Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.10.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93833	0.671
27DAP/17DAP	0.96698	0.952
39DAP/27DAP	2.16653	0.215
41DAP/39DAP	0.76328	0.235
42DAP/41DAP	1.28249	0.587
43DAP/42DAP	1.05314	1
47DAP/43DAP	0.90164	0.663
52DAP/47DAP	1.11124	0.967
57DAP/52DAP	1.24114	0.817

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13759	0.162
17DAP/reference	0.94233	0.419
27DAP/reference	1.18813	0.205
39DAP/reference	0.9371	0.35
41DAP/reference	0.97781	0.667
42DAP/reference	1.02238	0.756
43DAP/reference	0.98855	0.82
47DAP/reference	1.0257	1
52DAP/reference	1.00138	0.668
57DAP/reference	0.95616	0.415

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00884	0.899
27DAP/17DAP	0.84167	0.121
39DAP/27DAP	0.94121	0.721
41DAP/39DAP	1.15231	0.579
42DAP/41DAP	0.98974	0.812
43DAP/42DAP	0.98745	0.902
47DAP/43DAP	0.9953	0.985
52DAP/47DAP	0.9527	0.834
57DAP/52DAP	0.90595	0.441
57DAP/7DAP	0.70393	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10593	0.491
17DAP/reference	1.24164	0.361
27DAP/reference	1.05048	0.804
39DAP/reference	1.15666	0.297
41DAP/reference	1.14602	0.416
42DAP/reference	1.20548	0.132
43DAP/reference	1.1366	0.344
47DAP/reference	0.8455	0.128
52DAP/reference	1.30905	0.031
57DAP/reference	1.06156	0.654

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12286	0.507
17DAP/reference	1.31683	0.074
27DAP/reference	1.05072	1
39DAP/reference	0.88332	0.165
41DAP/reference	0.97121	0.441
42DAP/reference	1.0076	0.723
43DAP/reference	0.93945	0.423
47DAP/reference	0.9611	0.41
52DAP/reference	0.89001	0.111
57DAP/reference	1.03305	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10552	0.493
17DAP/reference	1.03876	0.944
27DAP/reference	1.06672	0.575
39DAP/reference	1.16309	0.307
41DAP/reference	1.04248	0.637
42DAP/reference	1.46955	0.041
43DAP/reference	1.14116	0.49
47DAP/reference	0.81683	0.076
52DAP/reference	1.18599	0.575
57DAP/reference	1.14521	0.316

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.80048	0.281
26DAP/20DAP	1.04369	1
34DAP/26DAP	1.15674	1
51DAP/34DAP	1.1385	0.898
52DAP/51DAP	0.88138	1
53DAP/52DAP	0.97376	0.854
55DAP/53DAP	0.77277	0.135
57DAP/55DAP	1.60293	0.065
62DAP/57DAP	0.92826	0.681
68DAP/62DAP	1.03109	1
68DAP/14DAP	1.04901	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.25931	0.055

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.78511
Mature Green Tomato/Ripe Tomato	1.0322	0.898
Immature Eggplant/Mature Eggplant	0.70951	0.125
Ripe Pepper/Ripe Tomato	4.59406
Mature Eggplant/Ripe Tomato	6.98356	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00759
1-1-2/M82	0.93294	1
12-2/M82	0.96079	0.955
12-4/M82	1.10244
1-3/M82	0.87454
2-1-1/M82	1.6662	0.332
2-1/M82	N/A	N/A
2-6/M82	1.15232	0.594
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	0.78134
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.00067	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.03061
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.27843	0.277
IL2-6/WTpooled	0.87549	0.383
IL7-5/WTpooled	0.9607	1
IL7-3/WTpooled	1.21017	0.362
IL12-4/WTpooled	0.96868	0.71
IL1-4/WTpooled	1.11313	1
WT/WTpooled	0.94272	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	0.9576	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94781	1
DC3000/delta hrp 6h	1.25091	1
DC3000/delta hrp 12h	1.12515	1
DC3000/delta hrp 24h	1.04593	0.69

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.93161	0.955
DC3000 delta B/DC3000 delta AB	0.82678	0.055

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.92135	1
Exp 36h	0.77057	0.41
Exp 60h	0.8217	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97879	1
Var 0h	0.84418	0.933
Var 12h I row2-row1	0.80486	0.338
Var 12h NI row2-row1	1.11459	0.34
Var 36h I row2-row1	1.10427	0.489
Var 36h NI row2-row1	1.08233	1
Var 60h I row2-row1	0.95274	0.952
Var 60h NI row2-row1	0.79562	0.483
Time course 0hI-0hNI	1.04892	0.63
Time course 12hI-12hNI	0.92761	0.287
Time course 36hI-36hNI	0.90651	0.102
Time course 60hI-60hNI	0.73462	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)	1.002	1
transgenic ySAMdc/azygous control (breaker)	0.9418	0.49
transgenic ySAMdc/azygous control (red)	0.95768	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94731	0.362

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.58582	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.43839	0.088
Manapal/WT (break)	1.55123	0.183
Manapal/WT (red)	1.75023	0.142