Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.7.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09078	0.697
27DAP/17DAP	0.94672	0.902
39DAP/27DAP	0.83353	0.507
41DAP/39DAP	1.13868	0.597
42DAP/41DAP	0.99335	1
43DAP/42DAP	1.02376	1
47DAP/43DAP	1.13601	0.809
52DAP/47DAP	1.38236	0.381
57DAP/52DAP	0.76582	0.456

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77717	0.027
17DAP/reference	0.9406	0.419
27DAP/reference	0.97606	0.683
39DAP/reference	0.95727	0.565
41DAP/reference	0.83293	0.085
42DAP/reference	0.86754	0.016
43DAP/reference	0.93415	0.273
47DAP/reference	0.94309	0.279
52DAP/reference	1.11473	0.32
57DAP/reference	1.20577	0.084

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9748	0.613
27DAP/17DAP	0.94559	0.58
39DAP/27DAP	0.98844	0.943
41DAP/39DAP	1.01699	0.895
42DAP/41DAP	1.01859	0.991
43DAP/42DAP	1.04448	0.382
47DAP/43DAP	1.00988	0.926
52DAP/47DAP	0.97907	0.899
57DAP/52DAP	1.00097	0.926
57DAP/7DAP	0.94916	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8413	0.168
17DAP/reference	0.81837	0.056
27DAP/reference	0.80373	0.013
39DAP/reference	0.76668	0.012
41DAP/reference	0.81412	0.094
42DAP/reference	0.70387	0.01
43DAP/reference	0.71034	0.017
47DAP/reference	0.94013	0.504
52DAP/reference	0.67714	0.013
57DAP/reference	0.78525	0.019

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88361	0.231
17DAP/reference	0.84349	0.058
27DAP/reference	0.99115	0.619
39DAP/reference	0.98352	0.526
41DAP/reference	0.80541	0.1
42DAP/reference	1.02614	1
43DAP/reference	0.94912	0.43
47DAP/reference	0.91401	0.164
52DAP/reference	1.03033	0.988
57DAP/reference	0.88859	0.135

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79834	0.047
17DAP/reference	0.89178	0.268
27DAP/reference	0.80145	0.045
39DAP/reference	0.69111	0.008
41DAP/reference	0.92396	0.148
42DAP/reference	0.85533	0.108
43DAP/reference	0.79977	0.048
47DAP/reference	0.88478	0.306
52DAP/reference	0.76743	0.145
57DAP/reference	0.80614	0.06

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.86324	1
26DAP/20DAP	0.8827	0.512
34DAP/26DAP	1.04911	1
51DAP/34DAP	1.06182	0.692
52DAP/51DAP	0.96621	1
53DAP/52DAP	1.12095	0.47
55DAP/53DAP	0.95617	0.263
57DAP/55DAP	1.05332	0.881
62DAP/57DAP	1.23885	0.35
68DAP/62DAP	0.79887	0.109
68DAP/14DAP	0.90784	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.9084	0.072

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.13023	0.881
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.20587	0.293
Mature Eggplant/Ripe Tomato	0.24496	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.91689
1-1-2/M82	1.11022	1
12-2/M82	0.94854
12-4/M82	0.98163	1
1-3/M82	0.89097
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.96923
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	1.20778	1
4-3/M82	N/A	N/A
5-3/M82	1.10187	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.00133	1
9-3-2/M82	0.73575

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.05477	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.15891	0.362
IL12-4/WTpooled	0.93602	0.71
IL1-4/WTpooled	0.98902
WT/WTpooled	0.99103	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	0.96254	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99933	1
DC3000/delta hrp 6h	0.92311	0.95
DC3000/delta hrp 12h	1.23379	1
DC3000/delta hrp 24h	0.97502	0.861

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.16009	0.183
DC3000 delta B/DC3000 delta AB	1.08162	0.398

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.26346	1
Exp 36h	1.4622	0.693
Exp 60h	1.48014	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97772	1
Var 0h	0.9168	1
Var 12h I row2-row1	1.0763	0.324
Var 12h NI row2-row1	0.95454	0.82
Var 36h I row2-row1	1.01123	1
Var 36h NI row2-row1	0.93996	0.421
Var 60h I row2-row1	1.21687	1
Var 60h NI row2-row1	1.30214	0.904
Time course 0hI-0hNI	1.09471	0.852
Time course 12hI-12hNI	1.04849	0.81
Time course 36hI-36hNI	0.98026	0.549
Time course 60hI-60hNI	1.22189	0.013

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)	2.00842	0.339
transgenic ySAMdc/azygous control (breaker)	0.56971	0.142
transgenic ySAMdc/azygous control (red)	1.33835	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08704	0.177

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.15569	0.307
Manapal/WT (break)	1.35865	0.126
Manapal/WT (red)	N/A	N/A