Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.9.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94592	0.61
27DAP/17DAP	2.13429	0.399
39DAP/27DAP	0.84793	0.652
41DAP/39DAP	0.74383	0.196
42DAP/41DAP	1.89093	0.244
43DAP/42DAP	1.04857	1
47DAP/43DAP	0.84286	0.504
52DAP/47DAP	2.31371	0.064
57DAP/52DAP	0.71731	0.462

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77333	0.051
17DAP/reference	0.73478	0.057
27DAP/reference	1.02484	0.981
39DAP/reference	0.75063	0.06
41DAP/reference	0.68579	0.011
42DAP/reference	1.64005	0.001
43DAP/reference	0.88968	0.191
47DAP/reference	1.21882	0.433
52DAP/reference	1.00402	0.709
57DAP/reference	1.20515	0.105

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.52855	0.299
27DAP/17DAP	1.14356	0.794
39DAP/27DAP	0.91951	0.579
41DAP/39DAP	1.17187	0.603
42DAP/41DAP	0.94122	0.721
43DAP/42DAP	1.11426	0.627
47DAP/43DAP	1.23514	0.853
52DAP/47DAP	1.51352	0.15
57DAP/52DAP	1.57183	0.088
57DAP/7DAP	2.45745	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26214	0.205
17DAP/reference	1.36185	0.162
27DAP/reference	1.04958	0.804
39DAP/reference	1.25585	0.126
41DAP/reference	1.30064	0.022
42DAP/reference	1.18814	0.405
43DAP/reference	1.70911	0.012
47DAP/reference	0.84303	0.222
52DAP/reference	1.32876	0.055
57DAP/reference	2.47394	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86231	0.164
17DAP/reference	0.94053	0.389
27DAP/reference	0.89567	0.155
39DAP/reference	0.84044	0.14
41DAP/reference	1.17007	0.925
42DAP/reference	0.97085	0.482
43DAP/reference	0.96635	0.516
47DAP/reference	1.31284	0.095
52DAP/reference	0.85274	0.086
57DAP/reference	0.8867	0.18

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86628	0.158
17DAP/reference	1.01083	0.918
27DAP/reference	1.13653	0.227
39DAP/reference	1.25342	0.02
41DAP/reference	0.87745	0.055
42DAP/reference	1.07078	0.521
43DAP/reference	1.37847	0.01
47DAP/reference	1.13616	0.179
52DAP/reference	1.57519	0.053
57DAP/reference	1.39674	0.038

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93938	1
26DAP/20DAP	0.89451	0.512
34DAP/26DAP	1.19366	1
51DAP/34DAP	1.36492	0.869
52DAP/51DAP	0.75532
53DAP/52DAP	1.62188
55DAP/53DAP	1.21594	0.861
57DAP/55DAP	0.73437	0.1
62DAP/57DAP	0.84474	0.28
68DAP/62DAP	0.93565	0.81
68DAP/14DAP	1.31426

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.10558	0.7

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.3902
Mature Green Tomato/Ripe Tomato	0.25651	0.018
Immature Eggplant/Mature Eggplant	1.08297	0.311
Ripe Pepper/Ripe Tomato	0.47061	0.224
Mature Eggplant/Ripe Tomato	0.59162	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.88353
1-1-2/M82	0.36891
12-2/M82	3.1937	0.375
12-4/M82	0.62333	0.619
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.49691	0.695
3-2/M82	1.29879
4-1-1/M82	N/A	N/A
4-1/M82	1.36875
4-3-2/M82	N/A	N/A
4-3/M82	1.73515
5-3/M82	0.35341	0.374
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.29399
7-2/M82	1.39244
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	1.08294	0.788
IL7-5/WTpooled	0.46675
IL7-3/WTpooled	0.90795	1
IL12-4/WTpooled	0.94991	1
IL1-4/WTpooled	0.70806	0.699
WT/WTpooled	0.98225	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	1.91588	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08596	0.692
DC3000/delta hrp 6h	0.8974
DC3000/delta hrp 12h	1.24929	1
DC3000/delta hrp 24h	1.22358	0.118

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	3.51806

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.58541	0.489
Exp 60h	1.98145	0.215

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01144	1
Var 0h	0.80116	0.933
Var 12h I row2-row1	1.00165	1
Var 12h NI row2-row1	1.08416	1
Var 36h I row2-row1	1.14025	0.908
Var 36h NI row2-row1	0.75395	0.706
Var 60h I row2-row1	0.78141	0.439
Var 60h NI row2-row1	0.90389	0.69
Time course 0hI-0hNI	1.07149	0.764
Time course 12hI-12hNI	1.08255	0.49
Time course 36hI-36hNI	1.82214	0.009
Time course 60hI-60hNI	10.2815	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)	1.73368	0.397
transgenic ySAMdc/azygous control (breaker)	0.39167	0.134
transgenic ySAMdc/azygous control (red)	0.99773	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0699	0.155

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.11479	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.58122	0.172
Manapal/WT (break)	0.70064	1
Manapal/WT (red)	0.59378	0.315