Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.11.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00535	0.919
27DAP/17DAP	1.08701	0.871
39DAP/27DAP	0.82442	0.474
41DAP/39DAP	1.02749	0.918
42DAP/41DAP	1.09865	0.941
43DAP/42DAP	0.9057	0.801
47DAP/43DAP	1.06179	0.873
52DAP/47DAP	1.08264	0.883
57DAP/52DAP	1.10865	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01824	0.814
17DAP/reference	1.00183	1
27DAP/reference	0.99405	0.779
39DAP/reference	0.96925	0.587
41DAP/reference	0.96716	0.065
42DAP/reference	1.02941	0.449
43DAP/reference	1.0087	0.838
47DAP/reference	1.02167	0.612
52DAP/reference	1.05524	0.878
57DAP/reference	1.00765	0.876

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02341	0.736
27DAP/17DAP	0.9963	0.969
39DAP/27DAP	1.00177	0.874
41DAP/39DAP	0.96484	0.662
42DAP/41DAP	0.9781	0.776
43DAP/42DAP	1.01535	0.699
47DAP/43DAP	1.01356	0.897
52DAP/47DAP	0.97588	0.886
57DAP/52DAP	1.01205	0.978
57DAP/7DAP	1.0191	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93491	0.115
17DAP/reference	0.94245	0.012
27DAP/reference	0.94647	0.076
39DAP/reference	0.96872	0.056
41DAP/reference	0.97592	0.431
42DAP/reference	0.99529	0.675
43DAP/reference	0.99726	0.694
47DAP/reference	0.94813	0.222
52DAP/reference	0.98029	0.435
57DAP/reference	0.97992	0.367

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04594	0.276
17DAP/reference	1.09674	0.044
27DAP/reference	1.107	0.278
39DAP/reference	1.0033	1
41DAP/reference	1.03398	0.91
42DAP/reference	0.99177	0.655
43DAP/reference	1.09867	0.157
47DAP/reference	0.9872	0.527
52DAP/reference	1.02518	0.417
57DAP/reference	1.10181	0.286

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91971	0.127
17DAP/reference	0.958	0.364
27DAP/reference	0.931	0.036
39DAP/reference	0.95933	0.122
41DAP/reference	0.91991	0.028
42DAP/reference	0.89074	0.016
43DAP/reference	0.93212	0.081
47DAP/reference	0.93534	0.132
52DAP/reference	0.94373	0.424
57DAP/reference	0.96095	0.394

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00815	1
26DAP/20DAP	1.0098	1
34DAP/26DAP	1.01889	1
51DAP/34DAP	0.98132	0.927
52DAP/51DAP	0.96451	1
53DAP/52DAP	1.0728	0.712
55DAP/53DAP	0.85442	0.478
57DAP/55DAP	1.0535	0.854
62DAP/57DAP	1.00167	1
68DAP/62DAP	0.93545	0.641
68DAP/14DAP	0.94166	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.06413	0.306

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.71815	0.194
Mature Green Tomato/Ripe Tomato	0.80293	0.119
Immature Eggplant/Mature Eggplant	1.33175	0.056
Ripe Pepper/Ripe Tomato	0.9714	1
Mature Eggplant/Ripe Tomato	3.65976	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0198	1
1-1-2/M82	1.05565	1
12-2/M82	1.00154	1
12-4/M82	1.03009	1
1-3/M82	0.90929	0.378
2-1-1/M82	1.17097	0.689
2-1/M82	1.26567	0.345
2-6/M82	0.99732	1
3-2/M82	1.08846
4-1-1/M82	1.0279	1
4-1/M82	0.98647
4-3-2/M82	N/A	N/A
4-3/M82	1.00129	1
5-3/M82	1.02927	1
6-2/M82	0.9892	1
6-3/M82	1.05092	1
7-1/M82	0.93721	0.441
7-2/M82	0.96041	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	0.59545	0.321
IL2-6/WTpooled	1.07343	0.46
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.8324	1
IL12-4/WTpooled	0.8876	0.71
IL1-4/WTpooled	1.50012	1
WT/WTpooled	1.0674	0.686

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	0.90258	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05536	0.921
DC3000/delta hrp 6h	1.04186	1
DC3000/delta hrp 12h	0.89758	1
DC3000/delta hrp 24h	0.97901	0.897

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.01732	0.598
DC3000 delta B/DC3000 delta AB	1.05295	0.491

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.78491	1
Exp 36h	1.05931	1
Exp 60h	0.98009	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01392	1
Var 0h	1.0539	1
Var 12h I row2-row1	1.18399	0.198
Var 12h NI row2-row1	1.05589	1
Var 36h I row2-row1	0.95681	1
Var 36h NI row2-row1	0.90668	0.706
Var 60h I row2-row1	1.12995	1
Var 60h NI row2-row1	1.09275	0.904
Time course 0hI-0hNI	1.05528	0.833
Time course 12hI-12hNI	1.00914	0.88
Time course 36hI-36hNI	0.99843	0.826
Time course 60hI-60hNI	1.36745	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)	0.99429	0.789
transgenic ySAMdc/azygous control (breaker)	1.20563	1
transgenic ySAMdc/azygous control (red)	1.16143	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.06277	0.185

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.36997	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.65323	0.09
Manapal/WT (break)	1.36391	0.381
Manapal/WT (red)	1.56015	0.15