Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.13.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.44726	0.498
27DAP/17DAP	2.23709	0.625
39DAP/27DAP	1.17308	0.981
41DAP/39DAP	0.76526	0.225
42DAP/41DAP	1.26331	0.797
43DAP/42DAP	1.60052	0.299
47DAP/43DAP	6.2924	0.156
52DAP/47DAP	1.44503	0.545
57DAP/52DAP	1.20779	0.853

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.67078	0.027
17DAP/reference	0.88582	0.169
27DAP/reference	0.87103	0.095
39DAP/reference	0.94147	0.292
41DAP/reference	0.88596	0.065
42DAP/reference	0.88881	0.03
43DAP/reference	1.16011	0.012
47DAP/reference	2.94344	0.001
52DAP/reference	6.68809	0.007
57DAP/reference	3.67115	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.47388	0.049
27DAP/17DAP	1.61509	0.04
39DAP/27DAP	2.12155	0.043
41DAP/39DAP	0.42879	0.013
42DAP/41DAP	0.98827	0.812
43DAP/42DAP	1.21405	0.25
47DAP/43DAP	1.36768	0.042
52DAP/47DAP	1.84492	0.048
57DAP/52DAP	1.83668	0.038
57DAP/7DAP	1.83945	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.34741	0.039
17DAP/reference	0.43557	0.012
27DAP/reference	0.82078	0.117
39DAP/reference	0.63844	0.014
41DAP/reference	0.50362	0.011
42DAP/reference	0.5896	0.018
43DAP/reference	0.47292	0.01
47DAP/reference	0.46904	0.035
52DAP/reference	0.26965	0.009
57DAP/reference	0.23118	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.42944	0.009
17DAP/reference	0.49992	0.004
27DAP/reference	0.85265	0.15
39DAP/reference	0.7053	0.011
41DAP/reference	0.52824	0.024
42DAP/reference	0.69432	0.013
43DAP/reference	0.3838	0.002
47DAP/reference	0.62462	0.03
52DAP/reference	0.43833	0.003
57DAP/reference	0.46337	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.26141	0.018
17DAP/reference	0.56069	0.071
27DAP/reference	0.61458	0.031
39DAP/reference	0.53831	0.008
41DAP/reference	0.48293	0.018
42DAP/reference	0.77973	0.049
43DAP/reference	0.87119	0.092
47DAP/reference	1.79703	0.011
52DAP/reference	1.95383	0.055
57DAP/reference	8.3035	0.005

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.24807	0.966
26DAP/20DAP	0.80422	0.512
34DAP/26DAP	1.0942	0.819
51DAP/34DAP	1.10302	0.565
52DAP/51DAP	0.96692	1
53DAP/52DAP	0.89787	0.715
55DAP/53DAP	1.08258	0.908
57DAP/55DAP	0.93286	0.765
62DAP/57DAP	1.91824	0.257
68DAP/62DAP	0.95488	0.769
68DAP/14DAP	1.39167	0.521

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.00623	0.045

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.69136	0.184
Mature Green Tomato/Ripe Tomato	0.04765
Immature Eggplant/Mature Eggplant	0.89683	0.594
Ripe Pepper/Ripe Tomato	0.31006	0.224
Mature Eggplant/Ripe Tomato	0.06836	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.22144	0.591
1-1-2/M82	0.93829	1
12-2/M82	1.114	1
12-4/M82	0.91376	1
1-3/M82	3.49416	0.248
2-1-1/M82	1.13193	0.764
2-1/M82	0.99307	1
2-6/M82	1.03245	1
3-2/M82	0.66551	0.752
4-1-1/M82	1.06918	1
4-1/M82	0.69338
4-3-2/M82	1.13012	1
4-3/M82	1.02854	1
5-3/M82	0.85983	1
6-2/M82	0.2145	0.444
6-3/M82	1.19387	1
7-1/M82	0.91611	1
7-2/M82	1.07186
9-3-2/M82	1.44535	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.62865	0.243
IL2-6/WTpooled	1.84829	0.46
IL7-5/WTpooled	8.31557
IL7-3/WTpooled	0.5829	0.294
IL12-4/WTpooled	0.78529	0.71
IL1-4/WTpooled	1.49787	0.426
WT/WTpooled	1.00788	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	0.88296	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99917	1
DC3000/delta hrp 6h	0.74479
DC3000/delta hrp 12h	1.30663
DC3000/delta hrp 24h	0.97454	0.897

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	N/A	N/A

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	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	0.98036
Var 12h NI row2-row1	1.02187	1
Var 36h I row2-row1	0.95862	1
Var 36h NI row2-row1	1.02343
Var 60h I row2-row1	1.18136	1
Var 60h NI row2-row1	0.63225	1
Time course 0hI-0hNI	1.07703	0.833
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	1.2225	0.28
Time course 60hI-60hNI	0.87621

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)	0.9886	0.789
transgenic ySAMdc/azygous control (breaker)	0.74049	0.251
transgenic ySAMdc/azygous control (red)	0.60569	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.25423	0.055

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.15519	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.83211	1
Manapal/WT (break)	3.39117	0.14
Manapal/WT (red)	0.96749	0.728