Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.14.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.72134	0.103
27DAP/17DAP	0.90047	0.754
39DAP/27DAP	1.32088	0.365
41DAP/39DAP	0.91673	0.69
42DAP/41DAP	0.96667	1
43DAP/42DAP	1.09471	1
47DAP/43DAP	0.99269	0.92
52DAP/47DAP	1.00031	0.837
57DAP/52DAP	1.10074	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07925	0.421
17DAP/reference	1.03089	0.907
27DAP/reference	0.92898	0.406
39DAP/reference	1.02463	0.871
41DAP/reference	0.99261	0.814
42DAP/reference	0.9352	0.111
43DAP/reference	1.07552	0.678
47DAP/reference	0.87177	0.019
52DAP/reference	0.70411	0.013
57DAP/reference	0.84605	0.028

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.80725	0.093
27DAP/17DAP	1.26718	0.381
39DAP/27DAP	1.19734	0.751
41DAP/39DAP	1.06812	0.827
42DAP/41DAP	0.96247	0.721
43DAP/42DAP	1.12235	0.554
47DAP/43DAP	1.01597	0.997
52DAP/47DAP	1.14257	0.568
57DAP/52DAP	1.33425	0.085
57DAP/7DAP	1.04581	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07444	0.613
17DAP/reference	0.92742	0.295
27DAP/reference	0.89636	0.125
39DAP/reference	0.84865	0.146
41DAP/reference	0.93437	0.139
42DAP/reference	0.79277	0.027
43DAP/reference	1.09426	0.325
47DAP/reference	0.84885	0.066
52DAP/reference	0.83774	0.033
57DAP/reference	0.9248	0.109

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1225	0.456
17DAP/reference	1.09158	0.415
27DAP/reference	1.02292	1
39DAP/reference	0.88949	0.113
41DAP/reference	1.14929	0.149
42DAP/reference	0.8973	0.089
43DAP/reference	1.05431	0.575
47DAP/reference	1.026	0.916
52DAP/reference	0.78415	0.02
57DAP/reference	0.98027	0.61

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07505	0.532
17DAP/reference	1.03793	0.746
27DAP/reference	1.01024	0.883
39DAP/reference	0.90522	0.058
41DAP/reference	0.92853	0.293
42DAP/reference	0.96606	0.552
43DAP/reference	0.89751	0.12
47DAP/reference	0.74185	0.004
52DAP/reference	1.17647	0.657
57DAP/reference	0.69757	0.019

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94869	1
26DAP/20DAP	1.02965	1
34DAP/26DAP	0.96282	0.945
51DAP/34DAP	1.06971	0.924
52DAP/51DAP	1.20544	0.481
53DAP/52DAP	1.01517	0.944
55DAP/53DAP	1.07946	0.911
57DAP/55DAP	0.8114	0.181
62DAP/57DAP	0.92391	0.681
68DAP/62DAP	0.84614	0.641
68DAP/14DAP	0.70268	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.59459

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.80637	0.261
Mature Green Tomato/Ripe Tomato	1.79372	0.119
Immature Eggplant/Mature Eggplant	1.43659	0.05
Ripe Pepper/Ripe Tomato	1.04328	1
Mature Eggplant/Ripe Tomato	1.34459	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99697	1
1-1-2/M82	1.13464	1
12-2/M82	1.11711
12-4/M82	0.96934	1
1-3/M82	1.23444
2-1-1/M82	0.94309	1
2-1/M82	1.11797
2-6/M82	N/A	N/A
3-2/M82	1.02016	1
4-1-1/M82	1.1674
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.18334	1
5-3/M82	1.1459	0.572
6-2/M82	N/A	N/A
6-3/M82	1.17802	1
7-1/M82	0.95051	0.466
7-2/M82	1.15071	0.302
9-3-2/M82	1.20289

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.70162	0.243
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.29039	0.75
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.8728	0.699
WT/WTpooled	1.12663

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	1.37831	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98574	1
DC3000/delta hrp 6h	0.87892	0.95
DC3000/delta hrp 12h	0.97402	1
DC3000/delta hrp 24h	1.04396	0.582

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.67595	0.024
DC3000 delta B/DC3000 delta AB	0.68816	0.025

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04478	1
Exp 36h	1.18823	0.371
Exp 60h	1.18757	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9946	1
Var 0h	0.55643	1
Var 12h I row2-row1	1.08505	0.654
Var 12h NI row2-row1	1.32346	0.34
Var 36h I row2-row1	0.88718	1
Var 36h NI row2-row1	1.08279	1
Var 60h I row2-row1	0.69805	0.306
Var 60h NI row2-row1	0.88258	0.483
Time course 0hI-0hNI	0.99418	1
Time course 12hI-12hNI	1.95003	0.005
Time course 36hI-36hNI	2.45948	0.004
Time course 60hI-60hNI	3.52724	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)	1.10972	0.212
transgenic ySAMdc/azygous control (breaker)	0.94199	1
transgenic ySAMdc/azygous control (red)	1.12823	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98194	0.323

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.14332	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.0824	0.307
Manapal/WT (break)	1.09043	1
Manapal/WT (red)	0.87002	0.274