Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.15.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99817	0.847
27DAP/17DAP	1.15396	0.902
39DAP/27DAP	0.85742	0.529
41DAP/39DAP	1.61686	0.264
42DAP/41DAP	0.94077	1
43DAP/42DAP	1.02747	0.937
47DAP/43DAP	1.10623	0.415
52DAP/47DAP	1.19549	0.608
57DAP/52DAP	0.91607	0.92

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95719	0.379
17DAP/reference	1.00617	0.675
27DAP/reference	1.04816	0.384
39DAP/reference	1.01431	0.734
41DAP/reference	0.99561	1
42DAP/reference	0.89707	0.027
43DAP/reference	0.94595	0.41
47DAP/reference	0.89941	0.019
52DAP/reference	0.94644	0.393
57DAP/reference	0.89527	0.074

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96275	0.613
27DAP/17DAP	1.04057	0.942
39DAP/27DAP	1.15033	0.343
41DAP/39DAP	0.90636	0.781
42DAP/41DAP	1.01553	1
43DAP/42DAP	1.02683	0.664
47DAP/43DAP	1.04178	0.892
52DAP/47DAP	1.02011	0.939
57DAP/52DAP	0.97298	0.665
57DAP/7DAP	1.11222	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82473	0.108
17DAP/reference	0.87427	0.024
27DAP/reference	0.86202	0.01
39DAP/reference	0.85539	0.011
41DAP/reference	0.86584	0.05
42DAP/reference	0.82275	0.016
43DAP/reference	0.86103	0.011
47DAP/reference	0.79748	0.044
52DAP/reference	0.74091	0.04
57DAP/reference	0.88946	0.016

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98155	0.756
17DAP/reference	0.88849	0.134
27DAP/reference	0.83857	0.108
39DAP/reference	0.82824	0.042
41DAP/reference	0.84691	0.103
42DAP/reference	0.87571	0.039
43DAP/reference	0.978	0.62
47DAP/reference	0.95393	0.24
52DAP/reference	0.87144	0.012
57DAP/reference	1.05655	0.477

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85783	0.169
17DAP/reference	0.94811	0.488
27DAP/reference	0.8959	0.119
39DAP/reference	0.88033	0.031
41DAP/reference	0.91288	0.132
42DAP/reference	0.7878	0.036
43DAP/reference	0.73364	0.056
47DAP/reference	0.92612	0.306
52DAP/reference	0.82556	0.22
57DAP/reference	0.61242	0.023

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94668	1
26DAP/20DAP	0.91448	0.512
34DAP/26DAP	0.99734	1
51DAP/34DAP	1.0072	0.988
52DAP/51DAP	1.01788	0.888
53DAP/52DAP	0.96796	0.862
55DAP/53DAP	0.96499	0.784
57DAP/55DAP	1.05273	0.828
62DAP/57DAP	1.07785	0.833
68DAP/62DAP	1.01969	1
68DAP/14DAP	0.93811	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.85061	0.186

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.72932	0.286
Mature Green Tomato/Ripe Tomato	0.98899	0.715
Immature Eggplant/Mature Eggplant	7.32418
Ripe Pepper/Ripe Tomato	1.03261	1
Mature Eggplant/Ripe Tomato	0.49588	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.16832	0.591
1-1-2/M82	1.08675	1
12-2/M82	1.161	1
12-4/M82	1.01736	1
1-3/M82	0.99933	1
2-1-1/M82	1.04268
2-1/M82	1.29589
2-6/M82	1.04583	0.594
3-2/M82	0.90757	1
4-1-1/M82	1.04384	1
4-1/M82	1.03206	1
4-3-2/M82	0.98739	1
4-3/M82	1.09403	1
5-3/M82	1.03968	1
6-2/M82	0.9977	1
6-3/M82	0.98043	1
7-1/M82	0.90724	1
7-2/M82	1.2117	0.385
9-3-2/M82	1.01084	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.92502
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.99509	1
IL12-4/WTpooled	1.00842	1
IL1-4/WTpooled	0.83702	0.422
WT/WTpooled	1.22247	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	0.80479	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03964	0.921
DC3000/delta hrp 6h	0.88618	0.95
DC3000/delta hrp 12h	0.98643	1
DC3000/delta hrp 24h	1.05088	0.604

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.99491	1
DC3000 delta B/DC3000 delta AB	1.02606	0.646

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.84401	1
Exp 36h	0.93483	0.82
Exp 60h	1.00282	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9624	1
Var 0h	1.59882	0.98
Var 12h I row2-row1	1.14171	0.145
Var 12h NI row2-row1	0.94132	0.82
Var 36h I row2-row1	0.80495	0.805
Var 36h NI row2-row1	0.9507	0.743
Var 60h I row2-row1	1.36514	0.562
Var 60h NI row2-row1	1.34013	0.904
Time course 0hI-0hNI	1.16348	0.574
Time course 12hI-12hNI	1.07585	0.684
Time course 36hI-36hNI	0.89454	0.121
Time course 60hI-60hNI	0.82175	0.161

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)	0.96974	0.722
transgenic ySAMdc/azygous control (breaker)	0.88425	0.251
transgenic ySAMdc/azygous control (red)	1.43074	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00936	0.587

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.42157	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.90841	1
Manapal/WT (break)	0.79753	1
Manapal/WT (red)	0.62646	0.188