Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.11.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06195	0.867
27DAP/17DAP	1.26675	0.772
39DAP/27DAP	1.17116	0.873
41DAP/39DAP	1.2044	0.408
42DAP/41DAP	0.76078	0.774
43DAP/42DAP	0.9848	0.934
47DAP/43DAP	0.97337	0.825
52DAP/47DAP	1.12089	0.806
57DAP/52DAP	1.01974	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96183	0.432
17DAP/reference	1.04292	1
27DAP/reference	0.9775	0.654
39DAP/reference	1.05616	0.691
41DAP/reference	1.17496	0.079
42DAP/reference	0.8266	0.052
43DAP/reference	1.09246	0.217
47DAP/reference	0.8622	0.01
52DAP/reference	0.73842	0.042
57DAP/reference	0.8333	0.059

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90507	0.47
27DAP/17DAP	1.2335	0.411
39DAP/27DAP	0.91333	0.382
41DAP/39DAP	0.86402	0.495
42DAP/41DAP	0.88332	0.276
43DAP/42DAP	1.29419	0.147
47DAP/43DAP	1.13292	0.572
52DAP/47DAP	0.99895	0.93
57DAP/52DAP	1.37565	0.064
57DAP/7DAP	1.16019	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98321	0.55
17DAP/reference	1.17636	0.077
27DAP/reference	1.04758	0.974
39DAP/reference	1.08396	0.96
41DAP/reference	1.19637	0.524
42DAP/reference	1.19189	0.405
43DAP/reference	1.21378	0.083
47DAP/reference	1.04127	1
52DAP/reference	1.24883	0.247
57DAP/reference	1.07876	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1639	0.501
17DAP/reference	1.15738	0.285
27DAP/reference	0.88442	0.181
39DAP/reference	1.02093	0.621
41DAP/reference	0.9859	0.505
42DAP/reference	0.97	0.482
43DAP/reference	1.45211	0.021
47DAP/reference	1.07237	0.069
52DAP/reference	1.06406	0.596
57DAP/reference	1.10953	0.786

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95006	0.422
17DAP/reference	1.18363	0.462
27DAP/reference	1.15087	0.096
39DAP/reference	1.13834	0.307
41DAP/reference	1.06044	0.554
42DAP/reference	0.99667	0.816
43DAP/reference	0.88045	0.246
47DAP/reference	1.22041	0.562
52DAP/reference	1.3948	0.759
57DAP/reference	0.78726	0.057

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04299	0.966
26DAP/20DAP	0.90759
34DAP/26DAP	1.00767	1
51DAP/34DAP	0.90765	0.611
52DAP/51DAP	1.14918	0.596
53DAP/52DAP	0.8174	0.535
55DAP/53DAP	1.11162	0.991
57DAP/55DAP	0.80702	0.271
62DAP/57DAP	0.98716	0.994
68DAP/62DAP	1.74867	0.653
68DAP/14DAP	0.93699	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.22152	0.439

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.0047	1
Mature Green Tomato/Ripe Tomato	0.61985	0.03
Immature Eggplant/Mature Eggplant	1.02411	1
Ripe Pepper/Ripe Tomato	1.66738	0.258
Mature Eggplant/Ripe Tomato	1.79069	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0541	0.742
1-1-2/M82	0.71802
12-2/M82	0.81969
12-4/M82	0.84045	0.358
1-3/M82	0.99782	1
2-1-1/M82	0.9123	1
2-1/M82	0.72446	0.519
2-6/M82	0.83926	1
3-2/M82	1.05759
4-1-1/M82	1.17501	1
4-1/M82	1.11448
4-3-2/M82	1.06472
4-3/M82	0.96649	0.72
5-3/M82	0.9642	1
6-2/M82	0.65042
6-3/M82	1.06177	1
7-1/M82	0.84314	1
7-2/M82	0.75733	0.417
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.26383	1
IL2-6/WTpooled	1.03317	1
IL7-5/WTpooled	1.09638	1
IL7-3/WTpooled	0.94003	1
IL12-4/WTpooled	0.90574	0.71
IL1-4/WTpooled	1.07825	1
WT/WTpooled	0.89788	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	0.95288	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99879
DC3000/delta hrp 6h	3.86564	1
DC3000/delta hrp 12h	1.04163	1
DC3000/delta hrp 24h	1.2082	0.165

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.9575	0.71

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.08391	1
Var 0h	0.45791	0.261
Var 12h I row2-row1	0.89467	0.357
Var 12h NI row2-row1	1.33454	0.266
Var 36h I row2-row1	1.2537	0.41
Var 36h NI row2-row1	0.89338	0.584
Var 60h I row2-row1	0.97918	1
Var 60h NI row2-row1	0.90305	1
Time course 0hI-0hNI	1.08425	0.603
Time course 12hI-12hNI	0.99176	0.994
Time course 36hI-36hNI	1.00723	0.975
Time course 60hI-60hNI	1.29314	0.008

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)	1.08946	0.326
transgenic ySAMdc/azygous control (breaker)	0.67584	0.142
transgenic ySAMdc/azygous control (red)	0.97595	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.92756	0.191

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.74142	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.82833	1
Manapal/WT (break)	1.03688	1
Manapal/WT (red)	0.58972	0.181