Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.10.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.52887	0.014
27DAP/17DAP	0.83979	0.602
39DAP/27DAP	1.63086	0.046
41DAP/39DAP	0.72736	0.119
42DAP/41DAP	1.15179	0.825
43DAP/42DAP	0.92404	0.801
47DAP/43DAP	1.50729	0.349
52DAP/47DAP	1.06724	0.879
57DAP/52DAP	1.26688	0.839

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.39855	0.013
17DAP/reference	0.90711	0.321
27DAP/reference	0.86383	0.078
39DAP/reference	0.99995	0.885
41DAP/reference	1.0138	1
42DAP/reference	1.14621	0.022
43DAP/reference	1.17713	0.064
47DAP/reference	1.90893	0.001
52DAP/reference	1.33008	0.016
57DAP/reference	1.2436	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97883	0.732
27DAP/17DAP	0.98705	0.943
39DAP/27DAP	0.95858	0.514
41DAP/39DAP	1.21751	0.417
42DAP/41DAP	0.98995	0.83
43DAP/42DAP	0.91767	0.351
47DAP/43DAP	1.03647	0.892
52DAP/47DAP	0.9857	0.925
57DAP/52DAP	1.17011	0.451
57DAP/7DAP	1.12953	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.64969	0.024
17DAP/reference	1.22533	0.016
27DAP/reference	1.141	0.246
39DAP/reference	1.36825	0.006
41DAP/reference	1.1561	0.056
42DAP/reference	1.00815	0.828
43DAP/reference	1.17838	0.028
47DAP/reference	1.08188	0.561
52DAP/reference	1.29499	0.052
57DAP/reference	1.33856	0.117

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.28472	0.35
17DAP/reference	1.02755	0.92
27DAP/reference	1.01662	1
39DAP/reference	0.99273	0.603
41DAP/reference	0.87682	0.108
42DAP/reference	0.96941	0.392
43DAP/reference	0.88086	0.229
47DAP/reference	1.20691	0.023
52DAP/reference	0.76828	0.005
57DAP/reference	0.87713	0.099

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.58774	0.033
17DAP/reference	1.09042	0.72
27DAP/reference	0.97634	0.416
39DAP/reference	0.99634	0.819
41DAP/reference	0.97798	0.56
42DAP/reference	1.05704	0.743
43DAP/reference	1.2027	0.081
47DAP/reference	1.17982	0.155
52DAP/reference	1.96203	0.056
57DAP/reference	1.40385	0.015

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.39793	0.56
26DAP/20DAP	1.39078	0.162
34DAP/26DAP	1.00214	0.998
51DAP/34DAP	0.90806	0.482
52DAP/51DAP	1.09766	0.313
53DAP/52DAP	0.9769	0.897
55DAP/53DAP	1.04643	0.976
57DAP/55DAP	1.22334	0.424
62DAP/57DAP	0.83942	0.28
68DAP/62DAP	0.82326	0.378
68DAP/14DAP	0.60446	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.96062	0.52

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.29045	0.058
Mature Green Tomato/Ripe Tomato	0.5543	0.019
Immature Eggplant/Mature Eggplant	1.26279	0.061
Ripe Pepper/Ripe Tomato	0.83819	0.224
Mature Eggplant/Ripe Tomato	0.77994	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0184	0.5
1-1-2/M82	1.12397	1
12-2/M82	0.85452	0.678
12-4/M82	0.96261	1
1-3/M82	2.34859
2-1-1/M82	0.97276	0.465
2-1/M82	0.9229
2-6/M82	1.0632
3-2/M82	0.91216	0.752
4-1-1/M82	1.08324	1
4-1/M82	1.49499
4-3-2/M82	1.20773
4-3/M82	1.31562	0.268
5-3/M82	1.19626	0.572
6-2/M82	0.83037	1
6-3/M82	1.02129	1
7-1/M82	1.34747	1
7-2/M82	N/A	N/A
9-3-2/M82	1.30708	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.85034	0.321
IL2-6/WTpooled	0.98941	1
IL7-5/WTpooled	0.47185	1
IL7-3/WTpooled	0.88035	0.294
IL12-4/WTpooled	1.00852	1
IL1-4/WTpooled	1.02995	0.426
WT/WTpooled	1.03991	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	1.29654	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07734	0.758
DC3000/delta hrp 6h	1.01059	1
DC3000/delta hrp 12h	0.91955	1
DC3000/delta hrp 24h	1.08903	0.502

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.19389	0.044
DC3000 delta B/DC3000 delta AB	0.94405	0.638

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.90096	1
Exp 36h	1.12278	1
Exp 60h	0.95879	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00139	1
Var 0h	0.51892	0.782
Var 12h I row2-row1	1.10526	0.736
Var 12h NI row2-row1	1.02347	1
Var 36h I row2-row1	1.13647	0.298
Var 36h NI row2-row1	0.86256	0.706
Var 60h I row2-row1	0.91289	0.439
Var 60h NI row2-row1	0.89382	0.516
Time course 0hI-0hNI	0.81553	0.071
Time course 12hI-12hNI	1.09907	0.168
Time course 36hI-36hNI	1.0007	0.611
Time course 60hI-60hNI	1.56742	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)	0.85071	0.297
transgenic ySAMdc/azygous control (breaker)	0.95033	0.49
transgenic ySAMdc/azygous control (red)	1.01742	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.16915	0.092

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.9922	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.9912	1
Manapal/WT (break)	1.15369	0.381
Manapal/WT (red)	1.1317	0.413