Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.6.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.24297	0.545
27DAP/17DAP	0.88106	0.764
39DAP/27DAP	1.0321	0.82
41DAP/39DAP	1.08827	0.833
42DAP/41DAP	1.07603	0.994
43DAP/42DAP	1.07022	1
47DAP/43DAP	1.15288	0.321
52DAP/47DAP	0.85923	0.605
57DAP/52DAP	1.22282	0.817

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96362	0.432
17DAP/reference	1.02101	0.717
27DAP/reference	1.0739	0.264
39DAP/reference	1.03068	0.615
41DAP/reference	1.14892	0.122
42DAP/reference	0.91133	0.107
43DAP/reference	1.08164	0.064
47DAP/reference	0.89792	0.012
52DAP/reference	0.96283	0.393
57DAP/reference	0.94677	0.248

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0375	0.87
27DAP/17DAP	0.96708	0.878
39DAP/27DAP	1.07868	0.698
41DAP/39DAP	0.92179	0.713
42DAP/41DAP	0.93539	0.552
43DAP/42DAP	1.07839	0.413
47DAP/43DAP	1.03292	0.884
52DAP/47DAP	1.05548	0.799
57DAP/52DAP	0.85445	0.324
57DAP/7DAP	1.1148	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06974	0.718
17DAP/reference	0.76467	0.072
27DAP/reference	1.05006	0.804
39DAP/reference	0.98247	0.552
41DAP/reference	0.97504	0.512
42DAP/reference	0.91748	0.16
43DAP/reference	1.21528	0.167
47DAP/reference	0.82475	0.128
52DAP/reference	1.13326	0.266
57DAP/reference	1.12361	0.198

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98297	0.756
17DAP/reference	1.06911	0.406
27DAP/reference	1.13048	0.31
39DAP/reference	0.98088	0.497
41DAP/reference	1.0287	1
42DAP/reference	1.05647	0.744
43DAP/reference	0.89942	0.269
47DAP/reference	1.06044	0.589
52DAP/reference	0.91038	0.351
57DAP/reference	1.21143	0.221

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11288	0.32
17DAP/reference	0.92446	0.186
27DAP/reference	1.06785	0.392
39DAP/reference	1.00721	0.889
41DAP/reference	1.11556	0.286
42DAP/reference	1.08124	0.356
43DAP/reference	1.08748	0.59
47DAP/reference	0.98561	0.574
52DAP/reference	0.86045	0.268
57DAP/reference	1.05704	0.436

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00196	1
26DAP/20DAP	0.81532	0.512
34DAP/26DAP	0.88931	0.898
51DAP/34DAP	1.34537	0.126
52DAP/51DAP	0.96883	1
53DAP/52DAP	1.05426	0.753
55DAP/53DAP	1.13062	0.319
57DAP/55DAP	1.12596	0.854
62DAP/57DAP	0.88729	0.002
68DAP/62DAP	0.7986	0.101
68DAP/14DAP	1.30986

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.85518	0.145

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.36761	0.048
Immature Eggplant/Mature Eggplant	1.60796	0.051
Ripe Pepper/Ripe Tomato	0.7953
Mature Eggplant/Ripe Tomato	0.3401	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.3431	0.526
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.71003	0.358
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	0.89117
2-6/M82	0.97757	1
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.91175	1
4-3/M82	N/A	N/A
5-3/M82	1.03926	1
6-2/M82	N/A	N/A
6-3/M82	1.23981	1
7-1/M82	1.23499
7-2/M82	0.87758
9-3-2/M82	0.92379

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.16204
IL2-6/WTpooled	0.83289	0.383
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.01805	1
IL12-4/WTpooled	1.10627	0.785
IL1-4/WTpooled	0.97629	1
WT/WTpooled	0.9277	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	0.94083	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03296	0.921
DC3000/delta hrp 6h	0.92679	0.95
DC3000/delta hrp 12h	0.92123	1
DC3000/delta hrp 24h	0.79583	0.08

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.63164
DC3000 delta B/DC3000 delta AB	0.66093	0.031

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07112	1
Exp 36h	1.07	1
Exp 60h	1.07489	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04701	1
Var 0h	0.9934	1
Var 12h I row2-row1	0.98143	1
Var 12h NI row2-row1	0.83803	0.494
Var 36h I row2-row1	0.99733	1
Var 36h NI row2-row1	1.02528	1
Var 60h I row2-row1	1.07879	0.448
Var 60h NI row2-row1	1.07436	0.904
Time course 0hI-0hNI	1.0287	0.852
Time course 12hI-12hNI	0.93073	0.47
Time course 36hI-36hNI	0.79771	0.102
Time course 60hI-60hNI	0.7358	0.015

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)	1.11785	0.221
transgenic ySAMdc/azygous control (breaker)	0.62943	0.137
transgenic ySAMdc/azygous control (red)	0.9861	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.07583	0.13

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.10164	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.30786	0.105
Manapal/WT (break)	1.28962	0.381
Manapal/WT (red)	1.06336	0.164