Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.6.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95692	0.77
27DAP/17DAP	0.87046	0.697
39DAP/27DAP	0.76288	0.338
41DAP/39DAP	0.88859	0.627
42DAP/41DAP	0.98195	1
43DAP/42DAP	1.11804	0.985
47DAP/43DAP	0.9188	0.71
52DAP/47DAP	0.94297	0.74
57DAP/52DAP	1.04154	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94938	0.326
17DAP/reference	0.92318	0.104
27DAP/reference	0.98018	0.642
39DAP/reference	0.89894	0.031
41DAP/reference	0.9044	0.039
42DAP/reference	0.98572	0.384
43DAP/reference	0.98975	0.785
47DAP/reference	1.02232	0.575
52DAP/reference	1.27292	0.01
57DAP/reference	1.09087	0.038

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81314	0.323
27DAP/17DAP	1.1273	0.976
39DAP/27DAP	0.8757	0.287
41DAP/39DAP	0.92365	0.885
42DAP/41DAP	1.36657	0.622
43DAP/42DAP	0.94056	0.684
47DAP/43DAP	0.88127
52DAP/47DAP	1.45839	0.785
57DAP/52DAP	1.13191	0.772
57DAP/7DAP	2.22854	0.207

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0714
17DAP/reference	0.8968	0.389
27DAP/reference	1.17958	0.974
39DAP/reference	0.86531	0.109
41DAP/reference	0.84032	0.076
42DAP/reference	0.75159	0.028
43DAP/reference	0.994	0.665
47DAP/reference	1.15105	0.161
52DAP/reference	1.07445	0.74
57DAP/reference	1.20442	0.268

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91503	0.152
17DAP/reference	0.92349	0.089
27DAP/reference	1.09135	0.48
39DAP/reference	1.14143	0.436
41DAP/reference	1.28807	0.096
42DAP/reference	1.17601	0.054
43DAP/reference	0.89893	0.269
47DAP/reference	1.02394	0.639
52DAP/reference	1.05926	0.156
57DAP/reference	0.81842	0.016

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.6839	0.13
17DAP/reference	0.97721	0.763
27DAP/reference	1.12259	0.695
39DAP/reference	1.51512	0.116
41DAP/reference	1.27161	0.038
42DAP/reference	1.31756	0.019
43DAP/reference	1.21874	0.32
47DAP/reference	1.09267	0.443
52DAP/reference	0.94484	0.562
57DAP/reference	1.65479	0.007

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99622	1
26DAP/20DAP	N/A	N/A
34DAP/26DAP	0.91426	0.927
51DAP/34DAP	1.53864	0.445
52DAP/51DAP	0.86041
53DAP/52DAP	0.9358	0.868
55DAP/53DAP	0.84945	0.417
57DAP/55DAP	1.13419	0.461
62DAP/57DAP	1.07673	0.868
68DAP/62DAP	1.35434	0.132
68DAP/14DAP	1.46728	0.033

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	6.05425

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.22573	0.058
Mature Green Tomato/Ripe Tomato	6.77629	0.015
Immature Eggplant/Mature Eggplant	0.70601	0.069
Ripe Pepper/Ripe Tomato	0.92061	1
Mature Eggplant/Ripe Tomato	0.85057

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.83014
12-2/M82	N/A	N/A
12-4/M82	0.91019
1-3/M82	N/A	N/A
2-1-1/M82	2.14686
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.56985
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.7922
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	1.09516
7-1/M82	0.52429
7-2/M82	N/A	N/A
9-3-2/M82	0.88586

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.39692
IL2-6/WTpooled	1.10484
IL7-5/WTpooled	0.86599	0.559
IL7-3/WTpooled	1.10466	1
IL12-4/WTpooled	0.95931	1
IL1-4/WTpooled	1.37026	1
WT/WTpooled	1.0293	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05357	0.921
DC3000/delta hrp 6h	1.01514	0.95
DC3000/delta hrp 12h	1.0231	1
DC3000/delta hrp 24h	0.88471	0.438

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	0.89052	1
Exp 36h	0.91729	0.82
Exp 60h	0.90893	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	1.01597	1
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.15868	0.283
transgenic ySAMdc/azygous control (breaker)	0.8022	0.139
transgenic ySAMdc/azygous control (red)	1.17254	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00977	0.556

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.31967	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.4001	0.105
Manapal/WT (break)	1.45619	0.13
Manapal/WT (red)	1.31891	0.222