Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.1.13.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.67284	0.105
27DAP/17DAP	1.58018	0.738
39DAP/27DAP	1.33969	0.447
41DAP/39DAP	0.97683	0.761
42DAP/41DAP	0.82584	0.397
43DAP/42DAP	1.06234	1
47DAP/43DAP	0.90755	0.613
52DAP/47DAP	1.57268	0.441
57DAP/52DAP	0.67461	0.591

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13733	0.35
17DAP/reference	1.16451	0.02
27DAP/reference	1.1179	0.067
39DAP/reference	1.01016	0.871
41DAP/reference	1.06316	0.587
42DAP/reference	1.26113	0.006
43DAP/reference	1.05157	0.306
47DAP/reference	0.94147	0.174
52DAP/reference	0.87436	0.139
57DAP/reference	0.89093	0.165

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.63676	0.055
27DAP/17DAP	1.25135	0.133
39DAP/27DAP	1.1445	0.541
41DAP/39DAP	1.67689	0.034
42DAP/41DAP	0.84333	0.196
43DAP/42DAP	1.33132	0.049
47DAP/43DAP	1.17855	0.276
52DAP/47DAP	1.10294	0.718
57DAP/52DAP	1.77727	0.036
57DAP/7DAP	2.20309	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94955	0.361
17DAP/reference	1.08614	0.244
27DAP/reference	1.07605	0.246
39DAP/reference	1.04549	0.252
41DAP/reference	1.06349	0.325
42DAP/reference	1.05164	0.534
43DAP/reference	1.02855	0.707
47DAP/reference	1.26761	0.229
52DAP/reference	0.8487	0.038
57DAP/reference	0.91723	0.077

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05932	0.712
17DAP/reference	1.27084	0.396
27DAP/reference	0.97158	0.501
39DAP/reference	1.19283	0.335
41DAP/reference	1.61355	0.188
42DAP/reference	1.09562	0.38
43DAP/reference	1.18803	0.105
47DAP/reference	1.17543	0.019
52DAP/reference	0.97809	0.537
57DAP/reference	0.99936	0.834

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03849	0.659
17DAP/reference	1.04314	0.712
27DAP/reference	1.09056	0.312
39DAP/reference	1.14184	0.084
41DAP/reference	1.09181	0.162
42DAP/reference	1.06371	0.759
43DAP/reference	0.95402	0.484
47DAP/reference	1.18074	0.11
52DAP/reference	1.13722	0.473
57DAP/reference	0.94423	0.346

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.31056	0.966
26DAP/20DAP	1.59387	0.143
34DAP/26DAP	1.10153	1
51DAP/34DAP	0.82785	0.317
52DAP/51DAP	1.26987	0.651
53DAP/52DAP	0.97907	0.938
55DAP/53DAP	1.06144	0.82
57DAP/55DAP	0.98263	0.859
62DAP/57DAP	0.94203	0.994
68DAP/62DAP	0.99112	0.885
68DAP/14DAP	0.86663	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.76783	0.061

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.26213	0.019
Immature Eggplant/Mature Eggplant	3.98152	0.055
Ripe Pepper/Ripe Tomato	0.25461	0.224
Mature Eggplant/Ripe Tomato	0.23766	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0499
1-1-2/M82	1.02188	1
12-2/M82	1.0205	1
12-4/M82	1.12116	1
1-3/M82	1.08957	1
2-1-1/M82	1.06168	0.375
2-1/M82	1.13621	0.32
2-6/M82	1.22244	0.425
3-2/M82	0.96033
4-1-1/M82	1.18324	1
4-1/M82	0.77688
4-3-2/M82	1.14361
4-3/M82	1.40719	1
5-3/M82	0.87203	1
6-2/M82	1.9823	0.235
6-3/M82	0.92906	1
7-1/M82	1.14503	0.539
7-2/M82	1.12603	0.318
9-3-2/M82	1.21302

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.82814
IL2-6/WTpooled	1.12101	1
IL7-5/WTpooled	1.4139
IL7-3/WTpooled	0.65016	0.31
IL12-4/WTpooled	1.07952	1
IL1-4/WTpooled	1.11756	1
WT/WTpooled	0.8776	0.962

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	2.71432	0.117

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94425	1
DC3000/delta hrp 6h	1.20509	1
DC3000/delta hrp 12h	0.88273	1
DC3000/delta hrp 24h	2.60815	0.023

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.51807
DC3000 delta B/DC3000 delta AB	1.32578	0.212

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.07781	1
Var 0h	0.97483	1
Var 12h I row2-row1	1.20798	0.263
Var 12h NI row2-row1	1.63842	1
Var 36h I row2-row1	1.15435	0.742
Var 36h NI row2-row1	0.52001	0.645
Var 60h I row2-row1	1.01162	1
Var 60h NI row2-row1	0.85169	0.359
Time course 0hI-0hNI	1.18807	0.833
Time course 12hI-12hNI	1.17601	0.392
Time course 36hI-36hNI	2.29732	0.005
Time course 60hI-60hNI	5.92019	0.008

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)	1.56762	0.312
transgenic ySAMdc/azygous control (breaker)	1.00808	1
transgenic ySAMdc/azygous control (red)	1.05061	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95484	0.07

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.71941	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.10467	1
Manapal/WT (break)	0.9625	1
Manapal/WT (red)	0.71937	0.181