Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.16.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95291	0.713
27DAP/17DAP	1.15994	0.845
39DAP/27DAP	1.1654	0.755
41DAP/39DAP	0.86466	0.475
42DAP/41DAP	0.75656	0.774
43DAP/42DAP	0.9204	0.867
47DAP/43DAP	0.91878	0.736
52DAP/47DAP	1.5739	0.468
57DAP/52DAP	0.87228	0.8

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98662	0.616
17DAP/reference	1.03404	0.399
27DAP/reference	1.01278	0.934
39DAP/reference	0.94095	0.575
41DAP/reference	1.12567	0.041
42DAP/reference	0.95272	0.115
43DAP/reference	1.00043	1
47DAP/reference	0.93753	0.035
52DAP/reference	0.88152	0.105
57DAP/reference	0.95671	0.395

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89859	0.311
27DAP/17DAP	1.01566	1
39DAP/27DAP	1.11924	0.514
41DAP/39DAP	0.95618	0.945
42DAP/41DAP	1.01594	0.924
43DAP/42DAP	1.04298	0.788
47DAP/43DAP	1.02563	0.95
52DAP/47DAP	1.06144	0.826
57DAP/52DAP	1.00923	1
57DAP/7DAP	1.03596	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84484	0.086
17DAP/reference	0.83654	0.024
27DAP/reference	0.83666	0.01
39DAP/reference	0.89213	0.031
41DAP/reference	0.8346	0.027
42DAP/reference	0.90296	0.01
43DAP/reference	0.74266	0.011
47DAP/reference	0.86462	0.222
52DAP/reference	0.78533	0.011
57DAP/reference	0.80098	0.026

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97416	0.669
17DAP/reference	0.94294	0.326
27DAP/reference	0.89126	0.129
39DAP/reference	0.94893	0.359
41DAP/reference	0.9422	0.262
42DAP/reference	0.93414	0.261
43DAP/reference	1.05519	0.617
47DAP/reference	1.01937	0.795
52DAP/reference	0.94507	0.22
57DAP/reference	0.99217	0.754

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87641	0.071
17DAP/reference	0.93496	0.286
27DAP/reference	0.83981	0.036
39DAP/reference	0.81685	0.024
41DAP/reference	0.82828	0.031
42DAP/reference	0.75395	0.032
43DAP/reference	0.76948	0.032
47DAP/reference	0.96078	0.421
52DAP/reference	0.80525	0.158
57DAP/reference	0.62662	0.019

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9838	1
26DAP/20DAP	0.92856	0.317
34DAP/26DAP	1.07571	1
51DAP/34DAP	0.96524	0.785
52DAP/51DAP	1.01511	0.873
53DAP/52DAP	0.98723	0.917
55DAP/53DAP	1.00851	1
57DAP/55DAP	0.85164	0.351
62DAP/57DAP	0.99215	1
68DAP/62DAP	1.16622	0.8
68DAP/14DAP	0.98903	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.88878	0.341

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.06582	0.417
Mature Green Tomato/Ripe Tomato	1.14264	0.399
Immature Eggplant/Mature Eggplant	1.01214	0.683
Ripe Pepper/Ripe Tomato	0.91375	0.224
Mature Eggplant/Ripe Tomato	1.12762

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95268	0.944
1-1-2/M82	0.87257	1
12-2/M82	1.18108	1
12-4/M82	0.93442	1
1-3/M82	0.94679	0.501
2-1-1/M82	0.96146	1
2-1/M82	N/A	N/A
2-6/M82	1.01742	1
3-2/M82	0.97574
4-1-1/M82	1.11178	1
4-1/M82	1.20788
4-3-2/M82	0.95636	1
4-3/M82	0.81169	0.72
5-3/M82	0.87197	0.642
6-2/M82	0.90371	1
6-3/M82	1.06652	1
7-1/M82	1.31735
7-2/M82	0.98593	1
9-3-2/M82	0.70911

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.48881	0.365
IL2-6/WTpooled	1.09488	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.80697	0.418
IL12-4/WTpooled	1.06621	0.737
IL1-4/WTpooled	0.87755	0.834
WT/WTpooled	1.05142	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	1.37082

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07597	0.914
DC3000/delta hrp 6h	0.98711	0.95
DC3000/delta hrp 12h	1.52293	0.922
DC3000/delta hrp 24h	1.15347	0.057

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	0.8431	0.152

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04947	1
Exp 36h	1.1888	1
Exp 60h	1.12454	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96259	1
Var 0h	1.03026	0.936
Var 12h I row2-row1	1.08144	0.544
Var 12h NI row2-row1	1.1512	1
Var 36h I row2-row1	0.84956	0.805
Var 36h NI row2-row1	0.91991	0.706
Var 60h I row2-row1	1.36405	0.562
Var 60h NI row2-row1	1.19956	0.904
Time course 0hI-0hNI	1.13078	0.764
Time course 12hI-12hNI	1.13082	0.385
Time course 36hI-36hNI	1.08013	0.316
Time course 60hI-60hNI	1.30765	0.042

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)	0.85339	0.32
transgenic ySAMdc/azygous control (breaker)	0.94735	1
transgenic ySAMdc/azygous control (red)	0.97204	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99717	0.832

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.23614	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.98026	1
Manapal/WT (break)	0.89422	0.299
Manapal/WT (red)	0.97276	0.728