Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.6.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05001	0.786
27DAP/17DAP	1.21407	0.788
39DAP/27DAP	0.96958	0.719
41DAP/39DAP	1.29887	0.214
42DAP/41DAP	0.91498	1
43DAP/42DAP	0.9259	0.801
47DAP/43DAP	1.07399	0.481
52DAP/47DAP	1.22426	0.601
57DAP/52DAP	0.9084	0.81

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8412	0.047
17DAP/reference	0.91487	0.069
27DAP/reference	0.99399	0.797
39DAP/reference	1.01377	0.92
41DAP/reference	1.0141	0.963
42DAP/reference	0.8705	0.015
43DAP/reference	0.99156	0.805
47DAP/reference	0.92647	0.207
52DAP/reference	0.87561	0.06
57DAP/reference	0.90906	0.156

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91297	0.26
27DAP/17DAP	1.035	0.909
39DAP/27DAP	1.02463	0.758
41DAP/39DAP	1.0557	0.909
42DAP/41DAP	0.915	0.503
43DAP/42DAP	1.12581	0.052
47DAP/43DAP	0.95048	0.855
52DAP/47DAP	0.99503	0.962
57DAP/52DAP	0.95699	0.501
57DAP/7DAP	0.99443	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.55774	0.037
17DAP/reference	2.09066	0.006
27DAP/reference	2.39439	0.007
39DAP/reference	3.00938	0.005
41DAP/reference	2.87711	0.01
42DAP/reference	2.61928	0.006
43DAP/reference	2.7229	0.007
47DAP/reference	1.43927	0.413
52DAP/reference	2.69713	0.007
57DAP/reference	2.02533	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14913	0.258
17DAP/reference	0.94875	0.317
27DAP/reference	0.88716	0.09
39DAP/reference	0.92203	0.147
41DAP/reference	1.0077	0.702
42DAP/reference	0.91987	0.169
43DAP/reference	0.99754	0.681
47DAP/reference	0.92939	0.12
52DAP/reference	1.07038	0.259
57DAP/reference	1.00949	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.53659	0.022
17DAP/reference	1.25263	0.699
27DAP/reference	1.91988	0.02
39DAP/reference	1.92741	0.01
41DAP/reference	2.08065	0.011
42DAP/reference	1.71794	0.017
43DAP/reference	1.76976	0.047
47DAP/reference	1.05194	0.63
52DAP/reference	1.52936	0.209
57DAP/reference	1.32082	0.2

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09068	0.966
26DAP/20DAP	0.95153	0.512
34DAP/26DAP	1.03724	0.819
51DAP/34DAP	0.98814	0.893
52DAP/51DAP	0.99835	1
53DAP/52DAP	0.96391	0.803
55DAP/53DAP	0.95461	0.735
57DAP/55DAP	1.08927	0.474
62DAP/57DAP	1.10615	0.723
68DAP/62DAP	1.12906	0.367
68DAP/14DAP	1.55071	0.346

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.96228	0.466

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.17634	0.185
Immature Eggplant/Mature Eggplant	1.36218
Ripe Pepper/Ripe Tomato	0.82312	1
Mature Eggplant/Ripe Tomato	1.62817	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99275	1
1-1-2/M82	0.96415	1
12-2/M82	1.03099	1
12-4/M82	0.99598	1
1-3/M82	0.9335	0.501
2-1-1/M82	1.16915	0.689
2-1/M82	0.82211
2-6/M82	1.14266	0.452
3-2/M82	0.96545	1
4-1-1/M82	0.87486	1
4-1/M82	1.17536
4-3-2/M82	0.88957	1
4-3/M82	0.88841	1
5-3/M82	0.97352	1
6-2/M82	1.11987	1
6-3/M82	0.90462	0.982
7-1/M82	1.00315
7-2/M82	1.06918	1
9-3-2/M82	0.90203	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.0577	1
IL2-6/WTpooled	0.99755	1
IL7-5/WTpooled	0.91857	1
IL7-3/WTpooled	0.91833	1
IL12-4/WTpooled	0.90181	0.581
IL1-4/WTpooled	0.98283	1
WT/WTpooled	0.9766	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	1.00012	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9935	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.28893	1
DC3000/delta hrp 24h	1.01796	0.84

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.92995	0.273
DC3000 delta B/DC3000 delta AB	0.97074	0.456

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.58411	1
Exp 36h	1.46971	0.489
Exp 60h	1.30813	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98411	1
Var 0h	1.04827	1
Var 12h I row2-row1	1.05474	0.204
Var 12h NI row2-row1	0.90095	0.546
Var 36h I row2-row1	0.99656	1
Var 36h NI row2-row1	1.16904	1
Var 60h I row2-row1	1.32719	1
Var 60h NI row2-row1	1.23178	0.904
Time course 0hI-0hNI	1.06846	0.719
Time course 12hI-12hNI	0.97869	0.82
Time course 36hI-36hNI	0.90983	0.076
Time course 60hI-60hNI	0.84572	0.007

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)	0.91668	0.246
transgenic ySAMdc/azygous control (breaker)	0.54495	0.137
transgenic ySAMdc/azygous control (red)	0.95842	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00198	0.909

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.0045	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.7585	0.172
Manapal/WT (break)	0.84077	0.299
Manapal/WT (red)	1.34014	0.222