Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.12.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17673	0.463
27DAP/17DAP	1.4128	0.766
39DAP/27DAP	1.07944	0.919
41DAP/39DAP	1.03124	0.96
42DAP/41DAP	1.53049	0.196
43DAP/42DAP	1.07637	1
47DAP/43DAP	2.72859	0.172
52DAP/47DAP	1.80154	0.29
57DAP/52DAP	0.56525	0.431

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.35946	0.007
17DAP/reference	1.14442	0.143
27DAP/reference	1.04893	0.587
39DAP/reference	1.09272	0.557
41DAP/reference	1.16101	0.111
42DAP/reference	1.22815	0.001
43DAP/reference	0.92287	0.191
47DAP/reference	1.21508	0.002
52DAP/reference	1.11584	0.096
57DAP/reference	0.90985	0.165

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96113	0.629
27DAP/17DAP	0.99938	0.943
39DAP/27DAP	1.02222	0.758
41DAP/39DAP	0.99795	1
42DAP/41DAP	0.93161	0.538
43DAP/42DAP	1.08867	0.351
47DAP/43DAP	1.05002	0.765
52DAP/47DAP	0.99308	0.951
57DAP/52DAP	1.25177	0.167
57DAP/7DAP	1.21321	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.25456	0.106
17DAP/reference	1.06897	0.399
27DAP/reference	1.11785	0.041
39DAP/reference	1.11865	0.048
41DAP/reference	1.2355	0.02
42DAP/reference	1.12519	0.018
43DAP/reference	1.32204	0.014
47DAP/reference	1.11946	0.241
52DAP/reference	1.15385	0.058
57DAP/reference	1.08922	0.214

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19388	0.184
17DAP/reference	1.4034	0.008
27DAP/reference	1.35334	0.049
39DAP/reference	1.12032	0.366
41DAP/reference	1.0922	0.241
42DAP/reference	1.31653	0.017
43DAP/reference	0.92827	0.378
47DAP/reference	1.25362	0.009
52DAP/reference	1.08817	0.043
57DAP/reference	1.0601	0.705

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18333	0.066
17DAP/reference	1.05947	0.538
27DAP/reference	1.05319	0.357
39DAP/reference	1.00837	0.987
41DAP/reference	1.1937	0.058
42DAP/reference	1.25511	0.082
43DAP/reference	1.22661	0.121
47DAP/reference	1.02333	0.934
52DAP/reference	1.12881	0.341
57DAP/reference	1.14619	0.531

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.44943	0.786
26DAP/20DAP	1.03194	1
34DAP/26DAP	1.12728	0.542
51DAP/34DAP	1.00505	0.856
52DAP/51DAP	0.90229	1
53DAP/52DAP	0.96172	0.817
55DAP/53DAP	1.1102	0.781
57DAP/55DAP	1.00263	0.914
62DAP/57DAP	0.98872	0.994
68DAP/62DAP	0.94122	0.747
68DAP/14DAP	0.62908	0.09

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.89845	0.322

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.24473	0.113
Mature Green Tomato/Ripe Tomato	0.04093	0.017
Immature Eggplant/Mature Eggplant	0.85084	0.082
Ripe Pepper/Ripe Tomato	0.48955	0.293
Mature Eggplant/Ripe Tomato	0.42779	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
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	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.54117

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.00202	0.493
IL2-6/WTpooled	0.85788	0.383
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.03833	1
IL12-4/WTpooled	0.90547	1
IL1-4/WTpooled	1.17508
WT/WTpooled	0.93102	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	0.96059	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99606	1
DC3000/delta hrp 6h	1.16166	1
DC3000/delta hrp 12h	1.41727	1
DC3000/delta hrp 24h	0.87233	0.422

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.94949	0.436
DC3000 delta B/DC3000 delta AB	0.87798	0.183

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02022	1
Exp 36h	1.01321	1
Exp 60h	1.19135	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97798	1
Var 0h	0.96006	1
Var 12h I row2-row1	0.88577	0.565
Var 12h NI row2-row1	0.94848	0.82
Var 36h I row2-row1	1.05591	1
Var 36h NI row2-row1	1.03515	1
Var 60h I row2-row1	1.18566	1
Var 60h NI row2-row1	1.0574	0.904
Time course 0hI-0hNI	1.01352	0.852
Time course 12hI-12hNI	0.91946	0.511
Time course 36hI-36hNI	1.05435	0.975
Time course 60hI-60hNI	0.89417	0.081

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)	1.07639	0.261
transgenic ySAMdc/azygous control (breaker)	0.95929	1
transgenic ySAMdc/azygous control (red)	1.07663	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0396	0.273

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.97336	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.30395	0.093
Manapal/WT (break)	0.97289	1
Manapal/WT (red)	N/A	N/A