Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.7.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13628	0.786
27DAP/17DAP	1.16964	0.852
39DAP/27DAP	1.04503	0.919
41DAP/39DAP	1.18214	0.511
42DAP/41DAP	0.8751	1
43DAP/42DAP	0.95967	0.892
47DAP/43DAP	0.97138	0.876
52DAP/47DAP	1.25783	0.538
57DAP/52DAP	1.00362	0.976

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98734	0.645
17DAP/reference	1.00382	1
27DAP/reference	0.93759	0.349
39DAP/reference	0.99001	0.841
41DAP/reference	0.98781	0.814
42DAP/reference	0.92478	0.103
43DAP/reference	1.0551	0.118
47DAP/reference	0.89209	0.011
52DAP/reference	0.81702	0.05
57DAP/reference	0.78366	0.062

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.36422	0.058
27DAP/17DAP	1.37356	0.09
39DAP/27DAP	0.82691	0.058
41DAP/39DAP	0.95453	0.822
42DAP/41DAP	1.17484	0.495
43DAP/42DAP	0.3936	0.022
47DAP/43DAP	1.42362	0.024
52DAP/47DAP	0.91193	0.677
57DAP/52DAP	0.89476	0.531
57DAP/7DAP	0.67623	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05643	0.83
17DAP/reference	0.89985	0.144
27DAP/reference	0.94829	0.283
39DAP/reference	0.78097	0.011
41DAP/reference	0.89452	0.122
42DAP/reference	0.85673	0.13
43DAP/reference	0.64169	0.012
47DAP/reference	0.76911	0.128
52DAP/reference	0.68338	0.021
57DAP/reference	0.67946	0.015

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02236	0.874
17DAP/reference	1.02973	0.789
27DAP/reference	0.82577	0.119
39DAP/reference	0.85141	0.208
41DAP/reference	0.84791	0.121
42DAP/reference	0.83457	0.108
43DAP/reference	1.04607	0.704
47DAP/reference	0.93972	0.208
52DAP/reference	0.99372	0.666
57DAP/reference	1.24058	0.057

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90173	0.197
17DAP/reference	0.99742	0.763
27DAP/reference	0.76777	0.042
39DAP/reference	0.71191	0.015
41DAP/reference	0.76661	0.064
42DAP/reference	0.63983	0.016
43DAP/reference	0.61264	0.028
47DAP/reference	0.97203	0.494
52DAP/reference	0.71403	0.122
57DAP/reference	0.40913	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.24298	0.916
26DAP/20DAP	0.86236	1
34DAP/26DAP	1.00104	1
51DAP/34DAP	1.67458	0.037
52DAP/51DAP	0.84221	1
53DAP/52DAP	0.99029	0.929
55DAP/53DAP	1.10193	0.82
57DAP/55DAP	1.09221	0.927
62DAP/57DAP	1.49018	0.081
68DAP/62DAP	0.91292	0.747
68DAP/14DAP	0.88992	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.47766	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.98333
Mature Green Tomato/Ripe Tomato	2.51471	0.028
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.34101
Mature Eggplant/Ripe Tomato	3.91956	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.68093	0.708
1-1-2/M82	0.78243
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.01528
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.87801
9-3-2/M82	0.9486	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.27401	0.493
IL2-6/WTpooled	0.92556	1
IL7-5/WTpooled	0.9652	1
IL7-3/WTpooled	1.23949	1
IL12-4/WTpooled	1.06507	0.695
IL1-4/WTpooled	1.04519	1
WT/WTpooled	1.00107	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	2.04091	0.914
DC3000/delta hrp 6h	0.68278	0.95
DC3000/delta hrp 12h	1.13581	1
DC3000/delta hrp 24h	1.23269	0.243

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	1.31162	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04068	1
Exp 36h	1.25005	0.693
Exp 60h	0.96505	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01089	1
Var 0h	0.98131	1
Var 12h I row2-row1	0.98924	1
Var 12h NI row2-row1	0.86283	0.546
Var 36h I row2-row1	0.85977	0.805
Var 36h NI row2-row1	1.07071	1
Var 60h I row2-row1	2.44011	0.562
Var 60h NI row2-row1	1.35907	0.904
Time course 0hI-0hNI	1.18387	0.662
Time course 12hI-12hNI	1.11257	0.572
Time course 36hI-36hNI	0.87501	0.047
Time course 60hI-60hNI	0.9865	0.646

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)	0.97742	0.567
transgenic ySAMdc/azygous control (breaker)	0.97969	1
transgenic ySAMdc/azygous control (red)	1.09424	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0427	0.213

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.80944	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.85874	1
Manapal/WT (break)	0.78853	0.299
Manapal/WT (red)	N/A	N/A