Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.16.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1039	0.83
27DAP/17DAP	1.67526	0.474
39DAP/27DAP	4.70309	0.025
41DAP/39DAP	1.28365	0.212
42DAP/41DAP	1.30623	0.642
43DAP/42DAP	1.37986	0.505
47DAP/43DAP	1.66837	0.156
52DAP/47DAP	0.93011	0.772
57DAP/52DAP	2.13453	0.567

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.54253	0.024
17DAP/reference	0.70964	0.008
27DAP/reference	0.72454	0.024
39DAP/reference	1.17832	0.706
41DAP/reference	0.93669	0.341
42DAP/reference	1.30249	0.025
43DAP/reference	1.10594	0.175
47DAP/reference	2.43173	0.001
52DAP/reference	1.41283	0.032
57DAP/reference	1.56696	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.70025	0.372
27DAP/17DAP	0.92237	0.821
39DAP/27DAP	2.34847	0.05
41DAP/39DAP	0.61077	0.178
42DAP/41DAP	1.0816	1
43DAP/42DAP	1.32656	0.192
47DAP/43DAP	1.35265	0.231
52DAP/47DAP	1.15564	0.97
57DAP/52DAP	1.66186	0.232
57DAP/7DAP	3.29064

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84454	0.071
17DAP/reference	0.69603	0.014
27DAP/reference	0.84968	0.055
39DAP/reference	1.03635	1
41DAP/reference	1.37099	0.02
42DAP/reference	1.24668	0.132
43DAP/reference	1.2075	0.226
47DAP/reference	1.13519	0.595
52DAP/reference	1.78845	0.007
57DAP/reference	2.52556	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.48375	0.005
17DAP/reference	0.53692	0.004
27DAP/reference	0.746	0.036
39DAP/reference	0.81216	0.025
41DAP/reference	1.02854	1
42DAP/reference	1.02098	1
43DAP/reference	0.93537	0.394
47DAP/reference	3.30246	0.008
52DAP/reference	1.29655	0.007
57DAP/reference	1.69415	0.009

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.73732	0.026
17DAP/reference	0.70875	0.106
27DAP/reference	0.90466	0.045
39DAP/reference	1.25241	0.024
41DAP/reference	1.14281	0.115
42DAP/reference	1.4056	0.076
43DAP/reference	1.32518	0.067
47DAP/reference	2.32807	0.006
52DAP/reference	2.27478	0.03
57DAP/reference	1.24574	0.187

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03072	0.966
26DAP/20DAP	1.49594	0.212
34DAP/26DAP	1.49991	0.542
51DAP/34DAP	3.1685	0.026
52DAP/51DAP	0.72284	0.151
53DAP/52DAP	1.44424	0.029
55DAP/53DAP	0.50469	0.017
57DAP/55DAP	0.86836	0.468
62DAP/57DAP	2.34081	0.004
68DAP/62DAP	1.01147	1
68DAP/14DAP	2.91566	0.053

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.86081	0.211

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.03837	0.036
Mature Green Tomato/Ripe Tomato	0.24433	0.02
Immature Eggplant/Mature Eggplant	19.4121	0.05
Ripe Pepper/Ripe Tomato	1.86015	0.258
Mature Eggplant/Ripe Tomato	0.41228	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.84023	0.535
1-1-2/M82	1.47959	1
12-2/M82	1.0635	1
12-4/M82	1.31546	1
1-3/M82	4.70149	0.248
2-1-1/M82	0.93435	1
2-1/M82	0.96727	1
2-6/M82	1.21513	0.594
3-2/M82	1.12885	0.84
4-1-1/M82	1.84025	1
4-1/M82	1.81987	1
4-3-2/M82	2.51208	0.284
4-3/M82	1.04956	1
5-3/M82	0.44688	0.49
6-2/M82	0.66727	0.481
6-3/M82	1.10968	1
7-1/M82	0.88139	0.509
7-2/M82	2.42109	0.385
9-3-2/M82	2.16399	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	1.46073	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	1.03833	1
DC3000/delta hrp 12h	1.18393	1
DC3000/delta hrp 24h	0.98135	0.642

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.49455
DC3000 delta B/DC3000 delta AB	3.09955	0.083

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.15425	1
Exp 36h	1.10745	1
Exp 60h	1.03723	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98433	1
Var 0h	0.93007	1
Var 12h I row2-row1	0.89383	0.705
Var 12h NI row2-row1	1.92645	0.649
Var 36h I row2-row1	0.94039	1
Var 36h NI row2-row1	0.81051	0.645
Var 60h I row2-row1	0.48742	0.285
Var 60h NI row2-row1	0.56962	0.304
Time course 0hI-0hNI	1.20738	0.246
Time course 12hI-12hNI	1.41148	0.467
Time course 36hI-36hNI	3.88931	0.004
Time course 60hI-60hNI	19.228	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)	0.58963	0.315
transgenic ySAMdc/azygous control (breaker)	0.90641	0.49
transgenic ySAMdc/azygous control (red)	1.14095	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.58551	0.051

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.97294	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	4.69597	0.096
Manapal/WT (break)	5.46017	0.14
Manapal/WT (red)	1.45063	0.133