Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.2.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.62481	0.029
27DAP/17DAP	1.27482	0.799
39DAP/27DAP	2.09089	0.04
41DAP/39DAP	0.61601	0.045
42DAP/41DAP	1.1503	0.954
43DAP/42DAP	0.84937	0.721
47DAP/43DAP	0.80003	0.386
52DAP/47DAP	1.01049	0.908
57DAP/52DAP	1.70964	0.524

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27757	0.007
17DAP/reference	1.03263	0.631
27DAP/reference	0.95978	0.471
39DAP/reference	0.9573	0.554
41DAP/reference	0.92872	0.434
42DAP/reference	1.07731	0.098
43DAP/reference	1.08658	0.34
47DAP/reference	1.0986	0.081
52DAP/reference	1.08792	0.014
57DAP/reference	1.20652	0.037

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.12837	0.5
27DAP/17DAP	1.00398	0.969
39DAP/27DAP	0.94855	0.692
41DAP/39DAP	1.35984	0.59
42DAP/41DAP	1.08111	0.753
43DAP/42DAP	0.92275	0.383
47DAP/43DAP	0.99703	0.99
52DAP/47DAP	0.87722	0.203
57DAP/52DAP	1.15023	0.385
57DAP/7DAP	0.71535	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.05311	0.024
17DAP/reference	1.76086	0.006
27DAP/reference	1.58326	0.009
39DAP/reference	1.42427	0.006
41DAP/reference	1.44945	0.024
42DAP/reference	1.34025	0.046
43DAP/reference	1.41213	0.006
47DAP/reference	1.41406	0.017
52DAP/reference	1.89152	0.007
57DAP/reference	1.77409	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27397	0.265
17DAP/reference	1.17276	0.191
27DAP/reference	1.28583	0.05
39DAP/reference	1.32188	0.013
41DAP/reference	1.13269	0.177
42DAP/reference	1.09697	0.259
43DAP/reference	0.87882	0.263
47DAP/reference	1.27384	0.029
52DAP/reference	0.90916	0.111
57DAP/reference	1.10017	0.827

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.83712	0.019
17DAP/reference	1.15194	0.531
27DAP/reference	1.18405	0.088
39DAP/reference	1.3296	0.024
41DAP/reference	1.31797	0.025
42DAP/reference	1.43892	0.014
43DAP/reference	1.50204	0.022
47DAP/reference	1.12935	0.562
52DAP/reference	1.6641	0.03
57DAP/reference	1.68392	0.021

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9391	1
26DAP/20DAP	1.71264	0.103
34DAP/26DAP	0.92309	0.861
51DAP/34DAP	0.75774	0.101
52DAP/51DAP	0.90671	1
53DAP/52DAP	1.01611	0.998
55DAP/53DAP	0.5591	0.02
57DAP/55DAP	1.6792	0.079
62DAP/57DAP	1.05625	0.8
68DAP/62DAP	1.00899	0.914
68DAP/14DAP	1.33073	0.384

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.67767	0.041

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.986	0.847
Mature Green Tomato/Ripe Tomato	1.37731	0.331
Immature Eggplant/Mature Eggplant	1.29302	0.058
Ripe Pepper/Ripe Tomato	1.3696	1
Mature Eggplant/Ripe Tomato	1.86081	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9318	0.944
1-1-2/M82	1.34018	1
12-2/M82	0.59443
12-4/M82	0.91655	1
1-3/M82	2.14235	0.248
2-1-1/M82	0.80839	0.465
2-1/M82	1.02457
2-6/M82	1.13494	0.405
3-2/M82	1.17477
4-1-1/M82	1.31952	1
4-1/M82	0.62273
4-3-2/M82	2.11068
4-3/M82	1.34456	1
5-3/M82	1.12871	0.496
6-2/M82	N/A	N/A
6-3/M82	1.01804	1
7-1/M82	1.07428	1
7-2/M82	1.42293	0.385
9-3-2/M82	1.3038

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.99541	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.24208	1
IL12-4/WTpooled	1.06341	0.785
IL1-4/WTpooled	1.08768
WT/WTpooled	1.02083	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	1.06387	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0593	0.921
DC3000/delta hrp 6h	1.00963	0.95
DC3000/delta hrp 12h	0.97621	1
DC3000/delta hrp 24h	1.04932	0.71

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.13386	0.087
DC3000 delta B/DC3000 delta AB	1.30081	0.223

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94108	1
Exp 36h	1.08706	1
Exp 60h	1.00535	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00595	1
Var 0h	0.9752	1
Var 12h I row2-row1	0.84901	0.514
Var 12h NI row2-row1	1.18613	1
Var 36h I row2-row1	0.98562	1
Var 36h NI row2-row1	0.87907	0.706
Var 60h I row2-row1	0.85649	0.582
Var 60h NI row2-row1	0.81276	0.329
Time course 0hI-0hNI	0.84376	0.122
Time course 12hI-12hNI	0.99237	1
Time course 36hI-36hNI	1.32239	0.218
Time course 60hI-60hNI	1.41546	0.012

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)	0.87636	0.314
transgenic ySAMdc/azygous control (breaker)	1.32766	0.248
transgenic ySAMdc/azygous control (red)	1.18162	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03617	0.448

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.85426	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.83171	1
Manapal/WT (break)	0.95379	1
Manapal/WT (red)	1.2088	0.413