Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.16.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.4194	0.523
27DAP/17DAP	0.59111	0.035
39DAP/27DAP	1.15683	0.729
41DAP/39DAP	0.84323	0.482
42DAP/41DAP	0.99353	1
43DAP/42DAP	0.93858	0.877
47DAP/43DAP	1.8769	0.349
52DAP/47DAP	1.65568	0.31
57DAP/52DAP	0.97823	0.956

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08449	0.441
17DAP/reference	1.11721	0.528
27DAP/reference	0.90701	0.114
39DAP/reference	0.95703	0.575
41DAP/reference	1.03239	0.714
42DAP/reference	0.86892	0.02
43DAP/reference	1.01947	0.982
47DAP/reference	1.22815	0.081
52DAP/reference	1.69273	0.05
57DAP/reference	1.12863	0.186

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83826	0.428
27DAP/17DAP	1.3655	0.598
39DAP/27DAP	0.76744	0.179
41DAP/39DAP	1.05084	0.896
42DAP/41DAP	1.13391	0.651
43DAP/42DAP	1.08904	0.699
47DAP/43DAP	1.08664	0.805
52DAP/47DAP	1.05609	0.835
57DAP/52DAP	1.01438	0.897
57DAP/7DAP	1.0003	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00004	1
17DAP/reference	0.88862	0.072
27DAP/reference	0.85959	0.01
39DAP/reference	0.91712	0.027
41DAP/reference	0.90876	0.052
42DAP/reference	0.87838	0.046
43DAP/reference	1.05362	0.14
47DAP/reference	0.90963	0.168
52DAP/reference	1.00583	1
57DAP/reference	1.00463	0.831

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09457	0.416
17DAP/reference	1.03028	0.874
27DAP/reference	0.93662	0.327
39DAP/reference	1.01064	0.702
41DAP/reference	0.97742	0.493
42DAP/reference	0.95528	0.261
43DAP/reference	0.9303	0.385
47DAP/reference	0.92909	0.168
52DAP/reference	0.92113	0.143
57DAP/reference	0.88441	0.092

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87951	0.057
17DAP/reference	0.90378	0.217
27DAP/reference	0.9332	0.078
39DAP/reference	0.86744	0.011
41DAP/reference	1.03631	1
42DAP/reference	0.97348	0.671
43DAP/reference	0.90741	0.158
47DAP/reference	0.84647	0.026
52DAP/reference	1.01011	1
57DAP/reference	1.17162	0.167

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.92383	0.878
26DAP/20DAP	1.34699	0.778
34DAP/26DAP	0.8652	0.811
51DAP/34DAP	0.56311
52DAP/51DAP	1.03472	0.904
53DAP/52DAP	0.94086	0.807
55DAP/53DAP	1.00915	0.939
57DAP/55DAP	0.91341	0.647
62DAP/57DAP	1.05725	1
68DAP/62DAP	1.09881	0.85
68DAP/14DAP	0.87163

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.31738	0.439

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.47871	0.026
Immature Eggplant/Mature Eggplant	1.42865	0.078
Ripe Pepper/Ripe Tomato	0.17207	0.224
Mature Eggplant/Ripe Tomato	0.25604	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.62792
12-2/M82	N/A	N/A
12-4/M82	0.76295
1-3/M82	N/A	N/A
2-1-1/M82	0.97011
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	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.86841	0.447
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.94523
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	0.95719	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.88733	1
DC3000/delta hrp 6h	1.03074	1
DC3000/delta hrp 12h	0.95307	1
DC3000/delta hrp 24h	1.01958	0.779

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.9101	0.882
DC3000 delta B/DC3000 delta AB	1.60654	0.127

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0898	1
Exp 36h	0.93381	0.749
Exp 60h	1.09467	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99725	1
Var 0h	1.04526	0.936
Var 12h I row2-row1	0.93357	0.565
Var 12h NI row2-row1	1.09563	0.266
Var 36h I row2-row1	0.95847	1
Var 36h NI row2-row1	0.83686	0.549
Var 60h I row2-row1	0.90358	0.285
Var 60h NI row2-row1	0.86235	0.69
Time course 0hI-0hNI	0.91656	0.266
Time course 12hI-12hNI	1.09238	0.091
Time course 36hI-36hNI	1.05646	0.19
Time course 60hI-60hNI	1.29092	0.009

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)	1.14772	0.243
transgenic ySAMdc/azygous control (breaker)	0.79545	0.15
transgenic ySAMdc/azygous control (red)	1.0104	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99437	0.784

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.84463	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.9904	1
Manapal/WT (break)	1.09871	0.381
Manapal/WT (red)	1.57621	0.222