Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.10.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92011	0.578
27DAP/17DAP	1.14489	0.88
39DAP/27DAP	1.15975	0.804
41DAP/39DAP	0.90413	0.685
42DAP/41DAP	1.05338	0.962
43DAP/42DAP	0.95871	0.898
47DAP/43DAP	1.0138	0.979
52DAP/47DAP	1.47457	0.374
57DAP/52DAP	0.9798	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01558	0.844
17DAP/reference	1.16042	0.022
27DAP/reference	0.95303	0.497
39DAP/reference	1.06338	0.229
41DAP/reference	1.036	0.759
42DAP/reference	0.84105	0.02
43DAP/reference	0.9769	0.594
47DAP/reference	0.9467	0.258
52DAP/reference	0.79884	0.091
57DAP/reference	0.85937	0.051

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92534	0.56
27DAP/17DAP	1.23301	0.685
39DAP/27DAP	1.07387	0.728
41DAP/39DAP	1.08585	0.79
42DAP/41DAP	1.21215	0.487
43DAP/42DAP	1.29713	0.017
47DAP/43DAP	1.05667	0.805
52DAP/47DAP	1.10679	0.749
57DAP/52DAP	1.29674	0.308
57DAP/7DAP	1.31751	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19757	0.132
17DAP/reference	1.60354	0.006
27DAP/reference	1.45907	0.012
39DAP/reference	1.58493	0.008
41DAP/reference	1.28225	0.08
42DAP/reference	1.12997	0.059
43DAP/reference	2.58048	0.011
47DAP/reference	1.20814	0.717
52DAP/reference	1.6765	0.034
57DAP/reference	1.66717	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11651	0.276
17DAP/reference	1.10751	0.223
27DAP/reference	0.79161	0.067
39DAP/reference	0.85371	0.202
41DAP/reference	0.79337	0.07
42DAP/reference	0.72467	0.013
43DAP/reference	1.01679	0.814
47DAP/reference	0.98658	0.543
52DAP/reference	0.92197	0.327
57DAP/reference	1.25061	0.172

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.33956	0.046
17DAP/reference	1.25663	0.572
27DAP/reference	1.85504	0.028
39DAP/reference	1.62851	0.017
41DAP/reference	1.32531	0.074
42DAP/reference	1.20643	0.648
43DAP/reference	1.38256	0.349
47DAP/reference	0.9101	0.278
52DAP/reference	1.34089	0.252
57DAP/reference	0.62764	0.048

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98223	1
26DAP/20DAP	1.39381	0.558
34DAP/26DAP	1.40556	0.304
51DAP/34DAP	1.46486	0.073
52DAP/51DAP	0.99977	1
53DAP/52DAP	1.04299	0.99
55DAP/53DAP	1.59511	0.095
57DAP/55DAP	0.88478	0.486
62DAP/57DAP	1.25152	0.35
68DAP/62DAP	0.88837	0.668
68DAP/14DAP	0.70263	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.97662	0.077

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.56626	0.096
Immature Eggplant/Mature Eggplant	0.86795	0.448
Ripe Pepper/Ripe Tomato	0.40446	0.224
Mature Eggplant/Ripe Tomato	0.70616	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01998	0.877
1-1-2/M82	1.02863	1
12-2/M82	0.98369
12-4/M82	0.81396
1-3/M82	1.28905	0.188
2-1-1/M82	1.10316	0.457
2-1/M82	0.79209
2-6/M82	1.04644	0.594
3-2/M82	N/A	N/A
4-1-1/M82	1.0549	1
4-1/M82	0.97274
4-3-2/M82	1.26028
4-3/M82	1.3904
5-3/M82	1.05894	1
6-2/M82	1.07489	1
6-3/M82	0.97678	1
7-1/M82	1.47325	0.598
7-2/M82	1.00784	1
9-3-2/M82	1.23792

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.11131
IL2-6/WTpooled	1.25159	0.419
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.10653	1
IL12-4/WTpooled	0.77166	0.554
IL1-4/WTpooled	1.1176	0.426
WT/WTpooled	0.88371	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	1.03872	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98873	1
DC3000/delta hrp 6h	1.13662	1
DC3000/delta hrp 12h	1.16119	1
DC3000/delta hrp 24h	1.20017	0.136

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.8863

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9622	1
Exp 36h	0.87824	0.749
Exp 60h	1.22188	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.08084	1
Var 0h	1.497	1
Var 12h I row2-row1	0.96723	0.856
Var 12h NI row2-row1	1.17111	1
Var 36h I row2-row1	1.15692	0.489
Var 36h NI row2-row1	0.84689	0.413
Var 60h I row2-row1	1.00486	1
Var 60h NI row2-row1	0.89423	0.69
Time course 0hI-0hNI	0.94283	0.729
Time course 12hI-12hNI	1.07971	0.461
Time course 36hI-36hNI	1.11002	0.316
Time course 60hI-60hNI	1.46552	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)	1.26597	0.321
transgenic ySAMdc/azygous control (breaker)	0.8534	0.251
transgenic ySAMdc/azygous control (red)	1.04492	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99521	0.757

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.71114	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.93559	1
Manapal/WT (break)	0.88538	1
Manapal/WT (red)	0.96465	0.607