Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.3.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.51346	0.026
27DAP/17DAP	0.45455	0.027
39DAP/27DAP	0.9627	0.682
41DAP/39DAP	0.4422	0.041
42DAP/41DAP	1.08456	0.999
43DAP/42DAP	1.22806	0.772
47DAP/43DAP	0.71171	0.231
52DAP/47DAP	0.88738	0.675
57DAP/52DAP	1.22965	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.73984	0.006
17DAP/reference	1.01233	1
27DAP/reference	1.24218	0.031
39DAP/reference	0.37035	0.004
41DAP/reference	0.4522	0.011
42DAP/reference	1.11563	0.931
43DAP/reference	0.76117	0.013
47DAP/reference	0.96686	0.503
52DAP/reference	0.4227	0.013
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.35634	0.029
27DAP/17DAP	1.50017	0.187
39DAP/27DAP	0.66793	0.053
41DAP/39DAP	0.64264	0.108
42DAP/41DAP	1.10843	0.727
43DAP/42DAP	0.95598	0.684
47DAP/43DAP	0.97578	0.902
52DAP/47DAP	0.88212	0.575
57DAP/52DAP	1.01817	0.907
57DAP/7DAP	0.31073	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.25162	0.024
17DAP/reference	1.05575	1
27DAP/reference	0.76483	0.011
39DAP/reference	0.44447	0.011
41DAP/reference	0.39706	0.009
42DAP/reference	0.50245	0.012
43DAP/reference	0.36508	0.011
47DAP/reference	0.52981	0.066
52DAP/reference	0.37526	0.011
57DAP/reference	0.44086	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.3277	0.438
17DAP/reference	1.18715	0.311
27DAP/reference	0.9482	0.452
39DAP/reference	0.5858	0.014
41DAP/reference	0.65182	0.027
42DAP/reference	0.89048	0.261
43DAP/reference	0.46611	0.002
47DAP/reference	0.52959	0.009
52DAP/reference	0.49107	0.004
57DAP/reference	0.44995	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.56146	0.015
17DAP/reference	1.70118	0.135
27DAP/reference	1.65594	0.021
39DAP/reference	0.74437	0.05
41DAP/reference	0.61133	0.018
42DAP/reference	0.73675	0.134
43DAP/reference	0.8126	0.171
47DAP/reference	0.85831	0.145
52DAP/reference	0.60584	0.103
57DAP/reference	0.87931	0.217

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09006	0.966
26DAP/20DAP	1.94576	0.099
34DAP/26DAP	1.10928	1
51DAP/34DAP	0.74767	0.076
52DAP/51DAP	1.00795	1
53DAP/52DAP	0.78447	0.065
55DAP/53DAP	0.59329	0.022
57DAP/55DAP	0.94031	0.748
62DAP/57DAP	N/A	N/A
68DAP/62DAP	1.3708	0.081
68DAP/14DAP	0.68107	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.21116	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.23405	0.058
Mature Green Tomato/Ripe Tomato	4.08908	0.024
Immature Eggplant/Mature Eggplant	0.5763	0.069
Ripe Pepper/Ripe Tomato	19.4566	0.258
Mature Eggplant/Ripe Tomato	44.6848	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.65983
12-2/M82	N/A	N/A
12-4/M82	0.87222	0.358
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	0.98551	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.63639
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.00349	1
IL2-6/WTpooled	1.01375	1
IL7-5/WTpooled	0.92845	1
IL7-3/WTpooled	0.91771	0.31
IL12-4/WTpooled	0.84915	0.52
IL1-4/WTpooled	1.07595	1
WT/WTpooled	0.9242	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	0.75006	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91982	0.62
DC3000/delta hrp 6h	0.9406	0.95
DC3000/delta hrp 12h	1.40633	1
DC3000/delta hrp 24h	0.62059	0.136

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.54502	0.023
DC3000 delta B/DC3000 delta AB	0.57375	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07063	1
Exp 36h	0.884	0.539
Exp 60h	0.86067	0.32

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

hybridization	ratio	FDR (corrected p value)
self-self	1.07408	1
Var 0h	0.99673	1
Var 12h I row2-row1	0.86981	0.565
Var 12h NI row2-row1	0.97062	0.906
Var 36h I row2-row1	1.10021	0.489
Var 36h NI row2-row1	1.07647	1
Var 60h I row2-row1	0.88964	0.832
Var 60h NI row2-row1	0.96764	1
Time course 0hI-0hNI	1.02626	0.852
Time course 12hI-12hNI	0.96517	0.831
Time course 36hI-36hNI	0.82327	0.025
Time course 60hI-60hNI	0.2154	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)	0.64491	0.314
transgenic ySAMdc/azygous control (breaker)	1.11115	1
transgenic ySAMdc/azygous control (red)	1.11395	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.67037	0.14

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	3.30252	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.98015	0.084
Manapal/WT (break)	2.69278	0.13
Manapal/WT (red)	1.94747	0.222