Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.2.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	8.11039	0.037
27DAP/17DAP	1.73346	0.73
39DAP/27DAP	2.55186	0.021
41DAP/39DAP	0.76797	0.252
42DAP/41DAP	0.82681	1
43DAP/42DAP	1.21452	0.985
47DAP/43DAP	1.15695	0.943
52DAP/47DAP	0.91883	0.586
57DAP/52DAP	1.93694	0.963

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.6116	0.042
17DAP/reference	1.43927	0.546
27DAP/reference	1.86712	0.013
39DAP/reference	1.42178	0.035
41DAP/reference	1.11144	0.759
42DAP/reference	1.1595	0.011
43DAP/reference	1.22585	0.252
47DAP/reference	1.05059	0.885
52DAP/reference	0.64127	0.013
57DAP/reference	0.7941	0.086

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.63749	0.036
27DAP/17DAP	1.02077	0.969
39DAP/27DAP	1.65829	0.114
41DAP/39DAP	0.53844	0.083
42DAP/41DAP	1.31533	0.019
43DAP/42DAP	1.61522	0.022
47DAP/43DAP	0.68264	0.01
52DAP/47DAP	0.81763	0.498
57DAP/52DAP	0.61999	0.052
57DAP/7DAP	1.36692	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27285	0.097
17DAP/reference	1.23945	0.007
27DAP/reference	1.59293	0.008
39DAP/reference	2.06225	0.006
41DAP/reference	2.36044	0.008
42DAP/reference	3.35315	0.006
43DAP/reference	4.13094	0.006
47DAP/reference	3.00504	0.015
52DAP/reference	3.1924	0.007
57DAP/reference	2.4364	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.60259	0.008
17DAP/reference	0.8153	0.08
27DAP/reference	1.93617	0.012
39DAP/reference	1.25319	0.175
41DAP/reference	1.6222	0.007
42DAP/reference	1.37737	0.061
43DAP/reference	0.62555	0.027
47DAP/reference	1.15144	0.441
52DAP/reference	0.73947	0.009
57DAP/reference	0.5487	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.54513	0.028
17DAP/reference	0.73766	0.107
27DAP/reference	1.31682	0.062
39DAP/reference	2.57147	0.006
41DAP/reference	1.2971	0.033
42DAP/reference	1.57554	0.018
43DAP/reference	1.41568	0.25
47DAP/reference	1.2358	0.372
52DAP/reference	1.1453	0.549
57DAP/reference	1.76769	0.039

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08488	1
26DAP/20DAP	0.79697	0.512
34DAP/26DAP	0.76144	0.214
51DAP/34DAP	1.12507	0.666
52DAP/51DAP	0.53348	0.151
53DAP/52DAP	2.5898	0.05
55DAP/53DAP	0.7741	0.417
57DAP/55DAP	1.14968	0.947
62DAP/57DAP	0.66018	0.05
68DAP/62DAP	1.20168	0.336
68DAP/14DAP	2.30399	0.035

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	4.77505	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.42059	0.08
Mature Green Tomato/Ripe Tomato	5.01106	0.015
Immature Eggplant/Mature Eggplant	0.40614	0.062
Ripe Pepper/Ripe Tomato	8.12858	0.235
Mature Eggplant/Ripe Tomato	0.87754	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.80802	0.883
1-1-2/M82	1.36209	1
12-2/M82	1.28585	1
12-4/M82	0.79147	1
1-3/M82	0.53919
2-1-1/M82	0.69029	0.465
2-1/M82	N/A	N/A
2-6/M82	0.96157	1
3-2/M82	N/A	N/A
4-1-1/M82	0.86329	1
4-1/M82	0.58989
4-3-2/M82	1.08614	1
4-3/M82	0.92319	1
5-3/M82	1.3929	0.455
6-2/M82	1.34322
6-3/M82	1.00392	1
7-1/M82	1.3705
7-2/M82	1.90138
9-3-2/M82	1.14309

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.33386	0.456
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.80257	0.418
IL12-4/WTpooled	1.19062	0.532
IL1-4/WTpooled	1.04217
WT/WTpooled	1.06164	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	1.06514	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98817	1
DC3000/delta hrp 6h	0.89228	0.95
DC3000/delta hrp 12h	1.50459	1
DC3000/delta hrp 24h	0.37342	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.74929	0.436
DC3000 delta B/DC3000 delta AB	1.0477	0.714

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97645	1
Exp 36h	0.82436	0.699
Exp 60h	0.71878	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99604	1
Var 0h	1.25079	0.594
Var 12h I row2-row1	0.89432	0.627
Var 12h NI row2-row1	0.96823	0.906
Var 36h I row2-row1	1.79583	1
Var 36h NI row2-row1	0.85513	0.329
Var 60h I row2-row1	1.31882	0.543
Var 60h NI row2-row1	0.9551	1
Time course 0hI-0hNI	0.85312	0.247
Time course 12hI-12hNI	0.83398	0.259
Time course 36hI-36hNI	0.93728	0.396
Time course 60hI-60hNI	0.36063	0.006

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)	0.97981	0.722
transgenic ySAMdc/azygous control (breaker)	0.62889	0.134
transgenic ySAMdc/azygous control (red)	0.90501	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95671	0.071

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.55479	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.13395	0.14
Manapal/WT (break)	0.65121	1
Manapal/WT (red)	1.15882	0.413