Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.11.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15306	0.932
27DAP/17DAP	0.86717	0.63
39DAP/27DAP	1.23196	0.546
41DAP/39DAP	1.05747	0.873
42DAP/41DAP	1.11211	0.974
43DAP/42DAP	0.9135	0.801
47DAP/43DAP	1.29973	0.609
52DAP/47DAP	0.97965	0.837
57DAP/52DAP	0.80388	0.777

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9218	0.284
17DAP/reference	1.16414	0.041
27DAP/reference	1.09263	0.194
39DAP/reference	1.5664	0.04
41DAP/reference	1.23177	0.111
42DAP/reference	0.97838	0.359
43DAP/reference	1.068	0.617
47DAP/reference	1.19165	0.666
52DAP/reference	0.8578	0.172
57DAP/reference	0.92918	0.221

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.34661	0.063
27DAP/17DAP	0.83303	0.475
39DAP/27DAP	0.81675	0.132
41DAP/39DAP	0.98872	1
42DAP/41DAP	1.10076	0.904
43DAP/42DAP	0.87358	0.28
47DAP/43DAP	1.63819	0.822
52DAP/47DAP	0.91082	0.538
57DAP/52DAP	0.92407	0.581
57DAP/7DAP	1.09534	0.203

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18353	0.126
17DAP/reference	1.14482	0.244
27DAP/reference	1.12012	0.664
39DAP/reference	0.93927	0.411
41DAP/reference	0.90396	0.213
42DAP/reference	0.8222	0.044
43DAP/reference	1.06132	1
47DAP/reference	0.98755	0.671
52DAP/reference	0.99759	0.571
57DAP/reference	1.14195	0.331

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1579	0.151
17DAP/reference	1.25917	0.01
27DAP/reference	1.22706	0.471
39DAP/reference	0.93422	0.348
41DAP/reference	1.13411	0.129
42DAP/reference	1.13829	0.532
43DAP/reference	1.61465	0.027
47DAP/reference	1.40499	0.008
52DAP/reference	0.99115	0.619
57DAP/reference	1.24777	0.029

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02883	0.864
17DAP/reference	1.1589	0.326
27DAP/reference	1.00373	1
39DAP/reference	1.22215	0.157
41DAP/reference	1.08485	1
42DAP/reference	0.95189	0.552
43DAP/reference	1.10316	0.646
47DAP/reference	1.17757	0.07
52DAP/reference	1.24874	0.205
57DAP/reference	0.88298	0.253

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.12955	0.966
26DAP/20DAP	0.76846	0.512
34DAP/26DAP	1.48953	0.819
51DAP/34DAP	0.83133	0.188
52DAP/51DAP	1.32365	0.413
53DAP/52DAP	0.96964	0.882
55DAP/53DAP	0.90509	0.648
57DAP/55DAP	0.99983	0.902
62DAP/57DAP	1.0879	1
68DAP/62DAP	1.17771	0.105
68DAP/14DAP	0.92966	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.07964	0.908

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	5.48954	0.034
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.49749
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.91376	0.944
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.25562
1-3/M82	0.68795
2-1-1/M82	1.10727
2-1/M82	N/A	N/A
2-6/M82	1.08444
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.14612
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.84061	0.49
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.92674	0.881
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	0.95027	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.99132	1
IL12-4/WTpooled	1.10574	0.785
IL1-4/WTpooled	0.94337
WT/WTpooled	0.95071	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	0.8625	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0216	0.921
DC3000/delta hrp 6h	0.90144	0.95
DC3000/delta hrp 12h	1.09106	1
DC3000/delta hrp 24h	1.00398	1

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	0.80642	0.091

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.92989	0.328
Exp 36h	1.02407	1
Exp 60h	1.00648	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05429	1
Var 0h	0.84008	0.933
Var 12h I row2-row1	0.8483	0.418
Var 12h NI row2-row1	0.97341	0.713
Var 36h I row2-row1	1.05197	1
Var 36h NI row2-row1	0.73015	0.852
Var 60h I row2-row1	0.87231	0.832
Var 60h NI row2-row1	0.97009	1
Time course 0hI-0hNI	1.06316	0.799
Time course 12hI-12hNI	0.96536	0.739
Time course 36hI-36hNI	0.9395	0.366
Time course 60hI-60hNI	0.66386	0.015

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)	0.95447	0.722
transgenic ySAMdc/azygous control (breaker)	0.72643	0.125
transgenic ySAMdc/azygous control (red)	0.84225	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99935	0.94

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87967	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	0.8145	0.333
Manapal/WT (red)	1.02558	1