Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.2.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.21382	0.403
27DAP/17DAP	0.75188	0.273
39DAP/27DAP	0.85716	0.544
41DAP/39DAP	0.96664	0.849
42DAP/41DAP	1.04275	0.945
43DAP/42DAP	0.84358	0.467
47DAP/43DAP	1.43002	0.415
52DAP/47DAP	1.02781	0.88
57DAP/52DAP	1.26231	0.776

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83373	0.036
17DAP/reference	0.8046	0.041
27DAP/reference	0.98965	0.725
39DAP/reference	0.93774	0.234
41DAP/reference	0.66958	0.009
42DAP/reference	0.90222	0.048
43DAP/reference	0.94988	0.538
47DAP/reference	0.91042	0.137
52DAP/reference	0.97411	0.438
57DAP/reference	1.19933	0.022

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06336	0.675
27DAP/17DAP	0.94236	0.648
39DAP/27DAP	0.98165	0.881
41DAP/39DAP	0.98133	0.986
42DAP/41DAP	1.0545	0.824
43DAP/42DAP	1.04239	0.664
47DAP/43DAP	0.91935	0.637
52DAP/47DAP	0.92733	0.553
57DAP/52DAP	0.82589	0.229
57DAP/7DAP	1.26591	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95408	0.55
17DAP/reference	0.83211	0.295
27DAP/reference	1.10932	0.804
39DAP/reference	1.07815	0.909
41DAP/reference	1.24692	0.325
42DAP/reference	1.23086	0.132
43DAP/reference	0.8951	0.292
47DAP/reference	0.83156	0.101
52DAP/reference	1.2208	0.491
57DAP/reference	0.98382	0.53

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94153	0.518
17DAP/reference	0.77459	0.075
27DAP/reference	0.9564	0.452
39DAP/reference	0.83502	0.048
41DAP/reference	0.95153	0.299
42DAP/reference	0.99019	0.594
43DAP/reference	0.71922	0.039
47DAP/reference	1.00802	1
52DAP/reference	0.76954	0.005
57DAP/reference	0.45277	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.44232	0.086
17DAP/reference	1.44064	0.041
27DAP/reference	1.25906	0.312
39DAP/reference	1.39783	0.067
41DAP/reference	1.50986	0.023
42DAP/reference	1.52958	0.124
43DAP/reference	1.25661	0.064
47DAP/reference	0.99784	0.61
52DAP/reference	0.9227	0.538
57DAP/reference	1.3792	0.164

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.12201	0.966
26DAP/20DAP	0.99634	1
34DAP/26DAP	1.25344	0.819
51DAP/34DAP	0.9806	0.835
52DAP/51DAP	0.93196	1
53DAP/52DAP	0.90346	0.587
55DAP/53DAP	0.93732	0.648
57DAP/55DAP	1.56983	0.376
62DAP/57DAP	1.24715	0.767
68DAP/62DAP	1.935	0.039
68DAP/14DAP	1.85147	0.031

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.09743	0.198

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.57669	0.058
Mature Green Tomato/Ripe Tomato	1.46993	0.106
Immature Eggplant/Mature Eggplant	0.41972	0.062
Ripe Pepper/Ripe Tomato	2.04453
Mature Eggplant/Ripe Tomato	4.24849	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.78599
1-1-2/M82	0.98286	1
12-2/M82	0.75963
12-4/M82	0.84348	0.619
1-3/M82	1.60809
2-1-1/M82	0.9239
2-1/M82	N/A	N/A
2-6/M82	1.11051	0.695
3-2/M82	1.13582	0.388
4-1-1/M82	N/A	N/A
4-1/M82	0.7755
4-3-2/M82	1.07648	1
4-3/M82	0.99358
5-3/M82	1.17775	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.86363
7-2/M82	1.15105
9-3-2/M82	1.08996

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.06327	0.277
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.1684	1
IL7-3/WTpooled	1.10276	1
IL12-4/WTpooled	1.20454	0.785
IL1-4/WTpooled	1.04633	1
WT/WTpooled	0.85619	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	1.02004	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.81976	0.868
DC3000/delta hrp 6h	1.13193	0.978
DC3000/delta hrp 12h	1.14697	1
DC3000/delta hrp 24h	0.88041	0.246

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.70813	0.088
DC3000 delta B/DC3000 delta AB	0.82957	0.1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.99331	1
Exp 36h	0.79655	0.471
Exp 60h	0.75856	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98239	1
Var 0h	0.90672	1
Var 12h I row2-row1	0.97037	0.948
Var 12h NI row2-row1	1.0108	1
Var 36h I row2-row1	1.04238	0.742
Var 36h NI row2-row1	1.04721	1
Var 60h I row2-row1	0.93084
Var 60h NI row2-row1	0.94439	1
Time course 0hI-0hNI	0.9766	0.908
Time course 12hI-12hNI	0.98578	0.889
Time course 36hI-36hNI	1.09508	0.023
Time course 60hI-60hNI	1.00871	1

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)	1.14752	0.748
transgenic ySAMdc/azygous control (breaker)	4.36519	0.165
transgenic ySAMdc/azygous control (red)	1.51499	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.79782	0.131

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.70398	0.223

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	4.41391	0.087
Manapal/WT (break)	9.68477	0.183
Manapal/WT (red)	7.58734	0.15