Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.11.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07335	0.812
27DAP/17DAP	1.07628	0.872
39DAP/27DAP	0.88029	0.529
41DAP/39DAP	1.15585	0.63
42DAP/41DAP	0.87686	1
43DAP/42DAP	0.93357	0.846
47DAP/43DAP	0.96661	0.821
52DAP/47DAP	1.11169	0.869
57DAP/52DAP	1.11322	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02018	0.814
17DAP/reference	0.84196	0.278
27DAP/reference	1.01848	0.88
39DAP/reference	0.96026	0.6
41DAP/reference	0.95151	0.667
42DAP/reference	0.85729	0.026
43DAP/reference	0.99224	0.82
47DAP/reference	0.9602	0.224
52DAP/reference	0.8346	0.23
57DAP/reference	0.90262	0.248

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93257	0.56
27DAP/17DAP	1.05829	0.805
39DAP/27DAP	1.15804	0.296
41DAP/39DAP	0.97702	0.997
42DAP/41DAP	1.14775	0.795
43DAP/42DAP	1.0819	0.446
47DAP/43DAP	1.02316	0.914
52DAP/47DAP	0.94906	0.837
57DAP/52DAP	1.161	0.398
57DAP/7DAP	0.91588	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18516	0.147
17DAP/reference	1.17344	0.026
27DAP/reference	1.05893	0.06
39DAP/reference	1.26347	0.006
41DAP/reference	1.30203	0.045
42DAP/reference	1.34133	0.021
43DAP/reference	1.31053	0.01
47DAP/reference	1.04113	0.745
52DAP/reference	1.17957	0.121
57DAP/reference	1.14697	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02697	0.612
17DAP/reference	0.94763	0.399
27DAP/reference	0.91436	0.167
39DAP/reference	0.95745	0.33
41DAP/reference	1.11153	0.878
42DAP/reference	1.07587	1
43DAP/reference	0.91572	0.257
47DAP/reference	1.08882	0.572
52DAP/reference	0.99902	0.761
57DAP/reference	0.95139	0.194

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04106	0.644
17DAP/reference	0.99028	0.763
27DAP/reference	1.11822	0.115
39DAP/reference	1.06588	0.296
41DAP/reference	1.05551	0.554
42DAP/reference	1.01812	0.979
43DAP/reference	1.021	0.973
47DAP/reference	0.89645	0.139
52DAP/reference	1.14357	0.341
57DAP/reference	0.80313	0.143

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95403	0.997
26DAP/20DAP	1.01304	1
34DAP/26DAP	0.94739	0.848
51DAP/34DAP	1.02701	0.962
52DAP/51DAP	0.9375	1
53DAP/52DAP	1.09859	0.712
55DAP/53DAP	1.28978	0.196
57DAP/55DAP	1.09588	0.947
62DAP/57DAP	0.81793	0.28
68DAP/62DAP	0.93431	0.787
68DAP/14DAP	1.14297	0.541

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.99201	0.737

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.9795	0.648
Mature Green Tomato/Ripe Tomato	0.94687	0.487
Immature Eggplant/Mature Eggplant	1.0977	1
Ripe Pepper/Ripe Tomato	0.83706	0.293
Mature Eggplant/Ripe Tomato	0.35525	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04971	1
1-1-2/M82	0.95457	1
12-2/M82	1.11912	1
12-4/M82	0.99246	1
1-3/M82	0.99872	1
2-1-1/M82	1.08927	0.764
2-1/M82	1.34657	0.345
2-6/M82	1.0364	1
3-2/M82	0.95362	1
4-1-1/M82	0.98222	1
4-1/M82	1.09067	1
4-3-2/M82	1.03185	1
4-3/M82	1.14315	1
5-3/M82	1.00121	1
6-2/M82	1.06411	1
6-3/M82	1.02899	1
7-1/M82	0.98347	1
7-2/M82	1.01075	1
9-3-2/M82	0.93625	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.63179	0.243
IL2-6/WTpooled	1.76975	0.788
IL7-5/WTpooled	0.67948	1
IL7-3/WTpooled	0.7516	0.418
IL12-4/WTpooled	0.83128	1
IL1-4/WTpooled	0.81106	0.562
WT/WTpooled	1.00721	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	1.12303	0.193

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0339	0.921
DC3000/delta hrp 6h	1.01324	1
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	1.19869	0.336

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.28219	0.073
DC3000 delta B/DC3000 delta AB	1.02993	0.771

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02059	1
Exp 36h	1.00671	1
Exp 60h	1.19773	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	0.93888	1
Var 0h	1.25511	0.374
Var 12h I row2-row1	1.10302	0.58
Var 12h NI row2-row1	0.7556	0.713
Var 36h I row2-row1	1.01805	1
Var 36h NI row2-row1	1.7937	1
Var 60h I row2-row1	1.10997	0.562
Var 60h NI row2-row1	1.22175	0.904
Time course 0hI-0hNI	1.03428	0.867
Time course 12hI-12hNI	0.96763	0.738
Time course 36hI-36hNI	1.04486	0.28
Time course 60hI-60hNI	1.09826	0.16

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)	1.02648	0.511
transgenic ySAMdc/azygous control (breaker)	0.72838	0.173
transgenic ySAMdc/azygous control (red)	0.98484	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.92757	1
Manapal/WT (break)	0.93948	1
Manapal/WT (red)	0.89947	0.36