Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.9.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.3064	0.615
27DAP/17DAP	1.06745	0.905
39DAP/27DAP	0.8937	0.537
41DAP/39DAP	1.29619	0.32
42DAP/41DAP	1.13175	0.933
43DAP/42DAP	1.21286	0.861
47DAP/43DAP	0.79998	0.416
52DAP/47DAP	1.27875	0.772
57DAP/52DAP	0.96766	0.956

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0153	0.96
17DAP/reference	1.02036	0.653
27DAP/reference	0.98669	0.694
39DAP/reference	0.99903	0.941
41DAP/reference	0.93657	0.434
42DAP/reference	0.90119	0.043
43DAP/reference	1.12129	0.078
47DAP/reference	0.84768	0.007
52DAP/reference	0.76091	0.04
57DAP/reference	0.74339	0.014

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99432	0.847
27DAP/17DAP	1.06782	0.909
39DAP/27DAP	0.97708	0.852
41DAP/39DAP	1.08015	0.612
42DAP/41DAP	0.99547	0.887
43DAP/42DAP	1.05506	0.382
47DAP/43DAP	1.08674	0.147
52DAP/47DAP	1.09861	0.779
57DAP/52DAP	0.98221	0.776
57DAP/7DAP	1.12872	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92282	0.296
17DAP/reference	0.9264	0.192
27DAP/reference	0.94192	0.402
39DAP/reference	0.86354	0.146
41DAP/reference	0.90657	0.133
42DAP/reference	0.65849	0.014
43DAP/reference	0.74807	0.02
47DAP/reference	0.89728	0.293
52DAP/reference	0.71812	0.019
57DAP/reference	0.87655	0.093

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2312	0.054
17DAP/reference	1.09024	0.264
27DAP/reference	0.90749	0.181
39DAP/reference	0.84116	0.077
41DAP/reference	0.89313	0.081
42DAP/reference	0.82182	0.02
43DAP/reference	1.19353	0.076
47DAP/reference	0.91384	0.048
52DAP/reference	0.90803	0.047
57DAP/reference	1.19369	0.188

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19524	0.149
17DAP/reference	1.10318	0.241
27DAP/reference	1.06604	0.34
39DAP/reference	0.92547	0.179
41DAP/reference	0.9508	0.512
42DAP/reference	0.79947	0.087
43DAP/reference	0.75701	0.046
47DAP/reference	0.9682	0.421
52DAP/reference	1.8372	0.549
57DAP/reference	0.63676	0.03

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.11092	0.966
26DAP/20DAP	0.98395	1
34DAP/26DAP	1.16805	0.819
51DAP/34DAP	0.98943	0.863
52DAP/51DAP	1.04166	0.873
53DAP/52DAP	1.13847	0.37
55DAP/53DAP	1.15026	0.527
57DAP/55DAP	0.90268	0.548
62DAP/57DAP	1.16574	0.622
68DAP/62DAP	0.78618	0.314
68DAP/14DAP	1.18042	0.802

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.26151	0.064

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.29447	0.058
Mature Green Tomato/Ripe Tomato	0.80332	0.317
Immature Eggplant/Mature Eggplant	0.54687	0.063
Ripe Pepper/Ripe Tomato	1.007	1
Mature Eggplant/Ripe Tomato	1.76982	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.85728	0.708
1-1-2/M82	1.20868	1
12-2/M82	0.8512
12-4/M82	0.92274	0.619
1-3/M82	1.21058	1
2-1-1/M82	0.96285	1
2-1/M82	N/A	N/A
2-6/M82	1.27195
3-2/M82	0.93067	0.752
4-1-1/M82	1.0526
4-1/M82	0.95706
4-3-2/M82	0.93122	1
4-3/M82	N/A	N/A
5-3/M82	1.04797	1
6-2/M82	0.82765
6-3/M82	1.07503
7-1/M82	0.80752
7-2/M82	1.02402	1
9-3-2/M82	1.01947	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.22838	0.277
IL2-6/WTpooled	1.22234	0.441
IL7-5/WTpooled	1.45642	1
IL7-3/WTpooled	1.04728	1
IL12-4/WTpooled	1.0181	0.785
IL1-4/WTpooled	0.79647	0.562
WT/WTpooled	0.98297	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	0.85027	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98331	1
DC3000/delta hrp 6h	0.94448	0.95
DC3000/delta hrp 12h	0.97373	1
DC3000/delta hrp 24h	0.88227	0.212

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.81956	0.365
DC3000 delta B/DC3000 delta AB	0.99301	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.05206	1
Exp 36h	0.7445	0.449
Exp 60h	0.67141	0.278

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

hybridization	ratio	FDR (corrected p value)
self-self	1.06546	1
Var 0h	1.10047	1
Var 12h I row2-row1	1.05372	0.58
Var 12h NI row2-row1	0.95492	0.438
Var 36h I row2-row1	1.28551	0.742
Var 36h NI row2-row1	0.81943	0.469
Var 60h I row2-row1	0.94337	0.832
Var 60h NI row2-row1	0.98462	1
Time course 0hI-0hNI	0.96614	0.798
Time course 12hI-12hNI	1.06201	0.58
Time course 36hI-36hNI	1.33731	0.007
Time course 60hI-60hNI	1.34722	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)	0.8551	0.254
transgenic ySAMdc/azygous control (breaker)	1.73284	0.178
transgenic ySAMdc/azygous control (red)	1.17921	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96972	0.067

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.27175	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.47481	0.105
Manapal/WT (break)	1.59707	0.183
Manapal/WT (red)	1.59777	0.142