Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-8.1.14.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.68856	0.069
27DAP/17DAP	1.17178	0.859
39DAP/27DAP	1.30415	0.387
41DAP/39DAP	0.85666	0.455
42DAP/41DAP	0.85525	0.774
43DAP/42DAP	0.79202	0.454
47DAP/43DAP	0.8505	0.526
52DAP/47DAP	2.58644	0.277
57DAP/52DAP	1.03018	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81182	0.035
17DAP/reference	0.85094	0.026
27DAP/reference	0.83882	0.152
39DAP/reference	0.84668	0.149
41DAP/reference	0.66489	0.008
42DAP/reference	0.78598	0.001
43DAP/reference	0.89272	0.029
47DAP/reference	0.89832	0.09
52DAP/reference	1.08535	0.912
57DAP/reference	1.24508	0.01

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92498	0.509
27DAP/17DAP	1.05023	0.951
39DAP/27DAP	0.71501	0.066
41DAP/39DAP	0.87988	0.586
42DAP/41DAP	1.13917	0.526
43DAP/42DAP	0.9809	0.831
47DAP/43DAP	0.94493	0.701
52DAP/47DAP	0.81811	0.405
57DAP/52DAP	0.98594	0.756
57DAP/7DAP	0.80459	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9546	0.402
17DAP/reference	0.86033	0.039
27DAP/reference	0.91049	0.055
39DAP/reference	0.84222	0.049
41DAP/reference	0.7017	0.02
42DAP/reference	0.76524	0.033
43DAP/reference	0.7263	0.014
47DAP/reference	0.95895	0.504
52DAP/reference	0.78661	0.015
57DAP/reference	0.81729	0.023

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87728	0.176
17DAP/reference	0.64474	0.042
27DAP/reference	0.82982	0.031
39DAP/reference	0.78637	0.095
41DAP/reference	0.93119	0.25
42DAP/reference	0.79328	0.237
43DAP/reference	0.76186	0.077
47DAP/reference	0.82344	0.021
52DAP/reference	0.84026	0.04
57DAP/reference	0.60378	0.008

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79474	0.071
17DAP/reference	0.93697	0.389
27DAP/reference	0.97504	0.539
39DAP/reference	0.81702	0.016
41DAP/reference	0.83431	0.237
42DAP/reference	1.01606	0.994
43DAP/reference	0.85998	0.061
47DAP/reference	0.80366	0.023
52DAP/reference	0.78888	0.141
57DAP/reference	1.06737	0.971

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0596	0.966
26DAP/20DAP	1.10328	0.818
34DAP/26DAP	0.97367	0.97
51DAP/34DAP	1.0273	0.869
52DAP/51DAP	0.92796	1
53DAP/52DAP	0.77976	0.21
55DAP/53DAP	0.43598	0.144
57DAP/55DAP	0.95041	0.783
62DAP/57DAP	1.204	0.622
68DAP/62DAP	1.5352	0.047
68DAP/14DAP	1.44636	0.295

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.51511	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.29461	0.058
Mature Green Tomato/Ripe Tomato	1.55203	0.028
Immature Eggplant/Mature Eggplant	0.74182	0.089
Ripe Pepper/Ripe Tomato	0.93473	1
Mature Eggplant/Ripe Tomato	2.24247	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.14812	0.877
1-1-2/M82	1.04259	1
12-2/M82	1.41385	1
12-4/M82	0.93432	1
1-3/M82	0.95259	1
2-1-1/M82	0.50442	0.683
2-1/M82	1.0156	1
2-6/M82	1.08669	1
3-2/M82	0.89379	N/A
4-1-1/M82	0.67952	0.908
4-1/M82	0.86839	0.737
4-3-2/M82	0.9676	N/A
4-3/M82	0.62144	0.578
5-3/M82	0.85917	0.642
6-2/M82	1.00637	1
6-3/M82	1.2623	1
7-1/M82	1.11034	N/A
7-2/M82	0.94717	1
9-3-2/M82	0.95065	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.03504	0.493
IL2-6/WTpooled	0.89881	1
IL7-5/WTpooled	1.08736	0.792
IL7-3/WTpooled	1.28325	1
IL12-4/WTpooled	1.00681	1
IL1-4/WTpooled	1.0491	1
WT/WTpooled	1.00596	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	1.13163	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.14937	0.692
DC3000/delta hrp 6h	1.13252	1
DC3000/delta hrp 12h	0.90621	1
DC3000/delta hrp 24h	0.90882	0.323

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.03922	0.648
DC3000 delta B/DC3000 delta AB	0.7151	0.032

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93147	1
Exp 36h	1.00525	1
Exp 60h	0.87788	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04194	1
Var 0h	0.77991	0.933
Var 12h I row2-row1	1.05299	0.613
Var 12h NI row2-row1	1.21608	0.649
Var 36h I row2-row1	0.95715	0.285
Var 36h NI row2-row1	1.13714	1
Var 60h I row2-row1	0.86573	0.439
Var 60h NI row2-row1	1.03772	1
Time course 0hI-0hNI	1.04711	0.852
Time course 12hI-12hNI	0.96996	0.738
Time course 36hI-36hNI	0.95077	0.246
Time course 60hI-60hNI	0.79711	0.161

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)	0.93206	0.377
transgenic ySAMdc/azygous control (breaker)	0.77089	0.173
transgenic ySAMdc/azygous control (red)	1.22529	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.88582	0.126

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.59156	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.02759	1
Manapal/WT (break)	1.77336	0.381
Manapal/WT (red)	1.24761	0.413