Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.14.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.58477	0.045
27DAP/17DAP	1.67104	0.38
39DAP/27DAP	1.33816	0.903
41DAP/39DAP	1.19348	0.584
42DAP/41DAP	1.13677	0.941
43DAP/42DAP	0.92424	0.888
47DAP/43DAP	1.0597	0.926
52DAP/47DAP	1.50317	0.331
57DAP/52DAP	1.04142	0.988

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26039	0.009
17DAP/reference	1.26005	0.033
27DAP/reference	1.2998	0.014
39DAP/reference	1.10721	0.343
41DAP/reference	1.21157	0.085
42DAP/reference	1.361	0.006
43DAP/reference	1.16131	0.012
47DAP/reference	1.45273	0.001
52DAP/reference	1.43248	0.015
57DAP/reference	1.34134	0.035

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89308	0.428
27DAP/17DAP	0.92744	0.748
39DAP/27DAP	1.50764	0.062
41DAP/39DAP	2.44169	0.006
42DAP/41DAP	0.61366	0.021
43DAP/42DAP	1.04649	0.446
47DAP/43DAP	1.45214	0.016
52DAP/47DAP	1.0643	0.81
57DAP/52DAP	0.89229	0.428
57DAP/7DAP	1.0469	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.53355	0.033
17DAP/reference	1.68462	0.006
27DAP/reference	1.70365	0.012
39DAP/reference	1.72512	0.005
41DAP/reference	1.8784	0.01
42DAP/reference	1.72054	0.007
43DAP/reference	2.03709	0.007
47DAP/reference	1.58179	0.017
52DAP/reference	1.65503	0.007
57DAP/reference	1.81323	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9434	0.487
17DAP/reference	1.40088	0.007
27DAP/reference	1.61921	0.012
39DAP/reference	1.50899	0.011
41DAP/reference	1.37429	0.009
42DAP/reference	1.41805	0.009
43DAP/reference	1.16608	0.89
47DAP/reference	1.61406	0.008
52DAP/reference	1.385	0.008
57DAP/reference	1.23552	0.15

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.44315	0.027
17DAP/reference	1.09404	0.72
27DAP/reference	1.92149	0.015
39DAP/reference	1.78773	0.004
41DAP/reference	1.45745	0.027
42DAP/reference	1.37519	0.029
43DAP/reference	1.50041	0.012
47DAP/reference	1.21378	0.044
52DAP/reference	2.06389	0.036
57DAP/reference	1.6634	0.009

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.20523	0.786
26DAP/20DAP	0.86818	1
34DAP/26DAP	0.95738	0.98
51DAP/34DAP	1.09695	0.854
52DAP/51DAP	1.24131	0.387
53DAP/52DAP	1.04293	1
55DAP/53DAP	1.21872	0.33
57DAP/55DAP	2.22836	0.865
62DAP/57DAP	0.88423	0.162
68DAP/62DAP	1.13569	0.729
68DAP/14DAP	1.19113	0.384

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.16962	0.087

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.8807	0.377
Mature Green Tomato/Ripe Tomato	0.35937	0.148
Immature Eggplant/Mature Eggplant	0.99489	1
Ripe Pepper/Ripe Tomato	1.03539	1
Mature Eggplant/Ripe Tomato	0.15546	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.70152
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	0.65004
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	3.61266
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	0.25394
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.1708

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.70622	0.277
IL2-6/WTpooled	0.96823	1
IL7-5/WTpooled	1.93121	0.792
IL7-3/WTpooled	0.57612	0.31
IL12-4/WTpooled	0.81614	0.71
IL1-4/WTpooled	0.72344	0.562
WT/WTpooled	1.10845	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	2.71511	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11425	0.921
DC3000/delta hrp 6h	0.92911	0.95
DC3000/delta hrp 12h	0.97846	1
DC3000/delta hrp 24h	2.70425	0.192

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.70434
DC3000 delta B/DC3000 delta AB	2.02709	0.079

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.21871	1
Exp 36h	1.23127	0.693
Exp 60h	1.46557	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	1.16727	1
Var 0h	1.00138	1
Var 12h I row2-row1	0.74397	0.467
Var 12h NI row2-row1	2.47337	0.649
Var 36h I row2-row1	1.5514	0.309
Var 36h NI row2-row1	0.71297	0.478
Var 60h I row2-row1	1.32769	0.543
Var 60h NI row2-row1	0.59731	0.483
Time course 0hI-0hNI	0.93059	0.867
Time course 12hI-12hNI	0.92632	0.742
Time course 36hI-36hNI	8.44157	0.004
Time course 60hI-60hNI	6.97998	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)	1.16378	0.305
transgenic ySAMdc/azygous control (breaker)	0.46363	0.119
transgenic ySAMdc/azygous control (red)	0.86049	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.20057	0.089

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.76373	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.50492	0.172
Manapal/WT (break)	0.90737	1
Manapal/WT (red)	0.39092	0.184