993
47DAP/43DAP	1.0452	0.825
52DAP/47DAP	0.73794	0.378
57DAP/52DAP	1.03642	0.992

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00037	0.806
17DAP/reference	1.20588	0.012
27DAP/reference	1.03744	0.831
39DAP/reference	1.06744	0.125
41DAP/reference	1.14893	0.041
42DAP/reference	0.8646	0.034
43DAP/reference	1.02438	0.758
47DAP/reference	0.94826	0.09
52DAP/reference	0.75166	0.028
57DAP/reference	0.78964	0.078

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00411	0.826
27DAP/17DAP	1.03342	0.98
39DAP/27DAP	1.06397	0.799
41DAP/39DAP	0.9827	0.997
42DAP/41DAP	0.99641	0.872
43DAP/42DAP	0.97134	0.751
47DAP/43DAP	1.16553	0.396
52DAP/47DAP	0.92186	0.686
57DAP/52DAP	0.9858	0.742
57DAP/7DAP	1.04802	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06087	0.6
17DAP/reference	1.02649	0.822
27DAP/reference	1.14242	0.16
39DAP/reference	0.95547	0.307
41DAP/reference	0.78868	0.064
42DAP/reference	0.9636	0.436
43DAP/reference	0.98847	0.58
47DAP/reference	0.99786	1
52DAP/reference	0.94948	0.332
57DAP/reference	0.97718	0.477

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09193	0.276
17DAP/reference	1.04052	0.874
27DAP/reference	0.79648	0.069
39DAP/reference	0.79029	0.126
41DAP/reference	0.7958	0.052
42DAP/reference	0.83864	0.061
43DAP/reference	1.03611	0.787
47DAP/reference	0.91052	0.056
52DAP/reference	0.98551	0.537
57DAP/reference	1.35462	0.286

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1444	0.386
17DAP/reference	1.05255	0.685
27DAP/reference	1.09773	0.149
39DAP/reference	1.07243	0.613
41DAP/reference	1.16337	0.369
42DAP/reference	0.89227	0.287
43DAP/reference	1.11553	0.721
47DAP/reference	0.93141	0.348
52DAP/reference	0.9801	0.69
57DAP/reference	0.6586	0.029

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08698	0.966
26DAP/20DAP	1.62406	0.204
34DAP/26DAP	0.87527	0.763
51DAP/34DAP	0.89073	0.419
52DAP/51DAP	1.31182	0.638
53DAP/52DAP	1.01545	1
55DAP/53DAP	1.10806	0.477
57DAP/55DAP	1.06966	1
62DAP/57DAP	0.80026	0.466
68DAP/62DAP	0.88264	0.314
68DAP/14DAP	1.45216	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.48454	0.026

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.2701
Mature Green Tomato/Ripe Tomato	0.63882	0.028
Immature Eggplant/Mature Eggplant	1.46846
Ripe Pepper/Ripe Tomato	1.22249	1
Mature Eggplant/Ripe Tomato	0.83365	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.2358
1-1-2/M82	1.46611	1
12-2/M82	1.13177	1
12-4/M82	0.94742	0.319
1-3/M82	N/A	N/A
2-1-1/M82	0.90621
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	1.36748
4-1-1/M82	N/A	N/A
4-1/M82	1.56618
4-3-2/M82	N/A	N/A
4-3/M82	1.08331	1
5-3/M82	1.10065	1
6-2/M82	N/A	N/A
6-3/M82	0.92985	1
7-1/M82	1.16207	1
7-2/M82	0.94858	0.599
9-3-2/M82	0.88086

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.91456	1
IL2-6/WTpooled	0.90874	0.473
IL7-5/WTpooled	0.56978	0.559
IL7-3/WTpooled	0.56825	0.298
IL12-4/WTpooled	0.92178	1
IL1-4/WTpooled	0.96028	1
WT/WTpooled	1.08644	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	0.97987	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08424	0.921
DC3000/delta hrp 6h	0.92529	0.95
DC3000/delta hrp 12h	1.20868	1
DC3000/delta hrp 24h	1.08769	0.422

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	1.03472	0.761

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.84674	0.406
Exp 60h	1.08291	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9959	1
Var 0h	1.27806	0.782
Var 12h I row2-row1	1.09207	0.544
Var 12h NI row2-row1	0.9607	0.713
Var 36h I row2-row1	0.99043	1
Var 36h NI row2-row1	1.07659	1
Var 60h I row2-row1	1.19275	0.543
Var 60h NI row2-row1	1.0165	1
Time course 0hI-0hNI	1.04651	0.852
Time course 12hI-12hNI	0.96176	0.739
Time course 36hI-36hNI	1.09762	0.218
Time course 60hI-60hNI	0.98849	1

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)	0.97047	0.391
transgenic ySAMdc/azygous control (breaker)	1.01095	1
transgenic ySAMdc/azygous control (red)	0.94643	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.12177	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95862	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.81757	0.172
Manapal/WT (break)	0.87858	0.299
Manapal/WT (red)	0.93513	0.36