Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.14.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91485	0.543
27DAP/17DAP	0.90054	0.782
39DAP/27DAP	1.04335	0.949
41DAP/39DAP	1.15042	0.85
42DAP/41DAP	1.06639	0.967
43DAP/42DAP	0.99576	0.937
47DAP/43DAP	0.96353	0.794
52DAP/47DAP	1.41225	0.463
57DAP/52DAP	1.05727	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0437	0.522
17DAP/reference	0.97389	0.474
27DAP/reference	0.9833	0.417
39DAP/reference	1.00354	0.747
41DAP/reference	0.96685	0.341
42DAP/reference	1.01153	0.995
43DAP/reference	1.02661	0.403
47DAP/reference	0.96913	0.174
52DAP/reference	0.9908	0.618
57DAP/reference	0.96455	0.21

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08709	0.114
27DAP/17DAP	0.97824	0.821
39DAP/27DAP	0.98673	0.932
41DAP/39DAP	1.03111	0.837
42DAP/41DAP	1.02958	0.879
43DAP/42DAP	0.89203	0.065
47DAP/43DAP	1.0606	0.735
52DAP/47DAP	0.98027	0.902
57DAP/52DAP	1.02566	0.891
57DAP/7DAP	1.13625	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0406	0.613
17DAP/reference	1.13201	0.007
27DAP/reference	1.09716	0.03
39DAP/reference	1.15456	0.005
41DAP/reference	1.12592	0.02
42DAP/reference	1.12663	0.059
43DAP/reference	1.05869	0.14
47DAP/reference	1.15636	0.027
52DAP/reference	1.18507	0.021
57DAP/reference	1.19372	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00365	0.979
17DAP/reference	1.14781	0.048
27DAP/reference	1.11616	0.221
39DAP/reference	1.05934	0.3
41DAP/reference	1.09697	0.335
42DAP/reference	1.07687	0.61
43DAP/reference	1.06607	0.611
47DAP/reference	1.01343	0.621
52DAP/reference	1.02226	0.789
57DAP/reference	1.0296	0.786

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0536	0.347
17DAP/reference	1.0104	0.924
27DAP/reference	1.06655	0.164
39DAP/reference	1.10682	0.033
41DAP/reference	1.03689	0.343
42DAP/reference	1.09867	0.209
43DAP/reference	1.04601	0.515
47DAP/reference	0.99355	0.646
52DAP/reference	1.05517	0.509
57DAP/reference	1.18918	0.069

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02002	0.966
26DAP/20DAP	1.06526	0.905
34DAP/26DAP	0.98704	0.998
51DAP/34DAP	0.96344	0.688
52DAP/51DAP	0.98512	1
53DAP/52DAP	1.04092	0.697
55DAP/53DAP	1.04517	0.712
57DAP/55DAP	1.02411	0.96
62DAP/57DAP	1.05641	0.8
68DAP/62DAP	0.9424	0.722
68DAP/14DAP	0.91748	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.24801	0.017

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.10372	0.089
Mature Green Tomato/Ripe Tomato	1.34511	0.119
Immature Eggplant/Mature Eggplant	1.03228	0.398
Ripe Pepper/Ripe Tomato	0.91049	1
Mature Eggplant/Ripe Tomato	0.9078	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96633	0.961
1-1-2/M82	0.9622	1
12-2/M82	0.916	0.955
12-4/M82	1.04518	1
1-3/M82	1.12373	1
2-1-1/M82	1.06517	0.764
2-1/M82	0.95504	1
2-6/M82	0.95848	1
3-2/M82	0.99138	1
4-1-1/M82	1.17078	1
4-1/M82	0.95293	1
4-3-2/M82	0.96464	1
4-3/M82	1.07915	1
5-3/M82	1.19267	0.572
6-2/M82	1.01769	1
6-3/M82	1.03871	1
7-1/M82	0.96635	1
7-2/M82	1.06467	1
9-3-2/M82	0.94602	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.89182	0.321
IL2-6/WTpooled	0.93045	0.473
IL7-5/WTpooled	0.96463	1
IL7-3/WTpooled	0.84597	0.418
IL12-4/WTpooled	0.92132	0.71
IL1-4/WTpooled	0.9267	0.562
WT/WTpooled	1.02406	0.957

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	1.11999	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98346	1
DC3000/delta hrp 6h	0.96842	0.95
DC3000/delta hrp 12h	0.96495	1
DC3000/delta hrp 24h	1.1384	0.383

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.14373	0.076
DC3000 delta B/DC3000 delta AB	1.08727	0.389

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.90678	1
Exp 36h	1.31761	1
Exp 60h	1.22178	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03601	1
Var 0h	0.95758	1
Var 12h I row2-row1	1.10012	0.473
Var 12h NI row2-row1	1.06798	0.34
Var 36h I row2-row1	0.92646	1
Var 36h NI row2-row1	0.84069	0.421
Var 60h I row2-row1	1.01035	1
Var 60h NI row2-row1	0.91359	0.818
Time course 0hI-0hNI	0.95733	0.671
Time course 12hI-12hNI	1.07206	0.517
Time course 36hI-36hNI	1.23794	0.015
Time course 60hI-60hNI	1.49618	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)	0.99018	0.862
transgenic ySAMdc/azygous control (breaker)	1.25022	0.178
transgenic ySAMdc/azygous control (red)	1.14325	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.06163	0.194

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.07545	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.74888	1
Manapal/WT (break)	0.9123	1
Manapal/WT (red)	1.25929	0.133