Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.15.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95225	0.671
27DAP/17DAP	1.0188	0.93
39DAP/27DAP	1.20689	0.47
41DAP/39DAP	1.23025	0.488
42DAP/41DAP	1.49686	0.527
43DAP/42DAP	1.15944	0.892
47DAP/43DAP	1.25386	0.326
52DAP/47DAP	0.88938	0.678
57DAP/52DAP	0.64775	0.591

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79365	0.025
17DAP/reference	0.97772	0.664
27DAP/reference	0.96929	0.525
39DAP/reference	1.06944	0.534
41DAP/reference	0.99913	1
42DAP/reference	1.00561	1
43DAP/reference	0.95865	0.394
47DAP/reference	0.99081	0.568
52DAP/reference	1.03017	0.878
57DAP/reference	0.94361	0.34

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87563	0.509
27DAP/17DAP	0.99899	0.919
39DAP/27DAP	0.78175	0.222
41DAP/39DAP	1.28566	0.355
42DAP/41DAP	0.94062	0.659
43DAP/42DAP	1.15816	0.699
47DAP/43DAP	0.86082	0.112
52DAP/47DAP	0.97539	0.905
57DAP/52DAP	1.30021	0.236
57DAP/7DAP	1.67875	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79291	0.063
17DAP/reference	0.83255	0.011
27DAP/reference	0.80683	0.01
39DAP/reference	0.78228	0.013
41DAP/reference	0.84345	0.015
42DAP/reference	1.13367	1
43DAP/reference	0.76725	0.011
47DAP/reference	0.87363	0.222
52DAP/reference	0.68236	0.011
57DAP/reference	0.8376	0.054

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92212	0.277
17DAP/reference	0.86319	0.072
27DAP/reference	0.774	0.012
39DAP/reference	0.86415	0.14
41DAP/reference	0.84633	0.076
42DAP/reference	0.9394	0.355
43DAP/reference	0.97376	0.607
47DAP/reference	0.96196	0.319
52DAP/reference	0.91888	0.203
57DAP/reference	0.71013	0.013

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79271	0.034
17DAP/reference	0.86824	0.066
27DAP/reference	0.83166	0.053
39DAP/reference	0.84379	0.111
41DAP/reference	0.86386	0.043
42DAP/reference	0.84576	0.025
43DAP/reference	0.91131	0.068
47DAP/reference	1.27237	0.009
52DAP/reference	0.90189	0.31
57DAP/reference	0.99505	0.718

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.19422	0.966
26DAP/20DAP	1.85221	0.145
34DAP/26DAP	1.02651	1
51DAP/34DAP	1.26454	0.785
52DAP/51DAP	1.14103	0.783
53DAP/52DAP	0.99976	1
55DAP/53DAP	1.23865	0.764
57DAP/55DAP	0.68338	0.151
62DAP/57DAP	1.29116	1
68DAP/62DAP	0.86137	0.722
68DAP/14DAP	2.25937	0.311

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.93474	0.443

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.75181	0.234
Mature Green Tomato/Ripe Tomato	0.9758	0.715
Immature Eggplant/Mature Eggplant	0.52724	0.064
Ripe Pepper/Ripe Tomato	2.87004	1
Mature Eggplant/Ripe Tomato	2.04387	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.06665	0.972
12-2/M82	N/A	N/A
12-4/M82	1.11355	1
1-3/M82	2.28463
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.18385
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.85792	0.418
4-3-2/M82	1.34644	0.508
4-3/M82	0.72715
5-3/M82	0.97441	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.8174
7-2/M82	N/A	N/A
9-3-2/M82	1.47831	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.03643
IL2-6/WTpooled	0.90391
IL7-5/WTpooled	1.20492
IL7-3/WTpooled	0.81985
IL12-4/WTpooled	0.99171	1
IL1-4/WTpooled	1.29407	1
WT/WTpooled	1.11824	0.855

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	2.55903
DC3000/delta hrp 6h	1.08067	1
DC3000/delta hrp 12h	0.98758	1
DC3000/delta hrp 24h	1.18531	0.143

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	2.50553

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.13425	1
Exp 36h	0.74885	0.539
Exp 60h	0.86356	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	0.94021
Var 0h	1.38898	0.311
Var 12h I row2-row1	1.03016	0.379
Var 12h NI row2-row1	0.87473	0.82
Var 36h I row2-row1	0.87829
Var 36h NI row2-row1	0.88537
Var 60h I row2-row1	1.06969	1
Var 60h NI row2-row1	1.05451	1
Time course 0hI-0hNI	0.80535	0.497
Time course 12hI-12hNI	0.70312	0.628
Time course 36hI-36hNI	1.75464	0.799
Time course 60hI-60hNI	0.72242	0.319

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)	0.94666	0.324
transgenic ySAMdc/azygous control (breaker)	1.15837	0.248
transgenic ySAMdc/azygous control (red)	1.08325	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00142	1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.42444	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.29322	0.14
Manapal/WT (break)	1.03847	1
Manapal/WT (red)	1.10268	0.413