Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.20.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81884	0.29
27DAP/17DAP	1.01794	0.923
39DAP/27DAP	0.7355	0.435
41DAP/39DAP	1.36852	0.285
42DAP/41DAP	1.16783	0.691
43DAP/42DAP	1.00106	0.937
47DAP/43DAP	0.87564	0.595
52DAP/47DAP	1.03383	0.982
57DAP/52DAP	0.83988	0.784

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91287	0.39
17DAP/reference	1.06447	0.27
27DAP/reference	1.00529	1
39DAP/reference	1.00222	1
41DAP/reference	0.98247	0.814
42DAP/reference	0.92187	0.107
43DAP/reference	0.97297	0.555
47DAP/reference	0.96357	0.258
52DAP/reference	0.97976	0.53
57DAP/reference	1.13792	0.063

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01788	0.782
27DAP/17DAP	0.94408	0.854
39DAP/27DAP	1.13481	0.685
41DAP/39DAP	0.88329	0.398
42DAP/41DAP	1.04757	1
43DAP/42DAP	1.25892	0.513
47DAP/43DAP	1.00627	1
52DAP/47DAP	1.12504	0.779
57DAP/52DAP	1.05193	0.891
57DAP/7DAP	0.9318	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19454	0.101
17DAP/reference	1.7091	0.006
27DAP/reference	1.86265	0.006
39DAP/reference	1.79056	0.005
41DAP/reference	1.72312	0.014
42DAP/reference	2.04133	0.006
43DAP/reference	2.10801	0.006
47DAP/reference	1.14168	0.561
52DAP/reference	1.89347	0.008
57DAP/reference	1.6638	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93468	0.362
17DAP/reference	0.85871	0.047
27DAP/reference	0.87994	0.24
39DAP/reference	0.88093	0.069
41DAP/reference	0.92476	0.183
42DAP/reference	0.84303	0.016
43DAP/reference	0.99868	0.748
47DAP/reference	0.87465	0.026
52DAP/reference	0.92447	0.007
57DAP/reference	0.92054	0.194

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19614	0.158
17DAP/reference	1.13248	0.412
27DAP/reference	1.44659	0.038
39DAP/reference	1.28115	0.037
41DAP/reference	1.34636	0.032
42DAP/reference	1.52241	0.094
43DAP/reference	1.42367	0.121
47DAP/reference	0.91963	0.191
52DAP/reference	1.91186	0.072
57DAP/reference	0.88369	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00116	1
26DAP/20DAP	0.84864	1
34DAP/26DAP	1.41607	1
51DAP/34DAP	3.78827	0.028
52DAP/51DAP	2.30967	0.542
53DAP/52DAP	0.95591	0.75
55DAP/53DAP	0.83534	0.604
57DAP/55DAP	1.16754	0.915
62DAP/57DAP	0.93542	0.871
68DAP/62DAP	1.19707	0.523
68DAP/14DAP	1.15424	0.785

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.81895	0.439

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.94258	0.71
Mature Green Tomato/Ripe Tomato	0.78525	0.055
Immature Eggplant/Mature Eggplant	1.16974	0.19
Ripe Pepper/Ripe Tomato	0.89103	0.293
Mature Eggplant/Ripe Tomato	1.12687	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.85975	0.605
1-1-2/M82	1.07308
12-2/M82	N/A	N/A
12-4/M82	1.07155	1
1-3/M82	0.81349
2-1-1/M82	1.37066
2-1/M82	N/A	N/A
2-6/M82	0.9305
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.38636
4-3-2/M82	0.88697
4-3/M82	N/A	N/A
5-3/M82	0.84656	0.642
6-2/M82	N/A	N/A
6-3/M82	0.95734	1
7-1/M82	0.70023
7-2/M82	1.07236
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.96259	0.243
IL2-6/WTpooled	0.8957	0.473
IL7-5/WTpooled	1.44413	0.75
IL7-3/WTpooled	1.03561	1
IL12-4/WTpooled	0.95221	1
IL1-4/WTpooled	1.0407	1
WT/WTpooled	0.99517	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	1.08309	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05708	0.921
DC3000/delta hrp 6h	1.2499	1
DC3000/delta hrp 12h	0.9628	1
DC3000/delta hrp 24h	1.13725	0.136

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.88999
DC3000 delta B/DC3000 delta AB	1.79863	0.199

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9153	1
Exp 36h	1.41967	0.693
Exp 60h	1.32649	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05013	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.01773	1
Var 12h NI row2-row1	1.43407	0.649
Var 36h I row2-row1	1.19491	0.368
Var 36h NI row2-row1	0.96461	0.852
Var 60h I row2-row1	0.80061	0.832
Var 60h NI row2-row1	0.87595	0.866
Time course 0hI-0hNI	0.90546	0.379
Time course 12hI-12hNI	2.24748	0.381
Time course 36hI-36hNI	1.36275	0.28
Time course 60hI-60hNI	3.02984	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)	0.99855	1
transgenic ySAMdc/azygous control (breaker)	1.14848	1
transgenic ySAMdc/azygous control (red)	1.09467	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98152	0.313

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.08486	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.76543	0.172
Manapal/WT (break)	0.92194	1
Manapal/WT (red)	1.36213	0.164