Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.7.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94412	0.64
27DAP/17DAP	1.03134	0.952
39DAP/27DAP	1.30118	0.626
41DAP/39DAP	1.01006	0.798
42DAP/41DAP	0.85364	1
43DAP/42DAP	0.93152	0.867
47DAP/43DAP	1.24634	0.542
52DAP/47DAP	0.88012	0.662
57DAP/52DAP	1.06141	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15051	0.366
17DAP/reference	0.90219	0.091
27DAP/reference	0.86438	0.223
39DAP/reference	0.90069	0.234
41DAP/reference	0.87609	0.201
42DAP/reference	1.00863	0.665
43DAP/reference	1.01639	1
47DAP/reference	1.04209	1
52DAP/reference	1.1615	0.84
57DAP/reference	1.31302	0.012

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97986	0.763
27DAP/17DAP	1.04748	0.98
39DAP/27DAP	0.93152	0.437
41DAP/39DAP	1.04097	0.79
42DAP/41DAP	1.02212	1
43DAP/42DAP	1.0103	0.788
47DAP/43DAP	0.9359	0.647
52DAP/47DAP	1.04619	0.945
57DAP/52DAP	1.1545	0.398
57DAP/7DAP	0.62523	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16902	0.205
17DAP/reference	1.28606	0.102
27DAP/reference	1.2816	0.301
39DAP/reference	1.09529	0.282
41DAP/reference	1.01083	0.949
42DAP/reference	0.90683	0.151
43DAP/reference	1.26569	0.048
47DAP/reference	1.14774	0.149
52DAP/reference	1.15986	0.055
57DAP/reference	1.12931	0.043

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94361	0.457
17DAP/reference	1.1088	0.086
27DAP/reference	1.32046	0.087
39DAP/reference	1.54176	0.016
41DAP/reference	1.4436	0.133
42DAP/reference	1.22995	0.033
43DAP/reference	0.89009	0.314
47DAP/reference	1.16989	0.058
52DAP/reference	1.05512	1
57DAP/reference	0.94274	0.063

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08697	0.356
17DAP/reference	1.01948	0.918
27DAP/reference	1.02593	0.749
39DAP/reference	3.11536	0.175
41DAP/reference	0.94396	0.417
42DAP/reference	1.39611	0.034
43DAP/reference	1.56155	0.03
47DAP/reference	0.84342	0.022
52DAP/reference	1.55991	0.072
57DAP/reference	1.74188	0.034

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.139	0.966
26DAP/20DAP	1.08437	0.744
34DAP/26DAP	1.1095	1
51DAP/34DAP	1.12099	0.949
52DAP/51DAP	1.03054	0.925
53DAP/52DAP	0.71715	0.076
55DAP/53DAP	1.09498	0.893
57DAP/55DAP	0.86583	0.49
62DAP/57DAP	1.51097	0.002
68DAP/62DAP	1.19766	0.926
68DAP/14DAP	2.05527	0.311

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.51443	0.025

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.50734	0.058
Mature Green Tomato/Ripe Tomato	1.08553	0.814
Immature Eggplant/Mature Eggplant	1.08786	0.222
Ripe Pepper/Ripe Tomato	1.16305	1
Mature Eggplant/Ripe Tomato	1.3099	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.77656	0.69
1-1-2/M82	1.11754	1
12-2/M82	0.89507	0.862
12-4/M82	0.79551	1
1-3/M82	2.11654
2-1-1/M82	0.79355	0.465
2-1/M82	0.53468
2-6/M82	0.91704	1
3-2/M82	1.14917
4-1-1/M82	1.29503	0.977
4-1/M82	0.69986
4-3-2/M82	1.52691
4-3/M82	1.30781	1
5-3/M82	1.36799	0.496
6-2/M82	1.13201	1
6-3/M82	1.07127	1
7-1/M82	1.01	1
7-2/M82	1.22546	0.291
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	0.95038	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02549	0.921
DC3000/delta hrp 6h	1.05522	1
DC3000/delta hrp 12h	0.93594	1
DC3000/delta hrp 24h	1.04591	0.516

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.88423	0.232
DC3000 delta B/DC3000 delta AB	1.15952	0.279

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

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

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00749	1
Var 0h	0.456	0.933
Var 12h I row2-row1	0.88561	0.338
Var 12h NI row2-row1	1.1193	1
Var 36h I row2-row1	1.19357	0.283
Var 36h NI row2-row1	0.87162	0.584
Var 60h I row2-row1	1.04548	1
Var 60h NI row2-row1	0.85241	0.818
Time course 0hI-0hNI	0.95394	0.711
Time course 12hI-12hNI	0.92356	0.6
Time course 36hI-36hNI	1.29952	0.007
Time course 60hI-60hNI	1.01477	1

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)	0.86459	0.267
transgenic ySAMdc/azygous control (breaker)	1.2815	0.178
transgenic ySAMdc/azygous control (red)	1.12807	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.31858	0.086

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.90572	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.73739	0.172
Manapal/WT (break)	0.97784	1
Manapal/WT (red)	1.37793	0.164