Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.12.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11979	0.381
27DAP/17DAP	0.94102	0.908
39DAP/27DAP	1.4398	0.618
41DAP/39DAP	0.66285	0.113
42DAP/41DAP	1.48388	0.722
43DAP/42DAP	1.2455	0.875
47DAP/43DAP	1.12766	0.4
52DAP/47DAP	0.94666	0.774
57DAP/52DAP	0.83479	0.765

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0043	0.824
17DAP/reference	1.10531	0.258
27DAP/reference	1.37153	0.013
39DAP/reference	1.02051	0.747
41DAP/reference	0.97659	0.667
42DAP/reference	1.13018	0.003
43DAP/reference	1.18228	0.016
47DAP/reference	1.09812	0.125
52DAP/reference	1.06431	0.498
57DAP/reference	0.96743	0.186

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.29174	0.078
27DAP/17DAP	0.99398	0.969
39DAP/27DAP	1.02209	0.862
41DAP/39DAP	0.7968	0.465
42DAP/41DAP	1.24658	0.034
43DAP/42DAP	1.6182	0.014
47DAP/43DAP	0.93905	0.534
52DAP/47DAP	0.97712	0.9
57DAP/52DAP	0.85746	0.103
57DAP/7DAP	1.18836	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77563	0.072
17DAP/reference	0.72483	0.011
27DAP/reference	0.73555	0.01
39DAP/reference	0.89217	0.016
41DAP/reference	0.86815	0.103
42DAP/reference	1.04136	0.889
43DAP/reference	1.18565	0.178
47DAP/reference	1.17127	0.195
52DAP/reference	1.00446	0.802
57DAP/reference	1.05983	0.571

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81799	0.17
17DAP/reference	1.06627	0.557
27DAP/reference	1.19599	0.042
39DAP/reference	1.04467	1
41DAP/reference	1.01441	0.735
42DAP/reference	0.99149	0.594
43DAP/reference	0.78615	0.066
47DAP/reference	0.90244	0.039
52DAP/reference	0.80604	0.006
57DAP/reference	0.74631	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75239	0.065
17DAP/reference	0.97522	0.658
27DAP/reference	0.95448	0.337
39DAP/reference	1.03744	0.633
41DAP/reference	0.99654	0.754
42DAP/reference	1.91822	0.011
43DAP/reference	1.80609	0.006
47DAP/reference	1.83326	0.011
52DAP/reference	1.80267	0.058
57DAP/reference	2.83262	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.80223	0.611
26DAP/20DAP	0.89817	1
34DAP/26DAP	1.07396	1
51DAP/34DAP	0.60157	0.063
52DAP/51DAP	1.01439	0.836
53DAP/52DAP	1.02098	0.921
55DAP/53DAP	1.03498	0.976
57DAP/55DAP	1.0256	0.975
62DAP/57DAP	1.05961	0.902
68DAP/62DAP	0.92352	0.668
68DAP/14DAP	0.75838	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.85896	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.79313	0.238
Mature Green Tomato/Ripe Tomato	1.2067	0.095
Immature Eggplant/Mature Eggplant	0.471	0.064
Ripe Pepper/Ripe Tomato	1.15196	1
Mature Eggplant/Ripe Tomato	1.14093	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.16898	0.742
1-1-2/M82	1.37772	1
12-2/M82	0.90181	0.955
12-4/M82	1.44825	1
1-3/M82	1.59282	0.277
2-1-1/M82	0.75598	0.465
2-1/M82	0.57251	0.325
2-6/M82	1.28125	0.395
3-2/M82	0.86133	0.752
4-1-1/M82	1.64563	0.72
4-1/M82	2.01288	0.853
4-3-2/M82	1.3865	0.241
4-3/M82	1.2749	0.268
5-3/M82	1.05893	1
6-2/M82	1.4413	0.253
6-3/M82	1.03058	1
7-1/M82	1.08724	1
7-2/M82	1.43909	1
9-3-2/M82	1.02034

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.96059	1
IL2-6/WTpooled	1.10175	0.584
IL7-5/WTpooled	1.03119	1
IL7-3/WTpooled	0.92822	1
IL12-4/WTpooled	1.04903	1
IL1-4/WTpooled	1.02031	1
WT/WTpooled	0.96789	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	0.86633	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04869	0.921
DC3000/delta hrp 6h	0.9697	0.95
DC3000/delta hrp 12h	1.07475	1
DC3000/delta hrp 24h	0.88783	0.403

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.75087	0.025
DC3000 delta B/DC3000 delta AB	0.75825	0.031

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.19567	1
Exp 36h	0.93397	0.879
Exp 60h	1.04611	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01859	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.94426	0.363
Var 12h NI row2-row1	1.04622	1
Var 36h I row2-row1	0.93932	1
Var 36h NI row2-row1	1.03169	1
Var 60h I row2-row1	1.05711	0.562
Var 60h NI row2-row1	0.95336	1
Time course 0hI-0hNI	1.00716	1
Time course 12hI-12hNI	0.98547	0.935
Time course 36hI-36hNI	0.99761	0.768
Time course 60hI-60hNI	0.58452	0.009

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)	0.96959	0.662
transgenic ySAMdc/azygous control (breaker)	1.25632	1
transgenic ySAMdc/azygous control (red)	2.00855	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.32186	0.115

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.14374	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.17465	0.105
Manapal/WT (break)	1.84002	0.381
Manapal/WT (red)	3.17338	0.126