Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.3.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86758	0.389
27DAP/17DAP	1.10868	0.859
39DAP/27DAP	1.24737	0.946
41DAP/39DAP	1.10673	0.814
42DAP/41DAP	0.86853	1
43DAP/42DAP	0.91037	0.807
47DAP/43DAP	1.14618	0.856
52DAP/47DAP	1.0843	0.948
57DAP/52DAP	1.32568	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90533	0.284
17DAP/reference	0.87128	0.022
27DAP/reference	0.90506	0.201
39DAP/reference	0.88398	0.097
41DAP/reference	0.75295	0.026
42DAP/reference	0.94863	0.176
43DAP/reference	0.82256	0.047
47DAP/reference	1.00243	0.764
52DAP/reference	0.94264	0.283
57DAP/reference	1.15227	0.04

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01308	0.899
27DAP/17DAP	0.90113	0.684
39DAP/27DAP	0.94912	0.673
41DAP/39DAP	1.21469	0.612
42DAP/41DAP	0.83218	0.151
43DAP/42DAP	1.11201	0.585
47DAP/43DAP	1.13445	0.464
52DAP/47DAP	1.08105	0.856
57DAP/52DAP	1.12566	0.699
57DAP/7DAP	1.2624	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98683	0.613
17DAP/reference	1.25146	0.042
27DAP/reference	1.16106	0.107
39DAP/reference	1.39137	0.017
41DAP/reference	1.35377	0.038
42DAP/reference	1.42589	0.009
43DAP/reference	1.66275	0.007
47DAP/reference	1.31187	0.133
52DAP/reference	1.81226	0.007
57DAP/reference	2.38222	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85517	0.157
17DAP/reference	0.87425	0.066
27DAP/reference	0.80938	0.044
39DAP/reference	0.85004	0.085
41DAP/reference	0.97891	0.472
42DAP/reference	0.93576	0.321
43DAP/reference	1.02417	1
47DAP/reference	0.98105	0.527
52DAP/reference	0.92487	0.156
57DAP/reference	0.97848	0.581

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.136	0.142
17DAP/reference	1.12036	0.602
27DAP/reference	1.35381	0.029
39DAP/reference	1.20433	0.078
41DAP/reference	1.25086	0.027
42DAP/reference	1.26008	0.106
43DAP/reference	0.95983	0.484
47DAP/reference	0.89424	0.183
52DAP/reference	1.15976	0.664
57DAP/reference	1.00144	0.858

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.113	0.966
26DAP/20DAP	1.11944	1
34DAP/26DAP	1.27671	1
51DAP/34DAP	1.26454	0.613
52DAP/51DAP	1.00025	1
53DAP/52DAP	0.8392	0.595
55DAP/53DAP	1.49537	0.185
57DAP/55DAP	0.9399	0.821
62DAP/57DAP	N/A	N/A
68DAP/62DAP	1.14155	1
68DAP/14DAP	0.69588	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.58897	0.105

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.61119	0.196
Mature Green Tomato/Ripe Tomato	1.43349
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	1.30279	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.86986
12-2/M82	N/A	N/A
12-4/M82	0.72069	0.619
1-3/M82	1.55428
2-1-1/M82	0.90436
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	0.82099
5-3/M82	1.17791	1
6-2/M82	1.31521
6-3/M82	N/A	N/A
7-1/M82	0.81824
7-2/M82	1.68955
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.75104	0.321
IL2-6/WTpooled	0.85385
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.98967	1
IL12-4/WTpooled	1.40011	0.839
IL1-4/WTpooled	0.8863	0.834
WT/WTpooled	1.14954	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	0.78721	0.216

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.23645	0.724
DC3000/delta hrp 6h	0.85705	0.95
DC3000/delta hrp 12h	0.91765	1
DC3000/delta hrp 24h	1.21429	0.397

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.12713	0.598
DC3000 delta B/DC3000 delta AB	0.91445	0.605

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.06312	1
Exp 36h	2.00165	1
Exp 60h	1.02566	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95695	1
Var 0h	1.08562	0.98
Var 12h I row2-row1	1.02883	0.795
Var 12h NI row2-row1	1.02441	1
Var 36h I row2-row1	1.08751	0.908
Var 36h NI row2-row1	1.498	1
Var 60h I row2-row1	1.39286
Var 60h NI row2-row1	1.04229	1
Time course 0hI-0hNI	0.86757	0.16
Time course 12hI-12hNI	0.94606	0.501
Time course 36hI-36hNI	1.09216	0.114
Time course 60hI-60hNI	0.96495	0.646

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)	1.11581	0.654
transgenic ySAMdc/azygous control (breaker)	1.05549	1
transgenic ySAMdc/azygous control (red)	1.09399	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04035	0.261

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.73606	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.14903	1
Manapal/WT (red)	1.42905	0.222