Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.19.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85166	0.456
27DAP/17DAP	1.26252	0.809
39DAP/27DAP	3.2379	0.057
41DAP/39DAP	0.9947	0.772
42DAP/41DAP	1.51961	0.066
43DAP/42DAP	0.94699	0.877
47DAP/43DAP	0.82921	0.492
52DAP/47DAP	0.90705	0.702
57DAP/52DAP	1.43524	0.735

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85405	0.094
17DAP/reference	1.02426	0.717
27DAP/reference	1.02123	0.831
39DAP/reference	1.08102	0.262
41DAP/reference	0.84789	0.085
42DAP/reference	1.24806	0.003
43DAP/reference	1.0064	1
47DAP/reference	1.33769	0.011
52DAP/reference	1.06432	0.991
57DAP/reference	1.15948	0.118

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10698	0.975
27DAP/17DAP	1.20124	0.822
39DAP/27DAP	3.21223	0.039
41DAP/39DAP	2.58929	0.008
42DAP/41DAP	0.82188	0.143
43DAP/42DAP	0.6998	0.024
47DAP/43DAP	1.80843	0.012
52DAP/47DAP	0.7977	0.226
57DAP/52DAP	1.04176	0.926
57DAP/7DAP	1.63805

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74667	0.091
17DAP/reference	0.80189	0.108
27DAP/reference	1.05012	0.804
39DAP/reference	1.08959	1
41DAP/reference	0.78663	0.146
42DAP/reference	0.93802	0.355
43DAP/reference	1.07362	1
47DAP/reference	1.3127	0.102
52DAP/reference	1.61032	0.008
57DAP/reference	1.88552	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90578	0.19
17DAP/reference	1.01679	0.873
27DAP/reference	1.09861	0.607
39DAP/reference	1.12031	0.272
41DAP/reference	1.1299	0.285
42DAP/reference	1.20343	0.034
43DAP/reference	1.17409	0.424
47DAP/reference	1.05614	0.377
52DAP/reference	1.02454	1
57DAP/reference	1.12263	0.398

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94534	0.362
17DAP/reference	1.03372	0.638
27DAP/reference	1.01366	0.805
39DAP/reference	0.90515	0.163
41DAP/reference	0.89258	0.209
42DAP/reference	0.97786	0.671
43DAP/reference	0.97083	0.568
47DAP/reference	1.32326	0.012
52DAP/reference	1.56904	0.247
57DAP/reference	1.21041	0.56

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.90456	1
26DAP/20DAP	0.6968	0.317
34DAP/26DAP	1.79697	1
51DAP/34DAP	1.45757	0.429
52DAP/51DAP	0.9083	0.151
53DAP/52DAP	0.96631	0.876
55DAP/53DAP	1.06919	0.842
57DAP/55DAP	0.94895	0.825
62DAP/57DAP	1.09259	1
68DAP/62DAP	1.26178	0.962
68DAP/14DAP	1.43351	0.025

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	4.67014	0.022

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.58305	0.141
Mature Green Tomato/Ripe Tomato	0.76623	0.377
Immature Eggplant/Mature Eggplant	1.82949	0.05
Ripe Pepper/Ripe Tomato	0.35475	0.224
Mature Eggplant/Ripe Tomato	0.09198	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.3688	0.536
1-1-2/M82	1.36432	1
12-2/M82	1.39279	1
12-4/M82	0.59866	0.257
1-3/M82	0.61548	0.378
2-1-1/M82	0.73751	0.784
2-1/M82	1.11834	1
2-6/M82	0.29406	0.501
3-2/M82	0.32664	0.402
4-1-1/M82	0.37664	0.926
4-1/M82	0.67451	0.737
4-3-2/M82	0.29901	0.412
4-3/M82	0.21209	0.466
5-3/M82	1.1741	0.572
6-2/M82	0.31256	0.473
6-3/M82	1.20082	1
7-1/M82	1.03338	1
7-2/M82	0.53899	0.527
9-3-2/M82	0.44653	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	2.48752	0.277
IL2-6/WTpooled	0.95343	1
IL7-5/WTpooled	1.12888	0.792
IL7-3/WTpooled	3.79022	1
IL12-4/WTpooled	1.5735	0.516
IL1-4/WTpooled	3.39842	0.426
WT/WTpooled	0.9423	0.764

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	1.57846	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93539	1
DC3000/delta hrp 6h	0.94044	0.95
DC3000/delta hrp 12h	1.1139	1
DC3000/delta hrp 24h	1.00688	1

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	2.32825

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.15534	1
Exp 36h	1.90624	0.489
Exp 60h	1.95325	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99553	1
Var 0h	1.02337	1
Var 12h I row2-row1	0.86419	0.705
Var 12h NI row2-row1	1.23613
Var 36h I row2-row1	1.38044	0.742
Var 36h NI row2-row1	1.13636	1
Var 60h I row2-row1	1.13888	0.543
Var 60h NI row2-row1	0.85495	0.866
Time course 0hI-0hNI	1.08601	0.852
Time course 12hI-12hNI	1.04535	0.811
Time course 36hI-36hNI	3.25109	0.005
Time course 60hI-60hNI	4.93038	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)	1.00847	0.798
transgenic ySAMdc/azygous control (breaker)	2.82147	0.248
transgenic ySAMdc/azygous control (red)	1.4085	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.23982	0.061

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.348	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.91465	1
Manapal/WT (break)	0.94443	0.333
Manapal/WT (red)	0.96263	0.503