Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.16.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	6.88906	0.037
27DAP/17DAP	1.41954	0.801
39DAP/27DAP	2.71665	0.025
41DAP/39DAP	0.68701	0.127
42DAP/41DAP	0.88259	1
43DAP/42DAP	1.39455	0.982
47DAP/43DAP	1.05651	0.934
52DAP/47DAP	0.93189	0.565
57DAP/52DAP	1.67796	0.96

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.53032	0.025
17DAP/reference	1.64471	0.787
27DAP/reference	2.59685	0.011
39DAP/reference	1.5802	0.04
41DAP/reference	1.17167	0.624
42DAP/reference	1.38464	0.011
43DAP/reference	0.94379	0.519
47DAP/reference	1.28622	0.071
52DAP/reference	0.54241	0.013
57DAP/reference	0.57897	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03343	0.774
27DAP/17DAP	0.99976	1
39DAP/27DAP	1.29316	0.292
41DAP/39DAP	0.55144	0.112
42DAP/41DAP	1.26185	0.065
43DAP/42DAP	1.45157	0.024
47DAP/43DAP	0.76846	0.014
52DAP/47DAP	0.89533	0.357
57DAP/52DAP	0.82091	0.29
57DAP/7DAP	1.31026	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19484	0.235
17DAP/reference	1.07735	0.064
27DAP/reference	1.51144	0.023
39DAP/reference	2.00961	0.005
41DAP/reference	2.29351	0.008
42DAP/reference	2.75519	0.013
43DAP/reference	3.80519	0.006
47DAP/reference	2.92384	0.014
52DAP/reference	2.82878	0.008
57DAP/reference	2.03313	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.54135	0.008
17DAP/reference	0.69454	0.011
27DAP/reference	1.96212	0.016
39DAP/reference	1.62489	0.047
41DAP/reference	1.68614	0.006
42DAP/reference	1.72735	0.009
43DAP/reference	0.61613	0.027
47DAP/reference	0.93174	0.319
52DAP/reference	0.72025	0.006
57DAP/reference	0.37175	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.4889	0.026
17DAP/reference	0.69916	0.13
27DAP/reference	1.14832	0.392
39DAP/reference	2.363	0.009
41DAP/reference	1.29684	0.018
42DAP/reference	1.48141	0.015
43DAP/reference	1.36856	0.214
47DAP/reference	1.57177	0.171
52DAP/reference	1.52643	0.349
57DAP/reference	1.66356	0.106

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93814	1
26DAP/20DAP	0.83929	0.317
34DAP/26DAP	1.06879	1
51DAP/34DAP	1.04301	0.654
52DAP/51DAP	0.90432	1
53DAP/52DAP	1.22176	0.212
55DAP/53DAP	0.99007	0.876
57DAP/55DAP	0.96127	0.795
62DAP/57DAP	0.87887	0.28
68DAP/62DAP	1.06921	0.897
68DAP/14DAP	2.67923	0.094

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.09148	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.44805	0.085
Mature Green Tomato/Ripe Tomato	3.68919	0.015
Immature Eggplant/Mature Eggplant	0.48657	0.067
Ripe Pepper/Ripe Tomato	8.15429	0.258
Mature Eggplant/Ripe Tomato	0.56094	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.80701
1-1-2/M82	1.17437	1
12-2/M82	1.7214
12-4/M82	0.80882	1
1-3/M82	N/A	N/A
2-1-1/M82	0.8544	0.92
2-1/M82	0.45007	0.318
2-6/M82	1.91888
3-2/M82	0.57464
4-1-1/M82	0.38397
4-1/M82	1.12578
4-3-2/M82	1.02432	1
4-3/M82	1.08258	1
5-3/M82	1.33008	0.496
6-2/M82	1.21152
6-3/M82	N/A	N/A
7-1/M82	1.46289	0.578
7-2/M82	N/A	N/A
9-3-2/M82	1.20429	0.171

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.73976
IL2-6/WTpooled	1.1267	0.531
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.12625	0.362
IL12-4/WTpooled	2.87611	0.595
IL1-4/WTpooled	1.14469	1
WT/WTpooled	0.98745	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	1.07841	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94698	1
DC3000/delta hrp 6h	0.98254	0.95
DC3000/delta hrp 12h	1.42136	1
DC3000/delta hrp 24h	0.33605	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.04737	0.476
DC3000 delta B/DC3000 delta AB	1.0767	0.524

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.83086	0.328
Exp 36h	0.72722	0.337
Exp 60h	0.68761	0.253

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04752	1
Var 0h	1.36081	0.98
Var 12h I row2-row1	0.98962	1
Var 12h NI row2-row1	0.86713	0.403
Var 36h I row2-row1	1.00338	1
Var 36h NI row2-row1	0.95833	0.584
Var 60h I row2-row1	1.36205	0.562
Var 60h NI row2-row1	1.04872	1
Time course 0hI-0hNI	0.92511	0.555
Time course 12hI-12hNI	0.91763	0.546
Time course 36hI-36hNI	0.96427	0.494
Time course 60hI-60hNI	0.61495	0.009

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)	1.01	0.921
transgenic ySAMdc/azygous control (breaker)	0.53225	0.131
transgenic ySAMdc/azygous control (red)	0.87438	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98098	0.237

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.63296	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.12945	0.14
Manapal/WT (break)	0.47443	0.333
Manapal/WT (red)	1.18274	0.413