Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-6.2.12.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83567	0.285
27DAP/17DAP	0.96683	0.923
39DAP/27DAP	1.26368	0.473
41DAP/39DAP	0.85075	0.445
42DAP/41DAP	0.95413	1
43DAP/42DAP	1.1831	0.772
47DAP/43DAP	1.17837	0.49
52DAP/47DAP	1.0956	0.913
57DAP/52DAP	1.03258	0.993

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88371	0.149
17DAP/reference	1.07609	0.492
27DAP/reference	0.95469	0.497
39DAP/reference	0.9918	0.855
41DAP/reference	1.12645	0.102
42DAP/reference	0.77652	0.014
43DAP/reference	1.05032	0.569
47DAP/reference	0.81353	0.01
52DAP/reference	0.86121	0.21
57DAP/reference	0.92424	0.235

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86727	0.135
27DAP/17DAP	1.06914	0.859
39DAP/27DAP	0.85473	0.181
41DAP/39DAP	0.95899	0.875
42DAP/41DAP	0.965	0.717
43DAP/42DAP	1.14087	0.25
47DAP/43DAP	1.03619	0.914
52DAP/47DAP	0.97517	0.902
57DAP/52DAP	1.05646	0.703
57DAP/7DAP	1.11526	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96653	0.55
17DAP/reference	1.04734	0.822
27DAP/reference	1.06818	0.551
39DAP/reference	1.03859	0.909
41DAP/reference	0.86227	0.064
42DAP/reference	0.98519	0.531
43DAP/reference	0.99192	0.665
47DAP/reference	0.96846	0.671
52DAP/reference	0.88924	0.232
57DAP/reference	0.90504	0.183

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07437	0.776
17DAP/reference	1.2477	0.508
27DAP/reference	1.01394	0.765
39DAP/reference	0.81042	0.144
41DAP/reference	0.87999	0.242
42DAP/reference	0.86105	0.15
43DAP/reference	0.95103	0.67
47DAP/reference	1.00758	1
52DAP/reference	0.96014	0.576
57DAP/reference	1.15199	0.494

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99045	0.653
17DAP/reference	1.12068	0.221
27DAP/reference	1.16284	0.179
39DAP/reference	1.09969	0.264
41DAP/reference	1.09803	0.343
42DAP/reference	1.03777	0.816
43DAP/reference	0.85843	0.256
47DAP/reference	0.91723	0.269
52DAP/reference	1.15321	0.549
57DAP/reference	0.70238	0.039

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.45341	0.966
26DAP/20DAP	1.20246	0.256
34DAP/26DAP	0.96133	0.954
51DAP/34DAP	1.10669	0.445
52DAP/51DAP	1.0599	0.689
53DAP/52DAP	0.89298	0.393
55DAP/53DAP	1.14787	0.29
57DAP/55DAP	1.09324	0.997
62DAP/57DAP	0.69003	0.05
68DAP/62DAP	1.27196	0.657
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.84496	0.285

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.977	0.611
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.75478	1
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	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.16221	0.508
4-3/M82	N/A	N/A
5-3/M82	0.78006	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.34024	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.14991	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.85321	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.14657	1
IL12-4/WTpooled	1.05578	0.522
IL1-4/WTpooled	2.49132	1
WT/WTpooled	0.91846	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	0.7963	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.48725	0.724
DC3000/delta hrp 6h	1.21723	1
DC3000/delta hrp 12h	0.97071	N/A
DC3000/delta hrp 24h	1.04642	0.84

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.86318	0.293
DC3000 delta B/DC3000 delta AB	1.76761	0.311

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.87025	1
Exp 36h	1.02017	1
Exp 60h	0.92899	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03812	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.10929	0.613
Var 12h NI row2-row1	0.99421	1
Var 36h I row2-row1	0.71785	1
Var 36h NI row2-row1	1.02479	1
Var 60h I row2-row1	0.86035	0.374
Var 60h NI row2-row1	0.9908	1
Time course 0hI-0hNI	0.93084	0.45
Time course 12hI-12hNI	1.0135	0.816
Time course 36hI-36hNI	0.93419	0.306
Time course 60hI-60hNI	0.7709	0.015

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)	0.99256	0.862
transgenic ySAMdc/azygous control (breaker)	0.71573	0.173
transgenic ySAMdc/azygous control (red)	0.87616	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9787	0.237

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.99954	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.87569	0.083
Manapal/WT (break)	1.33136	0.381
Manapal/WT (red)	1.32783	0.222