Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.11.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0432	0.851
27DAP/17DAP	1.02777	0.905
39DAP/27DAP	1.03281	1
41DAP/39DAP	1.02063	0.964
42DAP/41DAP	1.06775	0.912
43DAP/42DAP	0.94722	0.801
47DAP/43DAP	0.82591	0.42
52DAP/47DAP	1.12538	0.832
57DAP/52DAP	1.10272	0.963

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9389	0.194
17DAP/reference	0.95957	0.393
27DAP/reference	0.98069	0.595
39DAP/reference	0.95752	0.5
41DAP/reference	1.00201	1
42DAP/reference	1.04143	0.287
43DAP/reference	0.97556	0.675
47DAP/reference	0.98906	0.535
52DAP/reference	1.02063	0.912
57DAP/reference	1.06011	0.366

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	N/A	N/A
27DAP/17DAP	1.01124	0.98
39DAP/27DAP	0.98796	0.997
41DAP/39DAP	1.01922	0.887
42DAP/41DAP	0.97877	0.816
43DAP/42DAP	1.03135	0.382
47DAP/43DAP	1.02489	0.897
52DAP/47DAP	1.00629	0.991
57DAP/52DAP	0.94355	0.405
57DAP/7DAP	0.88869

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89433	0.203
17DAP/reference	0.88527	0.011
27DAP/reference	0.84627	0.01
39DAP/reference	0.95416	0.146
41DAP/reference	0.93781	0.082
42DAP/reference	0.87109	0.151
43DAP/reference	0.88549	0.014
47DAP/reference	0.87754	0.044
52DAP/reference	0.89245	0.021
57DAP/reference	0.89625	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02525	0.495
17DAP/reference	0.97782	0.461
27DAP/reference	0.97281	0.452
39DAP/reference	1.03193	0.556
41DAP/reference	0.9429	0.237
42DAP/reference	1.07241	0.38
43DAP/reference	1.0609	0.503
47DAP/reference	1.07508	0.098
52DAP/reference	0.99632	0.666
57DAP/reference	1.01243	0.807

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85925	0.049
17DAP/reference	0.99354	0.81
27DAP/reference	0.90852	0.038
39DAP/reference	0.93145	0.076
41DAP/reference	0.87746	0.02
42DAP/reference	0.85827	0.016
43DAP/reference	0.89128	0.059
47DAP/reference	0.94636	0.306
52DAP/reference	0.86613	0.208
57DAP/reference	0.83435	0.184

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99851	1
26DAP/20DAP	1.02635	0.988
34DAP/26DAP	1.02059	1
51DAP/34DAP	1.05048	0.719
52DAP/51DAP	1.03087	0.638
53DAP/52DAP	1.19794
55DAP/53DAP	0.89753
57DAP/55DAP	0.95754	0.855
62DAP/57DAP	0.9767	0.871
68DAP/62DAP	1.5931
68DAP/14DAP	1.07941	0.436

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.00251	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.52011	0.122
Mature Green Tomato/Ripe Tomato	1.31656	0.363
Immature Eggplant/Mature Eggplant	1.78715	0.05
Ripe Pepper/Ripe Tomato	0.7786	0.293
Mature Eggplant/Ripe Tomato	0.33661	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.90503	0.934
1-1-2/M82	0.93787	1
12-2/M82	0.89026	0.955
12-4/M82	0.99952	1
1-3/M82	1.02778	1
2-1-1/M82	0.8823	0.465
2-1/M82	1.20533	0.345
2-6/M82	0.95322	1
3-2/M82	1.0226	1
4-1-1/M82	1.21732	0.966
4-1/M82	0.87952	1
4-3-2/M82	0.86398	0.487
4-3/M82	0.91203	0.72
5-3/M82	0.94122	1
6-2/M82	0.96903	1
6-3/M82	1.04462	1
7-1/M82	0.97233	0.803
7-2/M82	0.92199	0.796
9-3-2/M82	0.92693	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.71314	0.243
IL2-6/WTpooled	1.36644	0.659
IL7-5/WTpooled	0.97657	1
IL7-3/WTpooled	0.76915	0.418
IL12-4/WTpooled	1.15977	0.557
IL1-4/WTpooled	1.02244	1
WT/WTpooled	1.00124	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	1.34578	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98827	1
DC3000/delta hrp 6h	1.20585	1
DC3000/delta hrp 12h	0.97991
DC3000/delta hrp 24h	0.99125	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.06008	0.333
DC3000 delta B/DC3000 delta AB	1.037	0.655

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	1.01022	1
Var 0h	1.22005	0.98
Var 12h I row2-row1	1.17416	0.272
Var 12h NI row2-row1	0.92543	0.466
Var 36h I row2-row1	0.96757	1
Var 36h NI row2-row1	1.0199	1
Var 60h I row2-row1	1.07124	1
Var 60h NI row2-row1	1.09669	0.904
Time course 0hI-0hNI	0.99977	1
Time course 12hI-12hNI	1.00957	0.867
Time course 36hI-36hNI	0.89882	0.117
Time course 60hI-60hNI	1.05399	0.302

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)	0.78407	0.314
transgenic ySAMdc/azygous control (breaker)	0.8754	0.49
transgenic ySAMdc/azygous control (red)	1.21989	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97876	0.181

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.63059	0.172
Manapal/WT (break)	0.70418	0.299
Manapal/WT (red)	0.49343	0.183