Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.14.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.68801	0.059
27DAP/17DAP	1.18637	0.842
39DAP/27DAP	0.86728	0.549
41DAP/39DAP	1.06833	0.938
42DAP/41DAP	0.76511	0.774
43DAP/42DAP	1.18945	0.88
47DAP/43DAP	0.73966	0.234
52DAP/47DAP	0.95097	0.673
57DAP/52DAP	1.43381	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80981	0.045
17DAP/reference	0.85154	0.028
27DAP/reference	0.85153	0.249
39DAP/reference	0.89128	0.097
41DAP/reference	0.71709	0.011
42DAP/reference	0.95068	0.225
43DAP/reference	1.11758	0.152
47DAP/reference	0.90042	0.06
52DAP/reference	0.93944	0.21
57DAP/reference	0.98059	0.553

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.75726	0.105
27DAP/17DAP	1.29743	0.22
39DAP/27DAP	1.00832	0.881
41DAP/39DAP	0.98031	0.893
42DAP/41DAP	1.75015	0.334
43DAP/42DAP	3.02014	0.016
47DAP/43DAP	1.01564	0.951
52DAP/47DAP	0.95608	0.834
57DAP/52DAP	1.00568	0.848
57DAP/7DAP	1.25608	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87459	0.108
17DAP/reference	1.5982	0.006
27DAP/reference	1.60581	0.007
39DAP/reference	2.27293	0.005
41DAP/reference	2.13071	0.015
42DAP/reference	3.67966	0.006
43DAP/reference	4.04606	0.006
47DAP/reference	2.56982	0.195
52DAP/reference	3.51544	0.007
57DAP/reference	2.7501	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77151	0.064
17DAP/reference	0.64273	0.008
27DAP/reference	0.95667	0.381
39DAP/reference	0.75853	0.013
41DAP/reference	0.80447	0.013
42DAP/reference	0.80308	0.135
43DAP/reference	0.87189	0.186
47DAP/reference	0.90799	0.094
52DAP/reference	0.85613	0.086
57DAP/reference	0.81279	0.046

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.62091	0.112
17DAP/reference	0.87822	0.348
27DAP/reference	1.11264	0.408
39DAP/reference	1.61898	0.059
41DAP/reference	1.05157	0.296
42DAP/reference	1.82584	0.114
43DAP/reference	1.28053	0.314
47DAP/reference	0.97693	0.509
52DAP/reference	2.58951	0.123
57DAP/reference	1.18418	0.549

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00133	1
26DAP/20DAP	1.46175	0.437
34DAP/26DAP	1.22	0.542
51DAP/34DAP	1.07897	0.791
52DAP/51DAP	1.46119	0.413
53DAP/52DAP	0.87456	0.612
55DAP/53DAP	0.98032	0.82
57DAP/55DAP	1.04126	0.938
62DAP/57DAP	1.08392	0.868
68DAP/62DAP	1.59165	0.018
68DAP/14DAP	1.50909	0.436

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.23167	0.017

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.18134	0.028
Immature Eggplant/Mature Eggplant	1.53228	0.116
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	1.00334
12-4/M82	1.50101	0.694
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.00152
3-2/M82	2.39587
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.53415
5-3/M82	N/A	N/A
6-2/M82	2.22952
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.60184
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.97351	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.19411	1
IL12-4/WTpooled	1.19433	0.42
IL1-4/WTpooled	0.90595
WT/WTpooled	1.04951	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	1.09663	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0838	0.692
DC3000/delta hrp 6h	1.48192	1
DC3000/delta hrp 12h	1.0343	1
DC3000/delta hrp 24h	2.06413	0.031

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.00108	1
DC3000 delta B/DC3000 delta AB	0.83551	0.456

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.12378	1
Exp 36h	1.1929	0.693
Exp 60h	1.38648	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.991	1
Var 0h	1.08076	0.98
Var 12h I row2-row1	1.14942	0.613
Var 12h NI row2-row1	1.24831	0.649
Var 36h I row2-row1	0.84007	0.575
Var 36h NI row2-row1	1.01666	1
Var 60h I row2-row1	0.78288	0.306
Var 60h NI row2-row1	1.0721	0.904
Time course 0hI-0hNI	0.9424	0.516
Time course 12hI-12hNI	0.94213	0.382
Time course 36hI-36hNI	0.93691	0.29
Time course 60hI-60hNI	3.04636	0.012

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)	1.35255	0.321
transgenic ySAMdc/azygous control (breaker)	1.2649	1
transgenic ySAMdc/azygous control (red)	1.3187	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99309	0.673

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.96077	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.96897	0.084
Manapal/WT (break)	1.1861	1
Manapal/WT (red)	1.14068	0.413