Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.5.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.78389	0.206
27DAP/17DAP	0.49743	0.027
39DAP/27DAP	1.05615	0.876
41DAP/39DAP	0.73626	0.152
42DAP/41DAP	1.25498	0.702
43DAP/42DAP	1.29783	0.619
47DAP/43DAP	1.24774	0.569
52DAP/47DAP	0.55013	0.071
57DAP/52DAP	1.18159	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10351	0.522
17DAP/reference	1.11173	0.653
27DAP/reference	0.9755	0.683
39DAP/reference	1.04266	0.434
41DAP/reference	1.26152	0.312
42DAP/reference	1.30227	0.003
43DAP/reference	1.32823	0.133
47DAP/reference	1.58694	0.011
52DAP/reference	1.18576	0.407
57DAP/reference	1.24262	0.147

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95033	0.595
27DAP/17DAP	0.97293	0.878
39DAP/27DAP	0.87539	0.412
41DAP/39DAP	0.96991	0.934
42DAP/41DAP	1.14219	0.47
43DAP/42DAP	0.92619	0.293
47DAP/43DAP	1.11887	0.758
52DAP/47DAP	0.91073	0.528
57DAP/52DAP	1.09841	0.606
57DAP/7DAP	0.41346	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9859	0.613
17DAP/reference	0.94966	0.094
27DAP/reference	0.96406	0.303
39DAP/reference	1.10204	0.267
41DAP/reference	1.01933	0.836
42DAP/reference	1.06708	0.132
43DAP/reference	1.1917	0.034
47DAP/reference	1.23899	0.03
52DAP/reference	1.24568	0.028
57DAP/reference	1.20499	0.049

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85575	0.164
17DAP/reference	0.87521	0.326
27DAP/reference	0.88893	0.269
39DAP/reference	1.03862	0.978
41DAP/reference	1.08021	0.878
42DAP/reference	1.06439	0.519
43DAP/reference	1.03508	0.892
47DAP/reference	1.08274	0.467
52DAP/reference	0.87849	0.351
57DAP/reference	1.09829	0.221

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0847	0.072
17DAP/reference	1.81808	0.675
27DAP/reference	0.96708	0.566
39DAP/reference	0.92472	0.199
41DAP/reference	0.96149	0.371
42DAP/reference	1.19972	0.313
43DAP/reference	1.27872	0.128
47DAP/reference	1.85542	0.008
52DAP/reference	1.42025	0.186
57DAP/reference	1.23015	0.204

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	2.15813	0.496
26DAP/20DAP	1.18106	0.394
34DAP/26DAP	0.9469	0.879
51DAP/34DAP	1.03367	0.909
52DAP/51DAP	0.79765	0.151
53DAP/52DAP	0.95367	0.835
55DAP/53DAP	0.86593	0.111
57DAP/55DAP	1.70795	0.393
62DAP/57DAP	0.27911
68DAP/62DAP	1.27608	1
68DAP/14DAP	0.60478

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.56513	0.022

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.08531	0.417
Mature Green Tomato/Ripe Tomato	0.32771
Immature Eggplant/Mature Eggplant	1.95039	0.05
Ripe Pepper/Ripe Tomato	1.74128	0.256
Mature Eggplant/Ripe Tomato	1.0451	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.48767	0.742
1-1-2/M82	1.24926	1
12-2/M82	1.26327	1
12-4/M82	0.85876	0.619
1-3/M82	2.22789
2-1-1/M82	N/A	N/A
2-1/M82	0.82378
2-6/M82	1.29096
3-2/M82	1.11163	0.463
4-1-1/M82	1.11994	1
4-1/M82	0.82017	1
4-3-2/M82	0.74032
4-3/M82	1.75538	0.268
5-3/M82	0.75805	0.419
6-2/M82	1.0302
6-3/M82	1.0293	1
7-1/M82	0.58109
7-2/M82	1.96305	0.299
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.23283	0.277
IL2-6/WTpooled	1.21816	0.441
IL7-5/WTpooled	1.05209	1
IL7-3/WTpooled	1.20131	1
IL12-4/WTpooled	0.91257	0.71
IL1-4/WTpooled	1.12216	0.426
WT/WTpooled	0.96831	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	1.0895	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.12938	0.715
DC3000/delta hrp 6h	0.74774	0.808
DC3000/delta hrp 12h	1.03999	1
DC3000/delta hrp 24h	1.19927	0.107

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.52877	0.024
DC3000 delta B/DC3000 delta AB	0.56577	0.022

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.23615	0.254
Exp 36h	1.09241	1
Exp 60h	1.33222	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99557	1
Var 0h	1.10307	0.782
Var 12h I row2-row1	0.8275	0.338
Var 12h NI row2-row1	0.89642	0.494
Var 36h I row2-row1	0.99081	0.805
Var 36h NI row2-row1	1.24165	0.482
Var 60h I row2-row1	0.86749	0.285
Var 60h NI row2-row1	1.00419	1
Time course 0hI-0hNI	0.9324	0.294
Time course 12hI-12hNI	1.00697	1
Time course 36hI-36hNI	0.81133	0.023
Time course 60hI-60hNI	0.17592	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)	0.83567	0.246
transgenic ySAMdc/azygous control (breaker)	0.73159	0.173
transgenic ySAMdc/azygous control (red)	1.13713	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01656	0.587

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.76284	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.04454	0.096
Manapal/WT (break)	1.74563	0.183
Manapal/WT (red)	0.57251	0.184