Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.8.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.35208	0.646
27DAP/17DAP	3.73939	0.134
39DAP/27DAP	1.15629	1
41DAP/39DAP	0.68084	0.449
42DAP/41DAP	1.83484	0.477
43DAP/42DAP	1.31927	0.909
47DAP/43DAP	0.65698	0.212
52DAP/47DAP	1.70105	0.516
57DAP/52DAP	2.07575	0.688

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08994	0.052
17DAP/reference	0.97064	0.63
27DAP/reference	1.08877	0.252
39DAP/reference	0.86029	0.015
41DAP/reference	0.94695	0.026
42DAP/reference	1.45353	0.001
43DAP/reference	0.93923	0.302
47DAP/reference	0.98032	0.392
52DAP/reference	1.00279	1
57DAP/reference	0.8842	0.024

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97186	0.629
27DAP/17DAP	0.99584	0.969
39DAP/27DAP	1.07209	0.46
41DAP/39DAP	1.0903	0.69
42DAP/41DAP	0.99369	0.876
43DAP/42DAP	1.00552	0.83
47DAP/43DAP	0.99081	0.961
52DAP/47DAP	1.08732	0.703
57DAP/52DAP	1.13888	0.308
57DAP/7DAP	1.15714	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94106	0.246
17DAP/reference	1.08057	0.092
27DAP/reference	0.85338	0.01
39DAP/reference	0.98261	0.411
41DAP/reference	1.12056	0.131
42DAP/reference	1.13859	0.233
43DAP/reference	1.55121	0.007
47DAP/reference	0.86514	0.101
52DAP/reference	1.13064	0.013
57DAP/reference	1.97016	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99868	0.93
17DAP/reference	1.22055	0.03
27DAP/reference	1.03005	1
39DAP/reference	0.92175	0.183
41DAP/reference	1.43698	0.007
42DAP/reference	1.11984	0.17
43DAP/reference	1.15899	0.093
47DAP/reference	1.13917	0.011
52DAP/reference	0.85696	0.005
57DAP/reference	1.10355	0.244

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87476	0.044
17DAP/reference	1.01406	0.842
27DAP/reference	1.15288	0.057
39DAP/reference	1.09721	0.075
41DAP/reference	0.98409	0.56
42DAP/reference	0.98353	0.671
43DAP/reference	1.21677	0.033
47DAP/reference	1.20496	0.127
52DAP/reference	1.25329	0.278
57DAP/reference	1.40041	0.098

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.86913	0.733
26DAP/20DAP	0.92001	0.512
34DAP/26DAP	0.95143	0.811
51DAP/34DAP	1.12096	0.511
52DAP/51DAP	1.01364	0.888
53DAP/52DAP	1.01814	0.83
55DAP/53DAP	1.11162	0.162
57DAP/55DAP	0.98363	0.904
62DAP/57DAP	1.16873	0.158
68DAP/62DAP	0.80428	0.406
68DAP/14DAP	1.02506	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.98937	0.696

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.40204	0.08
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	1.32817	0.15
Ripe Pepper/Ripe Tomato	0.21468	0.224
Mature Eggplant/Ripe Tomato	0.26036	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9004	0.907
1-1-2/M82	N/A	N/A
12-2/M82	2.02115	0.61
12-4/M82	1.23363
1-3/M82	0.9629
2-1-1/M82	1.26168	0.457
2-1/M82	N/A	N/A
2-6/M82	1.27869	0.695
3-2/M82	N/A	N/A
4-1-1/M82	1.37231	1
4-1/M82	1.30263
4-3-2/M82	N/A	N/A
4-3/M82	1.63966
5-3/M82	0.58738	0.369
6-2/M82	1.3945	1
6-3/M82	0.91707	1
7-1/M82	N/A	N/A
7-2/M82	1.02502	1
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	1.16365	0.441
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.01084	1
IL12-4/WTpooled	0.96113	1
IL1-4/WTpooled	0.99444	1
WT/WTpooled	0.95116	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	1.55799	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06937	0.538
DC3000/delta hrp 6h	1.55979	0.978
DC3000/delta hrp 12h	1.10305	1
DC3000/delta hrp 24h	1.03531	0.743

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.01806	0.441
DC3000 delta B/DC3000 delta AB	1.06269	0.468

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.17691	1
Exp 36h	1.38973	0.489
Exp 60h	1.75453	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96388	1
Var 0h	4.07635	0.936
Var 12h I row2-row1	1.07596	0.194
Var 12h NI row2-row1	0.99615	1
Var 36h I row2-row1	1.03159	1
Var 36h NI row2-row1	0.99182	0.791
Var 60h I row2-row1	1.04599	1
Var 60h NI row2-row1	1.08683	0.904
Time course 0hI-0hNI	1.06558	0.799
Time course 12hI-12hNI	1.00702	0.885
Time course 36hI-36hNI	1.17734	0.006
Time course 60hI-60hNI	2.10709	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)	1.63356	0.397
transgenic ySAMdc/azygous control (breaker)	0.57523	0.131
transgenic ySAMdc/azygous control (red)	1.2058	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0329	0.05

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.14666	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.59105	0.172
Manapal/WT (break)	0.58428	1
Manapal/WT (red)	0.59858	0.181