Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.20.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0742	1
27DAP/17DAP	1.37265	0.647
39DAP/27DAP	0.79425	0.364
41DAP/39DAP	1.32113	0.162
42DAP/41DAP	0.92613	1
43DAP/42DAP	1.07099	1
47DAP/43DAP	1.19676	0.463
52DAP/47DAP	0.79188	0.488
57DAP/52DAP	1.08234	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88474	0.103
17DAP/reference	0.91193	0.091
27DAP/reference	0.87262	0.027
39DAP/reference	0.87326	0.019
41DAP/reference	0.85918	0.018
42DAP/reference	0.79927	0.001
43DAP/reference	0.86026	0.024
47DAP/reference	0.88592	0.021
52DAP/reference	0.88613	0.135
57DAP/reference	0.98889	0.639

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83187	0.211
27DAP/17DAP	1.16227	0.541
39DAP/27DAP	1.00778	1
41DAP/39DAP	0.9536	0.893
42DAP/41DAP	0.98355	0.791
43DAP/42DAP	1.03737	0.746
47DAP/43DAP	1.0207	0.95
52DAP/47DAP	1.17712	0.573
57DAP/52DAP	1.08742	0.832
57DAP/7DAP	0.88006	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11461	0.223
17DAP/reference	0.99841	0.693
27DAP/reference	0.92404	0.117
39DAP/reference	1.08212	0.511
41DAP/reference	1.03184	0.46
42DAP/reference	0.92977	0.086
43DAP/reference	1.11063	0.157
47DAP/reference	0.9751	0.671
52DAP/reference	1.26208	0.071
57DAP/reference	1.1474	0.07

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96685	0.592
17DAP/reference	0.85231	0.011
27DAP/reference	0.81848	0.071
39DAP/reference	0.78583	0.028
41DAP/reference	0.82978	0.033
42DAP/reference	0.95274	0.321
43DAP/reference	0.89334	0.206
47DAP/reference	0.96564	0.328
52DAP/reference	0.87569	0.101
57DAP/reference	0.84882	0.092

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92553	0.147
17DAP/reference	0.9974	0.855
27DAP/reference	1.01921	0.672
39DAP/reference	1.02963	0.528
41DAP/reference	0.99907	0.826
42DAP/reference	0.98259	0.671
43DAP/reference	0.86692	0.179
47DAP/reference	0.93982	0.231
52DAP/reference	0.86605	0.211
57DAP/reference	0.97417	0.475

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	3.10919	0.966
26DAP/20DAP	1.06559	1
34DAP/26DAP	1.07643	1
51DAP/34DAP	1.08244	0.677
52DAP/51DAP	1.05259	1
53DAP/52DAP	0.69567	0.276
55DAP/53DAP	1.79302	0.361
57DAP/55DAP	1.25338	0.961
62DAP/57DAP	1.10578	0.868
68DAP/62DAP	2.32983	0.034
68DAP/14DAP	1.99734	0.025

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.51213	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.26152	0.062
Mature Green Tomato/Ripe Tomato	1.03631	0.814
Immature Eggplant/Mature Eggplant	0.79356	0.064
Ripe Pepper/Ripe Tomato	5.66678	0.256
Mature Eggplant/Ripe Tomato	1.81977	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.22118	0.551
1-1-2/M82	0.92163	0.958
12-2/M82	0.96211
12-4/M82	0.93733	1
1-3/M82	0.79555	0.501
2-1-1/M82	1.34524	0.764
2-1/M82	N/A	N/A
2-6/M82	0.95795	0.501
3-2/M82	0.98651	1
4-1-1/M82	1.19062
4-1/M82	1.04936
4-3-2/M82	0.82185	1
4-3/M82	1.22454	1
5-3/M82	0.90897	1
6-2/M82	0.82303
6-3/M82	1.04776
7-1/M82	0.82003
7-2/M82	0.98298	1
9-3-2/M82	0.9924	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.78853	0.243
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.13849	0.792
IL7-3/WTpooled	1.15204	1
IL12-4/WTpooled	1.1841
IL1-4/WTpooled	0.73638	0.476
WT/WTpooled	0.94927	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	1.38792	0.222

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09473	0.692
DC3000/delta hrp 6h	0.96949	0.95
DC3000/delta hrp 12h	0.80036	1
DC3000/delta hrp 24h	1.11319	0.271

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.70947
DC3000 delta B/DC3000 delta AB	0.43826

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04074	1
Exp 36h	0.93305	0.434
Exp 60h	0.87857	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00194	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.90982	0.338
Var 12h NI row2-row1	1.01265	1
Var 36h I row2-row1	1.03677	1
Var 36h NI row2-row1	1.33331	1
Var 60h I row2-row1	0.89941	0.285
Var 60h NI row2-row1	1.17463	1
Time course 0hI-0hNI	1.01086	1
Time course 12hI-12hNI	0.88302	0.375
Time course 36hI-36hNI	0.8938	0.26
Time course 60hI-60hNI	1.07312	0.495

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)	1.11574	0.289
transgenic ySAMdc/azygous control (breaker)	1.66128	0.178
transgenic ySAMdc/azygous control (red)	1.00958	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.90548	0.052

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.69864	0.227

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.20137	0.14
Manapal/WT (break)	1.08808	0.381
Manapal/WT (red)	1.15844	0.15