Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.20.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9713	0.728
27DAP/17DAP	1.33733	0.755
39DAP/27DAP	0.8837	0.549
41DAP/39DAP	1.19558	0.535
42DAP/41DAP	0.86915	1
43DAP/42DAP	1.22262	0.636
47DAP/43DAP	1.27379	0.595
52DAP/47DAP	0.70912	0.32
57DAP/52DAP	1.06324	0.958

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.7178	0.007
17DAP/reference	0.94705	0.567
27DAP/reference	1.01341	0.909
39DAP/reference	1.70011	0.144
41DAP/reference	1.24219	0.05
42DAP/reference	1.16797	0.098
43DAP/reference	1.00389
47DAP/reference	0.90279	0.224
52DAP/reference	0.92765	0.371
57DAP/reference	1.03043	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1009	0.881
27DAP/17DAP	0.95526	0.878
39DAP/27DAP	1.27827	0.314
41DAP/39DAP	1.20337	0.214
42DAP/41DAP	1.02264	0.865
43DAP/42DAP	0.94736	0.751
47DAP/43DAP	1.2825	0.135
52DAP/47DAP	1.31715	0.489
57DAP/52DAP	1.65458	0.165
57DAP/7DAP	1.08339

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91951	0.168
17DAP/reference	0.84906	0.013
27DAP/reference	0.97632	0.43
39DAP/reference	0.82744	0.014
41DAP/reference	0.92552	0.16
42DAP/reference	0.9544	0.248
43DAP/reference	0.88642	0.049
47DAP/reference	1.19467	0.493
52DAP/reference	0.80437	0.026
57DAP/reference	0.8889	0.137

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.42766	0.106
17DAP/reference	1.1023	0.824
27DAP/reference	1.09749	0.516
39DAP/reference	1.10237	0.247
41DAP/reference	1.10187	0.204
42DAP/reference	1.20862	0.018
43DAP/reference	1.79537	0.07
47DAP/reference	1.16793	0.043
52DAP/reference	1.20108	0.259
57DAP/reference	1.12632	0.119

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83928	0.034
17DAP/reference	1.00071	0.81
27DAP/reference	0.83458	0.031
39DAP/reference	0.8148	0.046
41DAP/reference	1.42909	0.734
42DAP/reference	1.04258	0.877
43DAP/reference	1.03558	0.894
47DAP/reference	1.42181	0.265
52DAP/reference	1.03315	1
57DAP/reference	1.05142	0.909

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.29602	0.966
26DAP/20DAP	1.40004	0.453
34DAP/26DAP	1.17129	0.819
51DAP/34DAP	1.20275	0.706
52DAP/51DAP	1.46889	0.556
53DAP/52DAP	2.75693	0.819
55DAP/53DAP	1.31618	0.733
57DAP/55DAP	0.88742	0.56
62DAP/57DAP	1.32402	0.303
68DAP/62DAP	1.32569	0.316
68DAP/14DAP	0.80124	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.904	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.83521	0.323
Mature Green Tomato/Ripe Tomato	0.76961	0.132
Immature Eggplant/Mature Eggplant	1.12531	0.485
Ripe Pepper/Ripe Tomato	0.54135	0.224
Mature Eggplant/Ripe Tomato	0.384	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.69442	0.605
1-1-2/M82	0.98814	1
12-2/M82	1.32845	1
12-4/M82	0.64028	0.274
1-3/M82	N/A	N/A
2-1-1/M82	0.66249
2-1/M82	N/A	N/A
2-6/M82	0.53452	0.501
3-2/M82	1.03872
4-1-1/M82	N/A	N/A
4-1/M82	0.46884	1
4-3-2/M82	0.68774	0.698
4-3/M82	0.50552
5-3/M82	1.10029	1
6-2/M82	1.02073	1
6-3/M82	1.40079	1
7-1/M82	0.98978
7-2/M82	0.94839	1
9-3-2/M82	0.73455	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.14741	0.493
IL2-6/WTpooled	1.76103	0.46
IL7-5/WTpooled	1.06223	1
IL7-3/WTpooled	0.86542	0.418
IL12-4/WTpooled	1.5251	0.785
IL1-4/WTpooled	0.96293	0.699
WT/WTpooled	1.05057	0.911

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	1.45498	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0293	1
DC3000/delta hrp 6h	0.98652	0.95
DC3000/delta hrp 12h	1.07892	1
DC3000/delta hrp 24h	1.02227	1

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	1.0187	1
Exp 36h	1.22942	1
Exp 60h	1.08108	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01802
Var 0h	N/A	N/A
Var 12h I row2-row1	1.32313	0.296
Var 12h NI row2-row1	0.8725	0.713
Var 36h I row2-row1	1.42406	1
Var 36h NI row2-row1	1.03087	1
Var 60h I row2-row1	0.84342	0.374
Var 60h NI row2-row1	1.01074	1
Time course 0hI-0hNI	1.02426	1
Time course 12hI-12hNI	0.90172	0.562
Time course 36hI-36hNI	1.11692	0.101
Time course 60hI-60hNI	1.61858	0.008

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)	1.36853	0.347
transgenic ySAMdc/azygous control (breaker)	0.88303	0.49
transgenic ySAMdc/azygous control (red)	0.95882	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02366	0.301

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88193	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.04008	1
Manapal/WT (break)	0.66847	0.333
Manapal/WT (red)	0.84619	0.315