Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.14.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06945	0.964
27DAP/17DAP	1.39808	0.624
39DAP/27DAP	1.05965	0.915
41DAP/39DAP	1.49676	0.356
42DAP/41DAP	1.0603	0.978
43DAP/42DAP	1.15002	0.875
47DAP/43DAP	1.2104	0.618
52DAP/47DAP	1.22046	0.639
57DAP/52DAP	1.05061	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.51349	0.007
17DAP/reference	1.25726	0.012
27DAP/reference	1.26246	0.015
39DAP/reference	1.15338	0.229
41DAP/reference	1.35162	0.03
42DAP/reference	1.24387	0.041
43DAP/reference	1.13091	0.425
47DAP/reference	1.14485	0.136
52DAP/reference	1.48453	0.017
57DAP/reference	1.36076	0.056

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90868	0.363
27DAP/17DAP	1.03602	0.909
39DAP/27DAP	1.19829	0.231
41DAP/39DAP	0.99666	1
42DAP/41DAP	1.0581	0.74
43DAP/42DAP	0.98505	0.928
47DAP/43DAP	0.99641	0.99
52DAP/47DAP	1.04434	0.831
57DAP/52DAP	1.11543	0.466
57DAP/7DAP	1.16335	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.79768	0.025
17DAP/reference	1.35208	0.013
27DAP/reference	1.51463	0.008
39DAP/reference	1.36659	0.011
41DAP/reference	1.53331	0.034
42DAP/reference	1.34216	0.059
43DAP/reference	1.08731	0.511
47DAP/reference	1.00665	1
52DAP/reference	0.952	0.332
57DAP/reference	1.12599	0.268

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23651	0.22
17DAP/reference	1.37348	0.032
27DAP/reference	1.4553	0.063
39DAP/reference	1.40214	0.044
41DAP/reference	1.57511	0.007
42DAP/reference	1.52772	0.009
43DAP/reference	1.247	0.13
47DAP/reference	1.18766	0.01
52DAP/reference	1.28872	0.043
57DAP/reference	0.98889	0.61

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.48735	0.015
17DAP/reference	1.19167	0.488
27DAP/reference	1.10199	0.298
39DAP/reference	1.15561	0.02
41DAP/reference	1.15411	0.15
42DAP/reference	1.33197	0.121
43DAP/reference	1.59823	0.017
47DAP/reference	1.18812	0.265
52DAP/reference	1.0224	0.979
57DAP/reference	1.38582	0.045

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.32908	0.966
26DAP/20DAP	1.18957	0.504
34DAP/26DAP	1.05445	1
51DAP/34DAP	0.82668	0.111
52DAP/51DAP	1.12514	0.367
53DAP/52DAP	1.02271	0.944
55DAP/53DAP	1.21619	0.266
57DAP/55DAP	0.86291	0.427
62DAP/57DAP	1.01338	0.994
68DAP/62DAP	1.07977	0.885
68DAP/14DAP	0.99334	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.80368	0.05

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.78791
Immature Eggplant/Mature Eggplant	1.32059
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.92389
12-2/M82	N/A	N/A
12-4/M82	1.05387
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	0.92312	1
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	N/A	N/A
9-3-2/M82	1.10993	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.08964
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.70834
IL1-4/WTpooled	0.92819	1
WT/WTpooled	1.05686	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	1.04284	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	0.32016
DC3000/delta hrp 12h	1.0128	1
DC3000/delta hrp 24h	0.68872	0.049

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.04632
DC3000 delta B/DC3000 delta AB	0.99	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89264	1
Exp 36h	0.86314	0.749
Exp 60h	0.65493	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05393	1
Var 0h	1.39421	0.782
Var 12h I row2-row1	1.0831	0.692
Var 12h NI row2-row1	1.07577	1
Var 36h I row2-row1	0.8703	0.575
Var 36h NI row2-row1	0.84036	0.549
Var 60h I row2-row1	0.99813	1
Var 60h NI row2-row1	1.17367	0.904
Time course 0hI-0hNI	0.99121	1
Time course 12hI-12hNI	0.98259	0.827
Time course 36hI-36hNI	0.87868	0.269
Time course 60hI-60hNI	0.94768	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)	1.07093	0.218
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	0.95646	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.83363	0.038

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.36472	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.79255	0.09
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.97841	0.863