Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.18.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99136	0.823
27DAP/17DAP	1.18186	0.849
39DAP/27DAP	0.92751	0.641
41DAP/39DAP	1.10805	0.921
42DAP/41DAP	0.99643	1
43DAP/42DAP	0.95823	0.877
47DAP/43DAP	0.99164	0.895
52DAP/47DAP	1.44297	0.483
57DAP/52DAP	0.97676	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90101	0.224
17DAP/reference	0.77277	0.01
27DAP/reference	0.96361	0.595
39DAP/reference	0.77915	0.015
41DAP/reference	0.78104	0.013
42DAP/reference	0.91004	0.03
43DAP/reference	0.87321	0.028
47DAP/reference	0.94328	0.137
52DAP/reference	1.09701	0.878
57DAP/reference	1.10622	0.249

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.60596	0.438
27DAP/17DAP	1.05627	0.957
39DAP/27DAP	1.27605	0.308
41DAP/39DAP	1.03281	1
42DAP/41DAP	0.8742	0.407
43DAP/42DAP	0.81995	0.073
47DAP/43DAP	1.35486	0.593
52DAP/47DAP	1.17298	0.63
57DAP/52DAP	0.99443	0.862
57DAP/7DAP	1.9678	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19305	0.166
17DAP/reference	1.51282	0.015
27DAP/reference	1.43982	0.02
39DAP/reference	1.41763	0.01
41DAP/reference	1.12118	0.539
42DAP/reference	1.39293	0.059
43DAP/reference	1.3848	0.023
47DAP/reference	1.13137	0.632
52DAP/reference	1.3539	0.055
57DAP/reference	1.45161	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83619	0.072
17DAP/reference	0.81642	0.035
27DAP/reference	1.02114	1
39DAP/reference	0.9945	0.586
41DAP/reference	0.92745	0.121
42DAP/reference	0.92952	0.212
43DAP/reference	0.86149	0.092
47DAP/reference	0.90952	0.01
52DAP/reference	0.9892	0.576
57DAP/reference	0.78477	0.04

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.54135	0.016
17DAP/reference	1.03422	0.81
27DAP/reference	1.81753	0.033
39DAP/reference	1.57774	0.035
41DAP/reference	1.61998	0.022
42DAP/reference	1.16497	0.333
43DAP/reference	0.9694	0.523
47DAP/reference	0.9531	0.286
52DAP/reference	2.30603	0.179
57DAP/reference	1.39464	0.095

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04333	1
26DAP/20DAP	0.8141	1
34DAP/26DAP	0.86662	0.848
51DAP/34DAP	1.36562	0.854
52DAP/51DAP	1.29962	0.067
53DAP/52DAP	0.99498	0.978
55DAP/53DAP	1.51757	0.047
57DAP/55DAP	0.70824	0.053
62DAP/57DAP	1.21787	0.081
68DAP/62DAP	1.17792	0.914
68DAP/14DAP	1.49864	0.504

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.76673	0.083

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.89067	0.287
Immature Eggplant/Mature Eggplant	N/A	N/A
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	1.36823
1-1-2/M82	0.89882	1
12-2/M82	1.15946	1
12-4/M82	0.86279	1
1-3/M82	0.795	0.501
2-1-1/M82	0.92801
2-1/M82	N/A	N/A
2-6/M82	1.05445
3-2/M82	N/A	N/A
4-1-1/M82	0.92611	1
4-1/M82	0.52974
4-3-2/M82	1.04345
4-3/M82	0.42915
5-3/M82	1.12541	0.572
6-2/M82	1.56763	0.235
6-3/M82	0.86521
7-1/M82	1.11496
7-2/M82	1.08737
9-3-2/M82	1.05149

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.71997	0.321
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.33363	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.1218	1
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	1.36156

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00902	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.1679	1
DC3000/delta hrp 24h	0.97985	0.897

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.10068	1
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	0.91192	1
Var 0h	1.05531	0.98
Var 12h I row2-row1	0.99885	1
Var 12h NI row2-row1	0.56166	0.494
Var 36h I row2-row1	0.40272	1
Var 36h NI row2-row1	1.06402	1
Var 60h I row2-row1	1.01258	1
Var 60h NI row2-row1	1.58767	0.904
Time course 0hI-0hNI	1.02185	1
Time course 12hI-12hNI	1.08784	0.816
Time course 36hI-36hNI	1.06259	0.651
Time course 60hI-60hNI	2.13862	0.033

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)	0.96344	0.662
transgenic ySAMdc/azygous control (breaker)	0.95404	0.49
transgenic ySAMdc/azygous control (red)	1.12324	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00439	0.854

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.89694	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.91306	1
Manapal/WT (break)	1.13512	0.381
Manapal/WT (red)	0.52197	0.187