Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.16.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06442	0.964
27DAP/17DAP	1.15434	0.881
39DAP/27DAP	1.15799	0.888
41DAP/39DAP	1.15701	0.806
42DAP/41DAP	1.43622	0.599
43DAP/42DAP	0.8978	0.827
47DAP/43DAP	0.95955	0.724
52DAP/47DAP	1.35108	0.608
57DAP/52DAP	1.03022	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98148	0.526
17DAP/reference	1.02497	0.74
27DAP/reference	0.98854	0.725
39DAP/reference	1.01019	0.786
41DAP/reference	1.04399	0.667
42DAP/reference	0.90923	0.007
43DAP/reference	0.98034	0.611
47DAP/reference	0.92575	0.007
52DAP/reference	0.93367	0.283
57DAP/reference	0.90508	0.071

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98716	0.763
27DAP/17DAP	1.00756	0.988
39DAP/27DAP	1.02436	0.718
41DAP/39DAP	1.1024	0.88
42DAP/41DAP	1.01562	1
43DAP/42DAP	1.03132	0.627
47DAP/43DAP	1.03122	0.906
52DAP/47DAP	1.03204	0.892
57DAP/52DAP	0.99008	0.823
57DAP/7DAP	1.05538	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77599	0.07
17DAP/reference	0.73797	0.011
27DAP/reference	0.74263	0.01
39DAP/reference	0.82796	0.011
41DAP/reference	0.82706	0.025
42DAP/reference	0.79566	0.011
43DAP/reference	0.79243	0.011
47DAP/reference	0.79946	0.036
52DAP/reference	0.80132	0.012
57DAP/reference	0.85532	0.02

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97314	0.655
17DAP/reference	1.01415	0.806
27DAP/reference	0.85995	0.119
39DAP/reference	0.84252	0.113
41DAP/reference	1.0455	0.735
42DAP/reference	0.91504	0.169
43DAP/reference	1.08239	0.401
47DAP/reference	1.04095	0.544
52DAP/reference	0.99889	0.761
57DAP/reference	1.10068	0.188

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76631	0.035
17DAP/reference	0.90463	0.262
27DAP/reference	0.80818	0.038
39DAP/reference	0.86404	0.133
41DAP/reference	0.83278	0.023
42DAP/reference	0.67896	0.019
43DAP/reference	0.77018	0.052
47DAP/reference	0.95242	0.383
52DAP/reference	0.762	0.167
57DAP/reference	0.59511	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97502	1
26DAP/20DAP	0.93351	1
34DAP/26DAP	0.97707	0.97
51DAP/34DAP	0.93953	0.64
52DAP/51DAP	1.01106	0.925
53DAP/52DAP	1.04526	0.738
55DAP/53DAP	1.01607	0.939
57DAP/55DAP	0.96192	0.799
62DAP/57DAP	0.99318	1
68DAP/62DAP	0.97908	0.668
68DAP/14DAP	0.95722	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.85731	0.224

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.54494
Mature Green Tomato/Ripe Tomato	1.06295	0.814
Immature Eggplant/Mature Eggplant	1.10917	0.239
Ripe Pepper/Ripe Tomato	0.50557	0.293
Mature Eggplant/Ripe Tomato	3.23459	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95554	0.944
1-1-2/M82	0.95578	1
12-2/M82	1.0828	1
12-4/M82	0.97579	1
1-3/M82	0.81127	0.441
2-1-1/M82	1.1129	0.375
2-1/M82	N/A	N/A
2-6/M82	1.09767	0.594
3-2/M82	0.91045
4-1-1/M82	0.97007	1
4-1/M82	0.92348	1
4-3-2/M82	0.99414	1
4-3/M82	0.72176	0.72
5-3/M82	0.89791	0.49
6-2/M82	0.73138
6-3/M82	0.92989	1
7-1/M82	N/A	N/A
7-2/M82	1.04598	1
9-3-2/M82	0.68898	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.17674	0.365
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.90251	1
IL7-3/WTpooled	0.75653	1
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.77848	0.699
WT/WTpooled	0.97624	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	0.75141	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94269	0.849
DC3000/delta hrp 6h	0.93474	0.95
DC3000/delta hrp 12h	1.03985	1
DC3000/delta hrp 24h	0.99954	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.10137	0.355
DC3000 delta B/DC3000 delta AB	0.95593	0.657

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04746	1
Exp 36h	1.06693	1
Exp 60h	1.02059	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97977	1
Var 0h	0.86869	0.457
Var 12h I row2-row1	1.13136	0.272
Var 12h NI row2-row1	1.05168	1
Var 36h I row2-row1	0.86844	0.805
Var 36h NI row2-row1	0.97088	0.743
Var 60h I row2-row1	1.44974	0.562
Var 60h NI row2-row1	1.01964	1
Time course 0hI-0hNI	1.09795	0.662
Time course 12hI-12hNI	1.00923	0.88
Time course 36hI-36hNI	0.8939	0.265
Time course 60hI-60hNI	0.88604	0.319

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)	0.98419	0.614
transgenic ySAMdc/azygous control (breaker)	1.03686	1
transgenic ySAMdc/azygous control (red)	1.04806	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99687	0.784

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.93372	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.86716	0.172
Manapal/WT (break)	0.67217	0.299
Manapal/WT (red)	1.18048	0.222