Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-5.3.13.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.79613	0.133
27DAP/17DAP	0.89461	0.724
39DAP/27DAP	1.75467	0.133
41DAP/39DAP	0.99352	0.825
42DAP/41DAP	0.77319	1
43DAP/42DAP	0.67507	0.504
47DAP/43DAP	2.04536	0.233
52DAP/47DAP	1.60153	0.619
57DAP/52DAP	1.52101	0.927

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.66231	0.027
17DAP/reference	1.13735	0.653
27DAP/reference	1.07139	0.831
39DAP/reference	1.12461	0.07
41DAP/reference	1.09388	0.393
42DAP/reference	0.67057	0.001
43DAP/reference	0.80448	0.015
47DAP/reference	1.26145	0.243
52DAP/reference	1.58761	0.008
57DAP/reference	1.24468	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.30533	0.201
27DAP/17DAP	0.81536	0.114
39DAP/27DAP	1.25987	0.224
41DAP/39DAP	0.99826	0.968
42DAP/41DAP	0.9004	0.303
43DAP/42DAP	0.61484	0.022
47DAP/43DAP	0.99331	0.983
52DAP/47DAP	1.09615	0.649
57DAP/52DAP	0.76035	0.08
57DAP/7DAP	0.7991	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19101	0.231
17DAP/reference	1.26391	0.064
27DAP/reference	1.33376	0.107
39DAP/reference	1.07944	0.909
41DAP/reference	1.23717	0.251
42DAP/reference	1.14322	0.405
43DAP/reference	1.13538	0.325
47DAP/reference	1.26284	0.266
52DAP/reference	1.1666	0.043
57DAP/reference	1.117	0.41

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.69453	0.012
17DAP/reference	0.80481	0.014
27DAP/reference	1.15647	0.48
39DAP/reference	1.58186	0.011
41DAP/reference	0.58817	0.009
42DAP/reference	1.39207	0.01
43DAP/reference	0.79949	0.025
47DAP/reference	0.83207	0.061
52DAP/reference	0.69723	0.013
57DAP/reference	0.72628	0.011

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82046	0.047
17DAP/reference	0.94253	0.56
27DAP/reference	0.96034	0.376
39DAP/reference	0.81959	0.122
41DAP/reference	1.12867	0.777
42DAP/reference	1.01381	1
43DAP/reference	0.55159	0.125
47DAP/reference	0.5076	0.004
52DAP/reference	1.02415	1
57DAP/reference	0.84206	0.109

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.2689	0.966
26DAP/20DAP	0.93438	1
34DAP/26DAP	1.23462	0.819
51DAP/34DAP	1.09042	0.402
52DAP/51DAP	0.78013	1
53DAP/52DAP	1.33123	0.125
55DAP/53DAP	0.7659	0.025
57DAP/55DAP	0.97243	0.819
62DAP/57DAP	1.23964	0.257
68DAP/62DAP	1.01045	0.914
68DAP/14DAP	1.18903	0.223

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.54142	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.15575	0.058
Mature Green Tomato/Ripe Tomato	1.06079	0.814
Immature Eggplant/Mature Eggplant	2.42031	0.05
Ripe Pepper/Ripe Tomato	0.44904	0.224
Mature Eggplant/Ripe Tomato	0.33148	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.91251	0.907
1-1-2/M82	1.04345	1
12-2/M82	0.80893	0.955
12-4/M82	0.56737	0.33
1-3/M82	1.40826	0.255
2-1-1/M82	0.86283	0.683
2-1/M82	1.11282	1
2-6/M82	0.75239	0.501
3-2/M82	N/A	N/A
4-1-1/M82	1.29884	1
4-1/M82	0.94058	N/A
4-3-2/M82	0.81837	0.445
4-3/M82	0.72582	0.611
5-3/M82	0.86806	1
6-2/M82	0.41315	0.481
6-3/M82	1.37617	1
7-1/M82	0.83185	N/A
7-2/M82	1.07186	N/A
9-3-2/M82	0.91747	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.6243	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.12706	1
IL12-4/WTpooled	1.62674	0.516
IL1-4/WTpooled	0.87836	0.834
WT/WTpooled	0.98725	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	1.08107	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07567	0.846
DC3000/delta hrp 6h	0.99837	0.95
DC3000/delta hrp 12h	1.31108	1
DC3000/delta hrp 24h	0.73894	0.055

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.15986	0.313
DC3000 delta B/DC3000 delta AB	1.17194	0.324

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.29051	1
Exp 36h	0.77009	0.661
Exp 60h	0.73572	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9673	1
Var 0h	1.0158	1
Var 12h I row2-row1	1.33064	0.198
Var 12h NI row2-row1	0.99559	1
Var 36h I row2-row1	1.16696	0.908
Var 36h NI row2-row1	0.9898	0.852
Var 60h I row2-row1	0.78908	0.292
Var 60h NI row2-row1	0.96551	0.818
Time course 0hI-0hNI	1.16653	0.63
Time course 12hI-12hNI	1.85496	0.005
Time course 36hI-36hNI	1.19286	0.008
Time course 60hI-60hNI	1.13625	0.053

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)	0.99679	0.931
transgenic ySAMdc/azygous control (breaker)	0.90408	1
transgenic ySAMdc/azygous control (red)	2.05692	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08251	0.421

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.92802	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.78999	1
Manapal/WT (break)	1.92373	1
Manapal/WT (red)	1.12603	1