Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.1.12.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92927	0.578
27DAP/17DAP	1.17497	0.844
39DAP/27DAP	0.81704	0.474
41DAP/39DAP	1.54219	0.478
42DAP/41DAP	0.93078	1
43DAP/42DAP	0.73703	0.477
47DAP/43DAP	0.81896	0.42
52DAP/47DAP	1.32236	0.436
57DAP/52DAP	0.99632	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87489	0.103
17DAP/reference	0.93825	0.169
27DAP/reference	0.94909	0.257
39DAP/reference	0.98449	0.762
41DAP/reference	0.98386	0.814
42DAP/reference	1.01222	0.931
43DAP/reference	0.96927	0.653
47DAP/reference	0.92831	0.174
52DAP/reference	0.91674	0.237
57DAP/reference	0.88611	0.065

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85547	0.194
27DAP/17DAP	1.0599	0.9
39DAP/27DAP	0.97878	0.87
41DAP/39DAP	1.06706	0.914
42DAP/41DAP	0.86664	0.196
43DAP/42DAP	1.01136	1
47DAP/43DAP	1.02999	0.956
52DAP/47DAP	1.03763	0.933
57DAP/52DAP	0.97755	0.768
57DAP/7DAP	1.05399	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85497	0.129
17DAP/reference	0.84691	0.049
27DAP/reference	0.95892	0.348
39DAP/reference	0.89034	0.064
41DAP/reference	0.85551	0.049
42DAP/reference	0.86235	0.106
43DAP/reference	0.92242	0.22
47DAP/reference	0.82542	0.128
52DAP/reference	0.86503	0.046
57DAP/reference	0.84902	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97968	0.72
17DAP/reference	1.18651	0.083
27DAP/reference	1.0149	0.765
39DAP/reference	0.98328	0.554
41DAP/reference	0.97151	0.441
42DAP/reference	0.99312	0.534
43DAP/reference	1.37918	0.479
47DAP/reference	1.02272	0.413
52DAP/reference	1.12517	0.322
57DAP/reference	1.03503	0.887

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84071	0.362
17DAP/reference	1.06177	0.728
27DAP/reference	0.83362	0.034
39DAP/reference	0.8903	0.054
41DAP/reference	0.89626	0.148
42DAP/reference	1.26252	0.3
43DAP/reference	0.918	0.206
47DAP/reference	1.18683	0.05
52DAP/reference	1.33373	0.123
57DAP/reference	0.92216	0.372

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97061	1
26DAP/20DAP	0.79725	0.244
34DAP/26DAP	1.02542	1
51DAP/34DAP	0.94059	0.667
52DAP/51DAP	1.15638	0.722
53DAP/52DAP	0.92149	0.715
55DAP/53DAP	1.15257	0.382
57DAP/55DAP	0.86852	0.577
62DAP/57DAP	1.15039	0.024
68DAP/62DAP	1.01099	0.914
68DAP/14DAP	1.03412	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.11465	0.782

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.00166	0.058
Mature Green Tomato/Ripe Tomato	0.85364	0.02
Immature Eggplant/Mature Eggplant	1.09519	0.165
Ripe Pepper/Ripe Tomato	0.61723	0.224
Mature Eggplant/Ripe Tomato	1.19409	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03051	1
1-1-2/M82	1.00233	1
12-2/M82	1.02937
12-4/M82	0.96823	1
1-3/M82	0.8773	0.441
2-1-1/M82	1.10596
2-1/M82	N/A	N/A
2-6/M82	0.98969	1
3-2/M82	0.66903
4-1-1/M82	0.97533	1
4-1/M82	1.00648
4-3-2/M82	0.67781	0.487
4-3/M82	0.7256	0.611
5-3/M82	0.93831	1
6-2/M82	0.85087	1
6-3/M82	0.96811	1
7-1/M82	0.88481
7-2/M82	0.94112	1
9-3-2/M82	0.79055

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.96148	1
IL7-5/WTpooled	1.16545
IL7-3/WTpooled	0.92875	1
IL12-4/WTpooled	1.13085	0.695
IL1-4/WTpooled	1.35401	1
WT/WTpooled	1.00229	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	0.90326	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97972	1
DC3000/delta hrp 6h	0.7901	0.915
DC3000/delta hrp 12h	1.05931	1
DC3000/delta hrp 24h	0.99063	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.29512	0.042
DC3000 delta B/DC3000 delta AB	1.15177	0.274

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.80231	0.328
Exp 36h	1.03701	1
Exp 60h	0.95649	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.07691	1
Var 0h	1.00747	1
Var 12h I row2-row1	1.0532	0.506
Var 12h NI row2-row1	0.88485	0.627
Var 36h I row2-row1	0.86477	0.805
Var 36h NI row2-row1	0.83273	0.706
Var 60h I row2-row1	1.25375	1
Var 60h NI row2-row1	1.14126	0.904
Time course 0hI-0hNI	1.07654	0.486
Time course 12hI-12hNI	0.95329	0.575
Time course 36hI-36hNI	0.9043	0.036
Time course 60hI-60hNI	1.0683	0.187

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)	0.97023	0.454
transgenic ySAMdc/azygous control (breaker)	0.53172	0.137
transgenic ySAMdc/azygous control (red)	1.03081	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02494	0.17

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.99722	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.90836	1
Manapal/WT (break)	1.00851	1
Manapal/WT (red)	0.89989	0.607