Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.7.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90457	0.522
27DAP/17DAP	0.84076	0.572
39DAP/27DAP	1.08353	0.876
41DAP/39DAP	0.77537	0.365
42DAP/41DAP	1.00352	1
43DAP/42DAP	1.12167	0.993
47DAP/43DAP	2.22047	0.156
52DAP/47DAP	1.74989	0.178
57DAP/52DAP	0.86022	0.759

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90328	0.246
17DAP/reference	0.69278	0.007
27DAP/reference	0.87008	0.114
39DAP/reference	0.73296	0.036
41DAP/reference	0.70529	0.065
42DAP/reference	0.89277	0.091
43DAP/reference	0.86715	0.191
47DAP/reference	0.96987	0.392
52DAP/reference	1.1492	0.498
57DAP/reference	1.05325	0.18

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15713	0.464
27DAP/17DAP	0.81675	0.124
39DAP/27DAP	0.76451	0.087
41DAP/39DAP	0.99062	1
42DAP/41DAP	1.20893	0.065
43DAP/42DAP	0.79608	0.063
47DAP/43DAP	0.95296	0.764
52DAP/47DAP	2.43531	0.045
57DAP/52DAP	2.39796	0.035
57DAP/7DAP	1.92927	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91965	0.183
17DAP/reference	0.9748	0.518
27DAP/reference	0.81487	0.248
39DAP/reference	0.91831	0.307
41DAP/reference	0.90765	0.174
42DAP/reference	0.80486	0.275
43DAP/reference	0.90466	0.126
47DAP/reference	0.79944	0.128
52DAP/reference	0.91001	0.232
57DAP/reference	0.94929	0.291

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76242	0.009
17DAP/reference	0.77969	0.021
27DAP/reference	0.93389	0.407
39DAP/reference	1.17428	0.489
41DAP/reference	0.98431	0.481
42DAP/reference	0.9819	0.534
43DAP/reference	0.6611	0.009
47DAP/reference	0.72103	0.014
52DAP/reference	0.92543	0.22
57DAP/reference	0.67751	0.01

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02127	0.903
17DAP/reference	1.01949	0.934
27DAP/reference	1.15326	0.373
39DAP/reference	1.05169	0.885
41DAP/reference	1.19398	0.257
42DAP/reference	1.14923	0.416
43DAP/reference	1.25289	0.154
47DAP/reference	0.87401	0.174
52DAP/reference	0.87963	0.268
57DAP/reference	1.55141	0.026

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1143	1
26DAP/20DAP	1.07227	1
34DAP/26DAP	2.53021	0.819
51DAP/34DAP	0.88249	0.698
52DAP/51DAP	4.17613	0.033
53DAP/52DAP	0.74514	0.049
55DAP/53DAP	1.8024	0.039
57DAP/55DAP	0.3951	0.043
62DAP/57DAP	3.17671
68DAP/62DAP	3.43271
68DAP/14DAP	2.41903	0.02

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.26002	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.13992	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.96655
Mature Eggplant/Ripe Tomato	0.63759	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.09187
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.97766	1
1-3/M82	1.7561
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.77434
3-2/M82	N/A	N/A
4-1-1/M82	1.12849
4-1/M82	0.75716
4-3-2/M82	N/A	N/A
4-3/M82	1.10462	1
5-3/M82	1.15657	1
6-2/M82	N/A	N/A
6-3/M82	0.94334
7-1/M82	1.04428
7-2/M82	0.91508
9-3-2/M82	1.9397	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.31331	0.277
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.31683	0.792
IL7-3/WTpooled	2.02517	1
IL12-4/WTpooled	1.09042
IL1-4/WTpooled	1.18721	0.421
WT/WTpooled	0.90382	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	1.3088	1

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	0.93894	0.95
DC3000/delta hrp 12h	1.23842	1
DC3000/delta hrp 24h	0.86743	0.241

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.80373	0.023
DC3000 delta B/DC3000 delta AB	0.95991	0.729

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.10326	1
Exp 36h	0.87297	0.749
Exp 60h	0.87826	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9907	1
Var 0h	0.90052	1
Var 12h I row2-row1	0.76008	0.39
Var 12h NI row2-row1	0.95763	0.906
Var 36h I row2-row1	1.09308	1
Var 36h NI row2-row1	1.14493	1
Var 60h I row2-row1	0.97346	0.952
Var 60h NI row2-row1	0.99974	1
Time course 0hI-0hNI	0.95548	0.751
Time course 12hI-12hNI	0.97637	0.86
Time course 36hI-36hNI	0.97434	0.533
Time course 60hI-60hNI	0.38428	0.006

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)	0.97415	0.267
transgenic ySAMdc/azygous control (breaker)	1.21028	0.172
transgenic ySAMdc/azygous control (red)	0.90308	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9019	0.27

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.55638	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.28475	0.14
Manapal/WT (break)	1.03513	1
Manapal/WT (red)	1.30402	0.126