Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.19.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	16.4311	0.008
27DAP/17DAP	1.20068	0.845
39DAP/27DAP	1.47481	0.105
41DAP/39DAP	0.52173	0.041
42DAP/41DAP	0.73463	0.774
43DAP/42DAP	0.82896	0.799
47DAP/43DAP	0.47344	0.049
52DAP/47DAP	0.60493	0.139
57DAP/52DAP	1.32134	0.963

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91702	0.269
17DAP/reference	3.71807	0.01
27DAP/reference	7.83042	0.007
39DAP/reference	5.4677	0.064
41DAP/reference	6.38423	0.012
42DAP/reference	3.37074	0.001
43DAP/reference	0.9707	0.631
47DAP/reference	1.18487	0.039
52DAP/reference	0.96744	0.416
57DAP/reference	0.9796	0.526

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	3.00371	0.036
27DAP/17DAP	1.824	0.045
39DAP/27DAP	0.80718	0.239
41DAP/39DAP	1.32004	1
42DAP/41DAP	1.01572	0.801
43DAP/42DAP	0.54615	0.022
47DAP/43DAP	0.73084	0.082
52DAP/47DAP	1.32806	0.226
57DAP/52DAP	0.48593	0.047
57DAP/7DAP	1.40976	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.73895	0.589
17DAP/reference	3.12396	0.006
27DAP/reference	4.07627	0.006
39DAP/reference	2.76375	0.008
41DAP/reference	5.34545	0.007
42DAP/reference	2.51372	0.037
43DAP/reference	1.07585	0.974
47DAP/reference	1.25789	0.155
52DAP/reference	1.53396	0.015
57DAP/reference	1.41939	0.094

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.33366	0.007
17DAP/reference	4.58462	0.007
27DAP/reference	9.43088	0.012
39DAP/reference	7.26137	0.011
41DAP/reference	8.83942	0.005
42DAP/reference	8.3758	0.007
43DAP/reference	2.7501	0.045
47DAP/reference	2.97417	0.008
52DAP/reference	6.03345	0.005
57DAP/reference	1.54883	0.221

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.56389	0.065
17DAP/reference	1.70712	0.118
27DAP/reference	2.83806	0.012
39DAP/reference	3.08243	0.004
41DAP/reference	1.21664	0.425
42DAP/reference	1.06165	0.552
43DAP/reference	0.73456	0.12
47DAP/reference	0.47282	0.005
52DAP/reference	0.251	0.047
57DAP/reference	1.25865	0.758

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.49303
26DAP/20DAP	1.161	1
34DAP/26DAP	1.40857	1
51DAP/34DAP	0.89739	0.579
52DAP/51DAP	0.64154	0.151
53DAP/52DAP	0.90852	0.64
55DAP/53DAP	0.77823	0.181
57DAP/55DAP	0.90211	0.577
62DAP/57DAP	1.12233	0.868
68DAP/62DAP	1.14952	1
68DAP/14DAP	1.43994	0.558

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	11.4622	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.68633	0.187
Mature Green Tomato/Ripe Tomato	5.09593	0.02
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.08247	1
Mature Eggplant/Ripe Tomato	0.06303	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.87833
1-1-2/M82	1.55993	1
12-2/M82	0.16221
12-4/M82	2.74073
1-3/M82	1.25275
2-1-1/M82	0.73904
2-1/M82	N/A	N/A
2-6/M82	1.24991	1
3-2/M82	3.04093
4-1-1/M82	1.70458
4-1/M82	11.1124
4-3-2/M82	1.55025
4-3/M82	3.24598
5-3/M82	1.61621	0.572
6-2/M82	0.64769	1
6-3/M82	1.81195	1
7-1/M82	N/A	N/A
7-2/M82	2.00901	0.385
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.62052
IL2-6/WTpooled	1.06834	0.659
IL7-5/WTpooled	0.5704
IL7-3/WTpooled	0.93937	1
IL12-4/WTpooled	1.10672	0.525
IL1-4/WTpooled	1.06583	1
WT/WTpooled	0.98817	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	1.80405	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95835	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.05056	1
DC3000/delta hrp 24h	1.11666	0.336

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.60999	0.027
DC3000 delta B/DC3000 delta AB	0.58432	0.02

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	0.99795	1
Var 0h	1.20312	0.98
Var 12h I row2-row1	0.78349	0.363
Var 12h NI row2-row1	1.11602	1
Var 36h I row2-row1	1.07593	1
Var 36h NI row2-row1	0.79322	0.61
Var 60h I row2-row1	1.35245	1
Var 60h NI row2-row1	0.89633	0.932
Time course 0hI-0hNI	1.05151	0.852
Time course 12hI-12hNI	0.92594	0.568
Time course 36hI-36hNI	1.4453	0.005
Time course 60hI-60hNI	0.65619	0.026

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)	0.90849	0.454
transgenic ySAMdc/azygous control (breaker)	0.7971	0.251
transgenic ySAMdc/azygous control (red)	0.69555	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93571	0.237

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.0628	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.93317	1
Manapal/WT (break)	0.4083	0.299
Manapal/WT (red)	2.39328	0.15