Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.1.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81193	0.278
27DAP/17DAP	1.28274	0.686
39DAP/27DAP	2.31336	0.047
41DAP/39DAP	1.00857	1
42DAP/41DAP	0.92999	1
43DAP/42DAP	0.92891	0.874
47DAP/43DAP	0.90586	0.68
52DAP/47DAP	1.22181	0.707
57DAP/52DAP	0.79574	0.509

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26665	0.11
17DAP/reference	0.78217	0.012
27DAP/reference	0.97958	0.668
39DAP/reference	0.83678	0.1
41DAP/reference	0.79675	0.085
42DAP/reference	1.43029	0.001
43DAP/reference	1.02241	0.982
47DAP/reference	0.92332	0.055
52DAP/reference	0.96378	0.449
57DAP/reference	1.16458	0.159

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83461	0.057
27DAP/17DAP	1.07839	0.951
39DAP/27DAP	1.05132	0.548
41DAP/39DAP	1.0646	0.861
42DAP/41DAP	1.02352	1
43DAP/42DAP	1.32808	0.016
47DAP/43DAP	0.99134	0.961
52DAP/47DAP	0.98444	0.925
57DAP/52DAP	1.21023	0.357
57DAP/7DAP	0.72443	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.49783	0.035
17DAP/reference	1.28425	0.03
27DAP/reference	1.2297	0.049
39DAP/reference	1.07473	0.74
41DAP/reference	1.68247	0.014
42DAP/reference	1.76991	0.007
43DAP/reference	2.86267	0.006
47DAP/reference	1.84804	0.028
52DAP/reference	2.64753	0.007
57DAP/reference	2.03272	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96185	0.607
17DAP/reference	1.45566	0.027
27DAP/reference	1.55426	0.026
39DAP/reference	1.37276	0.016
41DAP/reference	1.44715	0.014
42DAP/reference	1.21988	0.015
43DAP/reference	1.32999	0.104
47DAP/reference	1.36466	0.023
52DAP/reference	1.04952	0.747
57DAP/reference	1.67961	0.017

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.25933	0.028
17DAP/reference	0.90232	0.358
27DAP/reference	1.50053	0.023
39DAP/reference	1.25898	0.017
41DAP/reference	1.19485	0.06
42DAP/reference	1.35404	0.052
43DAP/reference	1.48372	0.012
47DAP/reference	1.30718	0.147
52DAP/reference	1.29372	0.15
57DAP/reference	1.24033	0.171

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.34166	1
26DAP/20DAP	1.92488	0.176
34DAP/26DAP	0.75886	0.093
51DAP/34DAP	1.26138	0.073
52DAP/51DAP	0.9064	1
53DAP/52DAP	0.63982	0.049
55DAP/53DAP	0.81581	0.021
57DAP/55DAP	0.9128	0.601
62DAP/57DAP	1.27093	0.034
68DAP/62DAP	1.88132	0.206
68DAP/14DAP	1.69361	0.074

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.16134	0.043

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.40046	0.017
Immature Eggplant/Mature Eggplant	0.75171	0.134
Ripe Pepper/Ripe Tomato	0.11418	0.224
Mature Eggplant/Ripe Tomato	0.68981	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.86767	0.907
1-1-2/M82	1.15164	1
12-2/M82	1.4149	0.375
12-4/M82	1.13435	1
1-3/M82	1.42548	0.479
2-1-1/M82	1.43444	0.375
2-1/M82	1.59989	1
2-6/M82	2.11044	0.405
3-2/M82	0.9093	0.752
4-1-1/M82	1.24406	0.657
4-1/M82	0.75074
4-3-2/M82	1.16281
4-3/M82	1.17004	1
5-3/M82	0.53433	0.447
6-2/M82	2.10314	1
6-3/M82	0.95175	1
7-1/M82	0.64433	0.803
7-2/M82	1.6634	0.302
9-3-2/M82	1.57039

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.92568	1
IL2-6/WTpooled	1.19011	0.659
IL7-5/WTpooled	0.82473	1
IL7-3/WTpooled	0.9593	1
IL12-4/WTpooled	1.05817	0.891
IL1-4/WTpooled	1.09125	1
WT/WTpooled	1.03184	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	1.09658	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03759	0.921
DC3000/delta hrp 6h	0.97859	0.95
DC3000/delta hrp 12h	0.87751	1
DC3000/delta hrp 24h	0.95486	0.7

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.11529
DC3000 delta B/DC3000 delta AB	1.17648	0.208

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.40996	0.254
Exp 36h	1.15305	0.693
Exp 60h	1.61489	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01731	1
Var 0h	0.81089	0.933
Var 12h I row2-row1	0.85088	0.338
Var 12h NI row2-row1	1.08058	1
Var 36h I row2-row1	1.21249	0.298
Var 36h NI row2-row1	1.17135	0.482
Var 60h I row2-row1	0.8053	0.292
Var 60h NI row2-row1	0.98484	1
Time course 0hI-0hNI	1.04077	0.852
Time course 12hI-12hNI	0.95471	0.738
Time course 36hI-36hNI	1.11221	0.355
Time course 60hI-60hNI	0.6372	0.007

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)	0.90282	0.614
transgenic ySAMdc/azygous control (breaker)	0.85194	0.15
transgenic ySAMdc/azygous control (red)	1.01688	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.16527	0.042

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.71458	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.95779	1
Manapal/WT (break)	0.79045	0.333
Manapal/WT (red)	1.26201	0.164