Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.17.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82991	0.475
27DAP/17DAP	0.78275	0.402
39DAP/27DAP	0.78122	0.376
41DAP/39DAP	1.48506	0.357
42DAP/41DAP	2.99452	0.021
43DAP/42DAP	1.73623	0.714
47DAP/43DAP	2.68626	0.3
52DAP/47DAP	0.41107	0.04
57DAP/52DAP	2.08663	0.806

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0249	0.844
17DAP/reference	0.81213	0.224
27DAP/reference	1.24228	0.52
39DAP/reference	0.95348	0.575
41DAP/reference	0.87644	0.267
42DAP/reference	1.06464	0.869
43DAP/reference	0.88163	0.155
47DAP/reference	1.19372	0.34
52DAP/reference	1.55879	0.036
57DAP/reference	1.23592	0.136

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86316	0.35
27DAP/17DAP	1.32378	0.107
39DAP/27DAP	0.90517	0.572
41DAP/39DAP	0.84065	0.465
42DAP/41DAP	2.14447	0.282
43DAP/42DAP	2.33962	0.016
47DAP/43DAP	1.14355	0.678
52DAP/47DAP	1.57907	0.172
57DAP/52DAP	0.85016	0.304
57DAP/7DAP	1.70811	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.70203	0.296
17DAP/reference	1.03294	1
27DAP/reference	0.84271	0.019
39DAP/reference	0.71048	0.014
41DAP/reference	0.97564	0.512
42DAP/reference	0.80578	0.106
43DAP/reference	0.8348	0.019
47DAP/reference	0.89982	0.293
52DAP/reference	1.13513	0.563
57DAP/reference	1.01044	0.61

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90421	0.518
17DAP/reference	1.72952	0.484
27DAP/reference	1.11524	0.648
39DAP/reference	1.25375	0.175
41DAP/reference	1.13337	0.614
42DAP/reference	1.06389	0.61
43DAP/reference	0.96028	0.516
47DAP/reference	1.01318	0.812
52DAP/reference	1.11694	0.417
57DAP/reference	1.27888	0.26

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93998	0.455
17DAP/reference	0.98071	0.709
27DAP/reference	0.97497	0.566
39DAP/reference	0.88668	0.222
41DAP/reference	0.99846	0.754
42DAP/reference	1.17538	0.51
43DAP/reference	1.39235	0.056
47DAP/reference	1.02095	0.687
52DAP/reference	1.03076	0.8
57DAP/reference	1.65449	0.078

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.77152	1
26DAP/20DAP	0.65994	0.512
34DAP/26DAP	0.73307	0.682
51DAP/34DAP	1.03807	0.949
52DAP/51DAP	0.954	1
53DAP/52DAP	1.01317	0.944
55DAP/53DAP	0.91685	0.663
57DAP/55DAP	1.54704	0.841
62DAP/57DAP	1.23701	0.678
68DAP/62DAP	1.42839	0.759
68DAP/14DAP	0.94179	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	10.8696	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.32856	0.021
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.07354
Mature Eggplant/Ripe Tomato	0.09602	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.15439	0.574
1-1-2/M82	1.35481	1
12-2/M82	0.97778	1
12-4/M82	2.19279	1
1-3/M82	N/A	N/A
2-1-1/M82	1.86211
2-1/M82	N/A	N/A
2-6/M82	1.07608	1
3-2/M82	1.40533	0.84
4-1-1/M82	1.52972	1
4-1/M82	2.1969	1
4-3-2/M82	1.95957	0.508
4-3/M82	3.97043	0.268
5-3/M82	0.52111	0.642
6-2/M82	2.53353
6-3/M82	0.50734	0.659
7-1/M82	N/A	N/A
7-2/M82	1.13583
9-3-2/M82	2.19168	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.53484	0.247
IL2-6/WTpooled	2.29635	0.419
IL7-5/WTpooled	1.22321	1
IL7-3/WTpooled	0.47314	0.294
IL12-4/WTpooled	0.88098	1
IL1-4/WTpooled	0.74464	0.457
WT/WTpooled	0.97815	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	0.68241	0.256

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.87609	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.32499	1
DC3000/delta hrp 24h	0.65233

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.06505	0.648
DC3000 delta B/DC3000 delta AB	0.87211	0.103

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	0.99054	1
Var 0h	1.20699	0.98
Var 12h I row2-row1	0.79028	0.357
Var 12h NI row2-row1	0.83507	0.403
Var 36h I row2-row1	1.1585	1
Var 36h NI row2-row1	0.9608	0.791
Var 60h I row2-row1	0.6686	1
Var 60h NI row2-row1	1.14905	0.904
Time course 0hI-0hNI	0.99573	1
Time course 12hI-12hNI	0.91201	0.497
Time course 36hI-36hNI	0.67488	0.023
Time course 60hI-60hNI	0.14134	0.005

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	0.96205	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	3.18655	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.87439	1
Manapal/WT (break)	1.08817	1
Manapal/WT (red)	0.45722	0.181