Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.7.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91587	0.596
27DAP/17DAP	1.10877	0.859
39DAP/27DAP	1.14213	1
41DAP/39DAP	1.27906	0.359
42DAP/41DAP	1.24949	0.797
43DAP/42DAP	1.00635	0.937
47DAP/43DAP	0.90083	0.66
52DAP/47DAP	1.27319	0.466
57DAP/52DAP	0.86975	0.827

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9341	0.262
17DAP/reference	0.99035	0.819
27DAP/reference	0.94314	0.471
39DAP/reference	1.14707	0.096
41DAP/reference	1.15489	0.014
42DAP/reference	1.02306	0.645
43DAP/reference	1.22964	0.064
47DAP/reference	0.97484	0.473
52DAP/reference	1.09264	0.912
57DAP/reference	1.28459	0.07

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99902	0.899
27DAP/17DAP	1.04058	0.9
39DAP/27DAP	1.03169	0.691
41DAP/39DAP	1.00678	1
42DAP/41DAP	1.03033	0.947
43DAP/42DAP	1.04035	0.585
47DAP/43DAP	1.00433	1
52DAP/47DAP	0.96028	0.834
57DAP/52DAP	0.95402	0.626
57DAP/7DAP	1.42898	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8517	0.104
17DAP/reference	0.88822	0.012
27DAP/reference	0.82506	0.01
39DAP/reference	0.83164	0.011
41DAP/reference	0.86699	0.064
42DAP/reference	0.86007	0.01
43DAP/reference	0.79256	0.013
47DAP/reference	0.8769	0.222
52DAP/reference	0.76536	0.012
57DAP/reference	0.80227	0.013

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14336	0.127
17DAP/reference	0.97455	0.536
27DAP/reference	1.28543	0.123
39DAP/reference	1.28086	0.657
41DAP/reference	1.10762	0.439
42DAP/reference	1.17676	0.185
43DAP/reference	1.81062	0.133
47DAP/reference	1.33194	0.011
52DAP/reference	1.29255	0.006
57DAP/reference	1.22695	0.609

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8433	0.028
17DAP/reference	0.96526	0.528
27DAP/reference	0.92762	0.218
39DAP/reference	0.83127	0.018
41DAP/reference	0.8887	0.028
42DAP/reference	0.88782	0.134
43DAP/reference	0.96376	0.416
47DAP/reference	1.25095	0.081
52DAP/reference	0.81011	0.204
57DAP/reference	0.97538	0.564

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01069	1
26DAP/20DAP	0.91554	1
34DAP/26DAP	0.90726	0.712
51DAP/34DAP	0.95396	0.77
52DAP/51DAP	0.98288	1
53DAP/52DAP	0.97595	0.848
55DAP/53DAP	1.0687	0.911
57DAP/55DAP	1.10563	0.841
62DAP/57DAP	N/A	N/A
68DAP/62DAP	0.87243
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.80404	0.137

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.5509	0.024
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	0.97428	0.961
1-1-2/M82	0.89995
12-2/M82	1.10038	1
12-4/M82	0.99644	1
1-3/M82	0.94773	0.501
2-1-1/M82	1.14755	0.689
2-1/M82	N/A	N/A
2-6/M82	1.06683	1
3-2/M82	0.84459
4-1-1/M82	0.75552
4-1/M82	0.88406
4-3-2/M82	0.75434	0.487
4-3/M82	0.99432	1
5-3/M82	0.95751	1
6-2/M82	N/A	N/A
6-3/M82	1.20247
7-1/M82	N/A	N/A
7-2/M82	1.01685
9-3-2/M82	0.75332	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.84004	0.321
IL2-6/WTpooled	0.94205	1
IL7-5/WTpooled	1.79369	1
IL7-3/WTpooled	1.24942	0.362
IL12-4/WTpooled	1.11724	0.737
IL1-4/WTpooled	0.87364	0.834
WT/WTpooled	1.01897	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	1.07383	0.088

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00263	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.66816	1
DC3000/delta hrp 24h	1.03989	0.567

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.92932	0.132
DC3000 delta B/DC3000 delta AB	0.95634	0.605

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	0.9755	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	0.86311	1
Var 0h	0.91351	0.933
Var 12h I row2-row1	1.0393	0.613
Var 12h NI row2-row1	1.01207	1
Var 36h I row2-row1	0.96697	1
Var 36h NI row2-row1	0.97846	0.852
Var 60h I row2-row1	1.40632	1
Var 60h NI row2-row1	1.13036	0.904
Time course 0hI-0hNI	1.08835	0.833
Time course 12hI-12hNI	1.0681	0.698
Time course 36hI-36hNI	0.97987	0.569
Time course 60hI-60hNI	1.13114	0.187

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)	1.22401	0.321
transgenic ySAMdc/azygous control (breaker)	0.72335	0.132
transgenic ySAMdc/azygous control (red)	1.08122	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01893	0.495

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)	0.85085	1
Manapal/WT (break)	0.79968	0.333
Manapal/WT (red)	0.91837	0.607