Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.12.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02199	0.83
27DAP/17DAP	1.46127	0.677
39DAP/27DAP	1.6115	0.425
41DAP/39DAP	0.86002	0.482
42DAP/41DAP	1.1845	0.73
43DAP/42DAP	1.00307	0.937
47DAP/43DAP	1.19633	0.563
52DAP/47DAP	0.94347	0.783
57DAP/52DAP	1.12446	0.941

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93268	0.326
17DAP/reference	0.73717	0.018
27DAP/reference	0.72919	0.013
39DAP/reference	0.89539	0.267
41DAP/reference	0.84433	0.201
42DAP/reference	1.26528	0.003
43DAP/reference	1.38452	0.028
47DAP/reference	1.6958	0.001
52DAP/reference	1.58884	0.014
57DAP/reference	1.3451	0.014

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97603	0.716
27DAP/17DAP	1.07126	0.73
39DAP/27DAP	1.05122	0.663
41DAP/39DAP	1.03106	0.895
42DAP/41DAP	0.97951	0.774
43DAP/42DAP	1.21518	0.079
47DAP/43DAP	1.06468	0.61
52DAP/47DAP	1.01246	1
57DAP/52DAP	1.12233	0.489
57DAP/7DAP	1.18578	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01858	1
17DAP/reference	0.92527	0.064
27DAP/reference	0.97843	0.375
39DAP/reference	0.96539	0.083
41DAP/reference	0.94007	0.054
42DAP/reference	0.87608	0.02
43DAP/reference	0.928	0.145
47DAP/reference	1.29198	0.112
52DAP/reference	0.89112	0.057
57DAP/reference	0.85288	0.074

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91859	0.306
17DAP/reference	0.54513	0.006
27DAP/reference	0.87689	0.16
39DAP/reference	0.92724	0.168
41DAP/reference	1.04162	0.531
42DAP/reference	0.86252	0.098
43DAP/reference	0.79059	0.084
47DAP/reference	1.18407	0.169
52DAP/reference	0.75201	0.01
57DAP/reference	0.83998	0.04

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92089	0.183
17DAP/reference	0.89785	0.322
27DAP/reference	1.04584	0.552
39DAP/reference	1.04813	0.773
41DAP/reference	0.98691	0.56
42DAP/reference	0.95411	0.552
43DAP/reference	1.04425	0.84
47DAP/reference	1.70496	0.005
52DAP/reference	1.43934	0.182
57DAP/reference	1.49161	0.025

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.86572	0.981
26DAP/20DAP	1.13376	0.487
34DAP/26DAP	0.97236	0.988
51DAP/34DAP	1.07748	0.473
52DAP/51DAP	1.09899	0.439
53DAP/52DAP	1.10615	0.458
55DAP/53DAP	0.93213	0.663
57DAP/55DAP	0.94015	0.724
62DAP/57DAP	0.82584	0.466
68DAP/62DAP	1.10152	0.939
68DAP/14DAP	0.99751	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.63604	0.022

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.85766	0.356
Mature Green Tomato/Ripe Tomato	0.62508	0.051
Immature Eggplant/Mature Eggplant	1.74102	0.05
Ripe Pepper/Ripe Tomato	0.23696	0.224
Mature Eggplant/Ripe Tomato	0.17673	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.38803	0.591
1-1-2/M82	1.29668	1
12-2/M82	0.99983	1
12-4/M82	1.17291	1
1-3/M82	1.9465	0.248
2-1-1/M82	1.05675	0.764
2-1/M82	1.03473	1
2-6/M82	1.17279	0.452
3-2/M82	1.41786	0.443
4-1-1/M82	1.12212	1
4-1/M82	1.39875	1
4-3-2/M82	1.32169	0.508
4-3/M82	1.1164	1
5-3/M82	0.88428	0.364
6-2/M82	1.14527	0.235
6-3/M82	0.87358	1
7-1/M82	0.94231
7-2/M82	1.20101	0.324
9-3-2/M82	1.24507	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.79059	0.321
IL2-6/WTpooled	2.63891	0.395
IL7-5/WTpooled	1.08324	1
IL7-3/WTpooled	0.61444	0.31
IL12-4/WTpooled	1.63438	0.839
IL1-4/WTpooled	1.15233	1
WT/WTpooled	1.05485	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	1.0659	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08468	0.921
DC3000/delta hrp 6h	1.01613	0.95
DC3000/delta hrp 12h	1.00894	1
DC3000/delta hrp 24h	2.50735	0.025

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.08906	0.408
DC3000 delta B/DC3000 delta AB	1.20042	0.183

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.08724	1
Exp 36h	1.38767	0.326
Exp 60h	1.82569	0.226

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00838	1
Var 0h	1.08525	0.936
Var 12h I row2-row1	0.9941	1
Var 12h NI row2-row1	1.16284	0.649
Var 36h I row2-row1	1.17746	0.41
Var 36h NI row2-row1	0.79273	0.478
Var 60h I row2-row1	0.86253	0.306
Var 60h NI row2-row1	0.85324	0.866
Time course 0hI-0hNI	1.04018	0.63
Time course 12hI-12hNI	1.15972	0.034
Time course 36hI-36hNI	1.43252	0.005
Time course 60hI-60hNI	1.59814	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)	0.95194	0.301
transgenic ySAMdc/azygous control (breaker)	0.88703	0.173
transgenic ySAMdc/azygous control (red)	1.16912	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.07026	0.301

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87701	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.9743	1
Manapal/WT (break)	0.96662	1
Manapal/WT (red)	0.76181	0.188