Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.7.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06049	0.947
27DAP/17DAP	1.10346	0.89
39DAP/27DAP	0.91893	0.631
41DAP/39DAP	0.80441	0.401
42DAP/41DAP	1.25498	0.825
43DAP/42DAP	0.95688	0.9
47DAP/43DAP	0.91738	0.701
52DAP/47DAP	1.17735	0.699
57DAP/52DAP	1.34018	0.55

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17711	0.147
17DAP/reference	1.14912	0.427
27DAP/reference	1.18048	0.314
39DAP/reference	1.08042	0.445
41DAP/reference	1.00238	1
42DAP/reference	0.88556	0.12
43DAP/reference	0.95876	0.538
47DAP/reference	1.01695	1
52DAP/reference	1.22471	0.014
57DAP/reference	1.0625	0.682

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.61939	0.036
27DAP/17DAP	0.83526	0.475
39DAP/27DAP	1.08281	0.603
41DAP/39DAP	1.05046	1
42DAP/41DAP	0.98653	0.803
43DAP/42DAP	0.60994	0.022
47DAP/43DAP	0.97501	0.877
52DAP/47DAP	0.94512	0.824
57DAP/52DAP	0.85297	0.359
57DAP/7DAP	0.5238	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08069	0.793
17DAP/reference	1.1192	0.627
27DAP/reference	1.08665	0.974
39DAP/reference	0.95646	0.354
41DAP/reference	0.93937	0.213
42DAP/reference	1.00299	0.751
43DAP/reference	1.12342	0.034
47DAP/reference	1.06941	0.525
52DAP/reference	1.18777	0.062
57DAP/reference	1.11498	0.5

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98223	0.72
17DAP/reference	1.36974	0.036
27DAP/reference	1.34384	0.066
39DAP/reference	1.62535	0.011
41DAP/reference	1.45941	0.039
42DAP/reference	1.06384	0.519
43DAP/reference	1.06347	0.532
47DAP/reference	1.08588	0.218
52DAP/reference	1.17031	0.061
57DAP/reference	1.30656	0.755

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14139	0.469
17DAP/reference	1.08253	0.792
27DAP/reference	1.18232	0.644
39DAP/reference	1.28375	0.018
41DAP/reference	1.06889	1
42DAP/reference	1.45693	0.046
43DAP/reference	1.4	0.151
47DAP/reference	1.14115	0.294
52DAP/reference	1.6202	0.095
57DAP/reference	1.41111	0.033

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.77087	0.064
26DAP/20DAP	1.11064	0.855
34DAP/26DAP	1.02725	1
51DAP/34DAP	1.3512	0.458
52DAP/51DAP	0.86601	1
53DAP/52DAP	1.14554	0.458
55DAP/53DAP	0.90953	0.563
57DAP/55DAP	0.78831	0.197
62DAP/57DAP	0.89479	0.871
68DAP/62DAP	1.07714	0.962
68DAP/14DAP	1.0843	0.915

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.00741	0.466

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.28864	0.058
Mature Green Tomato/Ripe Tomato	1.96454	0.053
Immature Eggplant/Mature Eggplant	1.21302	0.165
Ripe Pepper/Ripe Tomato	1.08637	1
Mature Eggplant/Ripe Tomato	2.57763	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.78014	0.358
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	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.03262
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.40654	0.277
IL2-6/WTpooled	0.67563	0.358
IL7-5/WTpooled	1.10676	0.792
IL7-3/WTpooled	1.22603	0.362
IL12-4/WTpooled	1.23677	0.532
IL1-4/WTpooled	0.92885	0.834
WT/WTpooled	0.97937	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	1.43174	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02409	1
DC3000/delta hrp 6h	1.10654	1
DC3000/delta hrp 12h	1.23681	1
DC3000/delta hrp 24h	0.86881	0.269

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.88021	0.568
DC3000 delta B/DC3000 delta AB	1.22353	0.377

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.13435	1
Exp 36h	0.79675	0.623
Exp 60h	0.83087	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00122	1
Var 0h	1.03596	0.98
Var 12h I row2-row1	0.97081	0.77
Var 12h NI row2-row1	1.03933	1
Var 36h I row2-row1	1.05925	0.601
Var 36h NI row2-row1	0.99667	0.852
Var 60h I row2-row1	0.79235	0.293
Var 60h NI row2-row1	0.71694	0.756
Time course 0hI-0hNI	0.99996	1
Time course 12hI-12hNI	1.0395	0.747
Time course 36hI-36hNI	1.07775	0.316
Time course 60hI-60hNI	0.92639	0.319

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)	0.94058	0.428
transgenic ySAMdc/azygous control (breaker)	1.04072	1
transgenic ySAMdc/azygous control (red)	1.20064	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.9909	0.038

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.51918	0.172
Manapal/WT (break)	1.33819	0.183
Manapal/WT (red)	1.23572	0.222