Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.14.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.7186	0.11
27DAP/17DAP	1.20606	0.809
39DAP/27DAP	1.26007	0.638
41DAP/39DAP	0.90719	0.636
42DAP/41DAP	0.88988	1
43DAP/42DAP	0.76392	0.497
47DAP/43DAP	1.26463	0.49
52DAP/47DAP	1.49919	0.906
57DAP/52DAP	0.97962	0.963

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06873	0.685
17DAP/reference	0.91494	0.18
27DAP/reference	0.93719	0.444
39DAP/reference	1.03377	0.615
41DAP/reference	0.84841	0.049
42DAP/reference	0.93809	0.163
43DAP/reference	0.85837	0.061
47DAP/reference	1.06581	0.463
52DAP/reference	1.16862	0.092
57DAP/reference	1.20609	0.027

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.7794	0.141
27DAP/17DAP	0.99192	0.943
39DAP/27DAP	0.82019	0.063
41DAP/39DAP	0.87571	0.299
42DAP/41DAP	1.12049	0.47
43DAP/42DAP	1.13762	0.324
47DAP/43DAP	0.95328	0.764
52DAP/47DAP	0.97456	0.9
57DAP/52DAP	0.92717	0.532
57DAP/7DAP	0.89795	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88525	0.157
17DAP/reference	1.0581	0.134
27DAP/reference	0.99947	0.8
39DAP/reference	1.08194	0.351
41DAP/reference	1.00704	0.741
42DAP/reference	1.06109	0.534
43DAP/reference	0.95421	0.321
47DAP/reference	0.9802	0.671
52DAP/reference	0.80091	0.035
57DAP/reference	0.92324	0.097

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.127	0.226
17DAP/reference	1.08866	0.415
27DAP/reference	1.10052	0.388
39DAP/reference	0.98661	0.569
41DAP/reference	1.05723	0.862
42DAP/reference	1.19928	0.016
43DAP/reference	1.15983	0.562
47DAP/reference	1.05858	0.467
52DAP/reference	1.02079	0.838
57DAP/reference	0.86479	0.18

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97632	0.566
17DAP/reference	1.0679	0.665
27DAP/reference	1.03428	0.672
39DAP/reference	1.22177	0.05
41DAP/reference	1.11246	0.174
42DAP/reference	1.14696	0.158
43DAP/reference	1.08253	0.768
47DAP/reference	1.03241	0.901
52DAP/reference	0.95333	0.562
57DAP/reference	1.21106	0.062

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.11337	0.966
26DAP/20DAP	0.80315	0.512
34DAP/26DAP	1.14691	1
51DAP/34DAP	1.12695	0.473
52DAP/51DAP	0.90218	1
53DAP/52DAP	0.82914	0.133
55DAP/53DAP	0.62785	0.05
57DAP/55DAP	0.94116	0.664
62DAP/57DAP	1.00103	1
68DAP/62DAP	1.00736	0.914
68DAP/14DAP	1.09645	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.64455	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.86455	0.058
Mature Green Tomato/Ripe Tomato	1.7376	0.015
Immature Eggplant/Mature Eggplant	0.67845	0.064
Ripe Pepper/Ripe Tomato	0.60134	0.224
Mature Eggplant/Ripe Tomato	2.01768	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.28416	0.536
1-1-2/M82	1.37402	1
12-2/M82	1.13946	1
12-4/M82	0.98179	1
1-3/M82	0.75373
2-1-1/M82	0.67133
2-1/M82	0.7697
2-6/M82	0.90173	1
3-2/M82	0.79187
4-1-1/M82	0.83768	1
4-1/M82	1.50495
4-3-2/M82	0.92429
4-3/M82	0.54884	0.611
5-3/M82	0.88572	1
6-2/M82	0.82144
6-3/M82	1.02428	1
7-1/M82	1.16104
7-2/M82	0.63231
9-3-2/M82	0.90087

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	0.90971	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.13643	0.656
DC3000/delta hrp 6h	0.93205	0.95
DC3000/delta hrp 12h	1.07738	1
DC3000/delta hrp 24h	0.9884	0.966

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.76713	0.065
DC3000 delta B/DC3000 delta AB	0.92392	0.381

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.84205	1
Exp 36h	0.86613	0.406
Exp 60h	0.77	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01331	1
Var 0h	1.13105	0.98
Var 12h I row2-row1	1.4209	0.379
Var 12h NI row2-row1	1.16914	0.649
Var 36h I row2-row1	0.88187	0.575
Var 36h NI row2-row1	1.30522	1
Var 60h I row2-row1	0.82572	0.306
Var 60h NI row2-row1	1.17739	0.904
Time course 0hI-0hNI	1.05036	0.833
Time course 12hI-12hNI	0.93806	0.464
Time course 36hI-36hNI	0.84728	0.023
Time course 60hI-60hNI	0.96936	0.646

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)	0.88236	0.306
transgenic ySAMdc/azygous control (breaker)	0.82755	0.137
transgenic ySAMdc/azygous control (red)	1.27663	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9479	0.191

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.81628	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.12609	1
Manapal/WT (break)	1.95859	0.381
Manapal/WT (red)	1.32109	0.15