Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.12.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.4203	0.858
27DAP/17DAP	1.3875	0.671
39DAP/27DAP	1.45686	0.667
41DAP/39DAP	0.81533	0.357
42DAP/41DAP	1.36618	0.832
43DAP/42DAP	0.95518	0.867
47DAP/43DAP	1.00978	0.768
52DAP/47DAP	0.98032	0.865
57DAP/52DAP	1.05854	0.995

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.55187	0.089
17DAP/reference	1.1811	0.546
27DAP/reference	1.3431	0.018
39DAP/reference	0.88147	0.333
41DAP/reference	0.88436	0.267
42DAP/reference	4.22063	0.001
43DAP/reference	1.02535	0.812
47DAP/reference	1.01927	1
52DAP/reference	1.07448	0.912
57DAP/reference	0.97507	0.479

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98922	0.782
27DAP/17DAP	0.91461	0.724
39DAP/27DAP	0.93985	0.639
41DAP/39DAP	1.23592	0.197
42DAP/41DAP	1.0388	0.947
43DAP/42DAP	1.00821	0.83
47DAP/43DAP	1.07129	0.822
52DAP/47DAP	1.51729	0.167
57DAP/52DAP	2.62287	0.035
57DAP/7DAP	1.97763	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04646	1
17DAP/reference	1.40812	0.009
27DAP/reference	1.28316	0.088
39DAP/reference	1.63271	0.009
41DAP/reference	1.73422	0.011
42DAP/reference	1.61132	0.007
43DAP/reference	1.5433	0.022
47DAP/reference	1.08664	1
52DAP/reference	1.52824	0.008
57DAP/reference	1.72323	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.50001	0.226
17DAP/reference	2.2533	0.007
27DAP/reference	1.48327	0.023
39DAP/reference	1.36228	0.018
41DAP/reference	4.25856	0.005
42DAP/reference	1.79618	0.011
43DAP/reference	1.76918	0.107
47DAP/reference	2.26241	0.008
52DAP/reference	1.77277	0.006
57DAP/reference	1.96215	0.012

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.232	0.053
17DAP/reference	1.09141	0.712
27DAP/reference	1.4635	0.041
39DAP/reference	1.3395	0.016
41DAP/reference	1.46449	0.02
42DAP/reference	1.36538	0.307
43DAP/reference	2.07973	0.038
47DAP/reference	1.33213	0.405
52DAP/reference	1.98896	0.098
57DAP/reference	3.30471	0.005

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.12259	0.966
26DAP/20DAP	1.08634	0.793
34DAP/26DAP	0.83408	0.394
51DAP/34DAP	0.84095	0.458
52DAP/51DAP	1.0712	0.651
53DAP/52DAP	1.13143	0.868
55DAP/53DAP	0.89522	0.544
57DAP/55DAP	1.46738	0.666
62DAP/57DAP	1.02358	1
68DAP/62DAP	0.84035	0.263
68DAP/14DAP	0.59252	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.98125	0.665

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.83884	0.287
Immature Eggplant/Mature Eggplant	0.68924	0.081
Ripe Pepper/Ripe Tomato	0.1062	0.224
Mature Eggplant/Ripe Tomato	0.34099	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.83739
12-2/M82	N/A	N/A
12-4/M82	0.82405	0.619
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	1.45664
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	0.97735	1
5-3/M82	0.48301	0.49
6-2/M82	2.31256
6-3/M82	0.98323
7-1/M82	1.43714	0.992
7-2/M82	0.69785	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.8776	1
IL2-6/WTpooled	1.21447	0.395
IL7-5/WTpooled	0.52884
IL7-3/WTpooled	1.21289	1
IL12-4/WTpooled	0.9298	1
IL1-4/WTpooled	1.15567	1
WT/WTpooled	1.13817	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	1.05826	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04897	0.921
DC3000/delta hrp 6h	1.06917	1
DC3000/delta hrp 12h	1.30781	1
DC3000/delta hrp 24h	1.49976	0.212

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.00536	1
DC3000 delta B/DC3000 delta AB	0.84824	0.183

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.023	1
Exp 36h	N/A	N/A
Exp 60h	0.68883	0.253

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97736	1
Var 0h	1.00388	1
Var 12h I row2-row1	0.8976	0.357
Var 12h NI row2-row1	0.93725	0.906
Var 36h I row2-row1	1.15371	0.305
Var 36h NI row2-row1	1.06672	1
Var 60h I row2-row1	0.93624	0.952
Var 60h NI row2-row1	0.89813	0.572
Time course 0hI-0hNI	1.00961	0.852
Time course 12hI-12hNI	0.99441	1
Time course 36hI-36hNI	1.05017	0.722
Time course 60hI-60hNI	1.17119	0.06

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)	1.94793	0.482
transgenic ySAMdc/azygous control (breaker)	0.29382	0.15
transgenic ySAMdc/azygous control (red)	1.62273	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05447	0.317

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.29836	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.74456	1
Manapal/WT (break)	0.65843	1
Manapal/WT (red)	1.0178	1