Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.12.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14621	0.904
27DAP/17DAP	0.89653	0.766
39DAP/27DAP	1.01987	0.782
41DAP/39DAP	0.89639	0.571
42DAP/41DAP	0.99625	1
43DAP/42DAP	1.10646	1
47DAP/43DAP	0.95195	0.821
52DAP/47DAP	1.27579	0.615
57DAP/52DAP	1.10878	0.993

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.57866	0.008
17DAP/reference	0.99854	0.957
27DAP/reference	1.1013	0.721
39DAP/reference	1.11699	0.243
41DAP/reference	1.09403	0.338
42DAP/reference	1.15827	0.014
43DAP/reference	0.93082	0.377
47DAP/reference	1.23728	0.017
52DAP/reference	0.88519	0.223
57DAP/reference	0.97646	0.526

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99843	0.826
27DAP/17DAP	0.95379	0.854
39DAP/27DAP	0.97813	0.919
41DAP/39DAP	1.1002	0.781
42DAP/41DAP	0.89316	0.42
43DAP/42DAP	0.91622	0.28
47DAP/43DAP	0.88468	0.428
52DAP/47DAP	1.09669	0.734
57DAP/52DAP	1.08953	0.654
57DAP/7DAP	0.76354	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92611	0.296
17DAP/reference	0.87471	0.031
27DAP/reference	0.92941	0.135
39DAP/reference	1.04335	0.74
41DAP/reference	1.00366	0.811
42DAP/reference	1.03303	0.889
43DAP/reference	0.85299	0.038
47DAP/reference	1.04035	1
52DAP/reference	0.90478	0.115
57DAP/reference	0.97243	0.443

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24937	0.084
17DAP/reference	1.22508	0.023
27DAP/reference	1.07185	0.48
39DAP/reference	1.23719	0.207
41DAP/reference	0.97217	0.441
42DAP/reference	1.1981	0.259
43DAP/reference	1.31475	0.069
47DAP/reference	1.10477	0.343
52DAP/reference	0.97969	0.5
57DAP/reference	0.95872	0.488

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97677	0.566
17DAP/reference	1.15549	0.237
27DAP/reference	0.89078	0.097
39DAP/reference	1.0663	0.218
41DAP/reference	1.01259	0.939
42DAP/reference	1.09442	0.55
43DAP/reference	1.09912	0.815
47DAP/reference	1.07165	0.424
52DAP/reference	0.89817	0.351
57DAP/reference	1.25886	0.164

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.11342	1
26DAP/20DAP	0.9477	1
34DAP/26DAP	1.20338	0.106
51DAP/34DAP	1.47812	0.416
52DAP/51DAP	1.09571	0.606
53DAP/52DAP	0.80958	0.21
55DAP/53DAP	1.27457	0.382
57DAP/55DAP	1.03615	0.724
62DAP/57DAP	0.99963	1
68DAP/62DAP	1.86781	0.162
68DAP/14DAP	1.88183	0.065

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.65116	0.032

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.02389	0.666
Mature Green Tomato/Ripe Tomato	1.69825	0.024
Immature Eggplant/Mature Eggplant	0.56988	0.062
Ripe Pepper/Ripe Tomato	2.52162	1
Mature Eggplant/Ripe Tomato	1.71196	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00853	1
1-1-2/M82	N/A	N/A
12-2/M82	1.25654
12-4/M82	0.92455	0.33
1-3/M82	0.56957	0.376
2-1-1/M82	0.63356
2-1/M82	N/A	N/A
2-6/M82	0.91741	1
3-2/M82	N/A	N/A
4-1-1/M82	1.04264	1
4-1/M82	2.41082
4-3-2/M82	N/A	N/A
4-3/M82	1.08157	1
5-3/M82	0.97191	1
6-2/M82	0.55529	1
6-3/M82	1.14455	1
7-1/M82	0.72747
7-2/M82	0.77685	0.796
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	1.22565	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07204	0.921
DC3000/delta hrp 6h	1.04966	1
DC3000/delta hrp 12h	1.61501	1
DC3000/delta hrp 24h	0.98907	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.71172	0.028
DC3000 delta B/DC3000 delta AB	0.63945	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.1832	1
Exp 36h	0.67302	0.471
Exp 60h	0.46128	0.257

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02258	1
Var 0h	0.94483	1
Var 12h I row2-row1	0.74616	0.338
Var 12h NI row2-row1	1.06395	1
Var 36h I row2-row1	0.78028	1
Var 36h NI row2-row1	1.92898	1
Var 60h I row2-row1	1.16113	0.562
Var 60h NI row2-row1	0.93299	1
Time course 0hI-0hNI	0.97313	0.9
Time course 12hI-12hNI	0.97368	0.808
Time course 36hI-36hNI	0.91219	0.19
Time course 60hI-60hNI	0.22434	0.005

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)	1.00291	1
transgenic ySAMdc/azygous control (breaker)	1.37455	0.166
transgenic ySAMdc/azygous control (red)	1.04848	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93451	0.049

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.25256	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.54815	0.083
Manapal/WT (break)	2.52088	0.13
Manapal/WT (red)	1.64411	0.137