Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.6.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97054	0.77
27DAP/17DAP	1.05112	0.885
39DAP/27DAP	1.77399	0.064
41DAP/39DAP	0.79241	0.283
42DAP/41DAP	1.34682	0.871
43DAP/42DAP	1.46612	0.894
47DAP/43DAP	0.38865	0.049
52DAP/47DAP	1.08668	0.963
57DAP/52DAP	1.328	0.894

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01395	0.824
17DAP/reference	1.19794	0.427
27DAP/reference	0.92746	0.249
39DAP/reference	1.34967	0.294
41DAP/reference	0.97865	0.667
42DAP/reference	2.09173	0.001
43DAP/reference	1.73843	0.007
47DAP/reference	1.39711	0.002
52DAP/reference	0.99013	0.58
57DAP/reference	1.23649	0.016

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.50943	0.06
27DAP/17DAP	1.11218	0.73
39DAP/27DAP	0.91993	0.556
41DAP/39DAP	1.42677	0.763
42DAP/41DAP	1.21878	0.526
43DAP/42DAP	1.03201	0.478
47DAP/43DAP	0.97994	0.902
52DAP/47DAP	0.86469	0.397
57DAP/52DAP	0.90051	0.403
57DAP/7DAP	1.08759	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.48367	0.043
17DAP/reference	1.39445	0.007
27DAP/reference	1.19838	0.197
39DAP/reference	1.38785	0.073
41DAP/reference	1.46539	0.012
42DAP/reference	1.57014	0.018
43DAP/reference	1.83616	0.012
47DAP/reference	2.86438	0.014
52DAP/reference	2.01984	0.015
57DAP/reference	1.73098	0.029

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9405	0.503
17DAP/reference	1.45807	0.026
27DAP/reference	1.52712	0.021
39DAP/reference	1.36818	0.03
41DAP/reference	1.27434	0.011
42DAP/reference	1.66527	0.008
43DAP/reference	1.21061	0.785
47DAP/reference	1.65572	0.01
52DAP/reference	1.06459	0.393
57DAP/reference	1.18814	0.538

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06741	0.481
17DAP/reference	1.09249	0.712
27DAP/reference	1.0583	0.575
39DAP/reference	1.19335	0.015
41DAP/reference	1.28017	0.045
42DAP/reference	1.91949	0.01
43DAP/reference	2.77481	0.008
47DAP/reference	1.39786	0.104
52DAP/reference	1.3435	0.095
57DAP/reference	2.20605	0.008

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9979	1
26DAP/20DAP	2.91708	0.136
34DAP/26DAP	0.80004	0.509
51DAP/34DAP	1.44847	0.073
52DAP/51DAP	0.93977	1
53DAP/52DAP	0.5658	0.049
55DAP/53DAP	0.30544	0.016
57DAP/55DAP	0.8454	0.556
62DAP/57DAP	1.14882	0.098
68DAP/62DAP	0.98735	0.885
68DAP/14DAP	0.93285	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	8.61335	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.66078	0.058
Mature Green Tomato/Ripe Tomato	1.16893	0.948
Immature Eggplant/Mature Eggplant	1.03554	0.554
Ripe Pepper/Ripe Tomato	0.50719	0.224
Mature Eggplant/Ripe Tomato	0.58789	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.85559	0.605
1-1-2/M82	1.91443	1
12-2/M82	1.02366	1
12-4/M82	2.40758	1
1-3/M82	3.15437	0.479
2-1-1/M82	0.97674	0.92
2-1/M82	0.71656	0.325
2-6/M82	1.3166	0.385
3-2/M82	0.98345	1
4-1-1/M82	1.73351	1
4-1/M82	5.63455	0.853
4-3-2/M82	2.34394	0.508
4-3/M82	1.18608	1
5-3/M82	0.89267	1
6-2/M82	1.7136	1
6-3/M82	1.10662	1
7-1/M82	1.05585	0.539
7-2/M82	2.05149	0.385
9-3-2/M82	2.07785	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.60725
IL2-6/WTpooled	0.97476	1
IL7-5/WTpooled	0.97827	1
IL7-3/WTpooled	1.53028	1
IL12-4/WTpooled	1.0553	0.839
IL1-4/WTpooled	0.95332	1
WT/WTpooled	1.01756	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	1.25302	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97893	1
DC3000/delta hrp 6h	0.88959	0.95
DC3000/delta hrp 12h	1.09901	1
DC3000/delta hrp 24h	0.6914	0.045

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.94862	1
DC3000 delta B/DC3000 delta AB	0.65164	0.025

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.8397	1
Exp 36h	2.15901	0.693
Exp 60h	1.02657	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99683	1
Var 0h	0.93417	0.332
Var 12h I row2-row1	1.2192	0.736
Var 12h NI row2-row1	1.27898	0.649
Var 36h I row2-row1	0.98027	1
Var 36h NI row2-row1	1.87238	1
Var 60h I row2-row1	0.98967	1
Var 60h NI row2-row1	0.99113	1
Time course 0hI-0hNI	1.28423	0.155
Time course 12hI-12hNI	0.9197	0.393
Time course 36hI-36hNI	0.57769	0.023
Time course 60hI-60hNI	0.34296	0.005

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)	1.12349	0.286
transgenic ySAMdc/azygous control (breaker)	0.74631	0.251
transgenic ySAMdc/azygous control (red)	0.94196	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05719	0.086

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.74428	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.63468	0.172
Manapal/WT (break)	0.96843	1
Manapal/WT (red)	0.87995	0.315