Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.1.9.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.47451	0.015
27DAP/17DAP	0.77454	0.406
39DAP/27DAP	1.24998	0.533
41DAP/39DAP	0.6726	0.115
42DAP/41DAP	0.73993	0.774
43DAP/42DAP	1.1695	0.816
47DAP/43DAP	0.68915	0.109
52DAP/47DAP	1.06121	0.926
57DAP/52DAP	0.93818	0.899

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.40982	0.052
17DAP/reference	1.03905	0.148
27DAP/reference	1.09568	0.037
39DAP/reference	0.89216	0.076
41DAP/reference	0.98219	0.542
42DAP/reference	0.95139	0.069
43DAP/reference	0.99547	0.882
47DAP/reference	0.97951	0.366
52DAP/reference	0.80338	0.096
57DAP/reference	1.02052	0.762

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.68427	0.039
27DAP/17DAP	1.21499	0.447
39DAP/27DAP	0.74049	0.046
41DAP/39DAP	0.74199	0.066
42DAP/41DAP	0.91229	0.382
43DAP/42DAP	1.49746	0.014
47DAP/43DAP	0.86279	0.219
52DAP/47DAP	1.10067	0.71
57DAP/52DAP	1.06696	0.695
57DAP/7DAP	0.77388	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.35464	0.051
17DAP/reference	0.87384	0.108
27DAP/reference	1.16192	0.06
39DAP/reference	1.1259	0.538
41DAP/reference	0.98529	0.538
42DAP/reference	1.18881	0.233
43DAP/reference	1.02162	0.764
47DAP/reference	0.80635	0.036
52DAP/reference	1.08265	0.197
57DAP/reference	1.10308	0.308

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.161	0.279
17DAP/reference	1.28315	0.027
27DAP/reference	1.09542	0.316
39DAP/reference	0.89497	0.097
41DAP/reference	0.98428	0.531
42DAP/reference	0.87202	0.098
43DAP/reference	0.94322	0.352
47DAP/reference	0.92333	0.141
52DAP/reference	0.83439	0.005
57DAP/reference	0.93912	0.014

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30423	0.644
17DAP/reference	1.10305	0.585
27DAP/reference	1.02093	1
39DAP/reference	1.01031	1
41DAP/reference	1.00747	0.826
42DAP/reference	1.03508	0.943
43DAP/reference	0.90312	0.165
47DAP/reference	0.85275	0.008
52DAP/reference	0.87993	0.376
57DAP/reference	0.85526	0.035

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91144	1
26DAP/20DAP	1.15692	0.421
34DAP/26DAP	0.82726	0.224
51DAP/34DAP	0.71618	0.061
52DAP/51DAP	1.06302	0.413
53DAP/52DAP	0.85628	0.25
55DAP/53DAP	0.78063	0.023
57DAP/55DAP	0.94274	0.731
62DAP/57DAP	1.10682	0.622
68DAP/62DAP	0.93281	0.579
68DAP/14DAP	0.71261	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.81718	0.137

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.52451	0.058
Mature Green Tomato/Ripe Tomato	1.89752	0.053
Immature Eggplant/Mature Eggplant	0.5624	0.063
Ripe Pepper/Ripe Tomato	3.15267	0.251
Mature Eggplant/Ripe Tomato	5.31423	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96287	0.503
1-1-2/M82	1.05169	1
12-2/M82	N/A	N/A
12-4/M82	0.78582	0.358
1-3/M82	1.38869	0.277
2-1-1/M82	0.79325	0.565
2-1/M82	1.12387
2-6/M82	1.29797	0.385
3-2/M82	1.10226
4-1-1/M82	1.3027
4-1/M82	1.27924	0.853
4-3-2/M82	1.29895	0.508
4-3/M82	1.13405	1
5-3/M82	1.18145	0.572
6-2/M82	1.07673	1
6-3/M82	1.12345	1
7-1/M82	0.9063	0.803
7-2/M82	1.21037	0.318
9-3-2/M82	1.09143	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.718	0.229
IL2-6/WTpooled	0.98478	1
IL7-5/WTpooled	1.30045	1
IL7-3/WTpooled	1.47089	1
IL12-4/WTpooled	1.32133	0.516
IL1-4/WTpooled	1.11896	1
WT/WTpooled	1.01255	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	0.94622	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97933	1
DC3000/delta hrp 6h	0.80511	0.95
DC3000/delta hrp 12h	1.03269	1
DC3000/delta hrp 24h	0.68802	0.08

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.34327	0.023
DC3000 delta B/DC3000 delta AB	0.4257	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95241	1
Exp 36h	0.78506	0.41
Exp 60h	0.69807	0.257

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00464	1
Var 0h	2.25426	0.936
Var 12h I row2-row1	0.77421	0.338
Var 12h NI row2-row1	0.90769	0.713
Var 36h I row2-row1	0.98338	1
Var 36h NI row2-row1	1.08437	1
Var 60h I row2-row1	1.04998	1
Var 60h NI row2-row1	1.01866	1
Time course 0hI-0hNI	1.05263	0.799
Time course 12hI-12hNI	0.97277	0.815
Time course 36hI-36hNI	0.91168	0.119
Time course 60hI-60hNI	0.1963	0.005

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)	0.86904	0.338
transgenic ySAMdc/azygous control (breaker)	1.2242	1
transgenic ySAMdc/azygous control (red)	1.19194	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.8576	0.071

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	3.66818	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.1091	0.307
Manapal/WT (break)	1.30331	0.381
Manapal/WT (red)	1.0587	0.413