Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.6.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0232	0.904
27DAP/17DAP	1.0897	0.854
39DAP/27DAP	0.73187	0.361
41DAP/39DAP	1.35531	0.149
42DAP/41DAP	0.95786	1
43DAP/42DAP	1.06903	1
47DAP/43DAP	1.09162	0.746
52DAP/47DAP	0.90424	0.711
57DAP/52DAP	1.04734	0.993

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93923	0.145
17DAP/reference	1.03186	0.457
27DAP/reference	0.95158	0.17
39DAP/reference	1.04307	0.165
41DAP/reference	0.94808	0.434
42DAP/reference	1.04973	0.311
43DAP/reference	1.03435	0.547
47DAP/reference	1.00743	1
52DAP/reference	0.92556	0.21
57DAP/reference	0.96618	0.456

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89445	0.112
27DAP/17DAP	0.98511	0.748
39DAP/27DAP	1.01547	0.832
41DAP/39DAP	1.07378	0.88
42DAP/41DAP	1.03881	0.893
43DAP/42DAP	1.0968	0.192
47DAP/43DAP	1.01726	0.939
52DAP/47DAP	1.01752	0.965
57DAP/52DAP	0.98961	0.838
57DAP/7DAP	0.94006	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1091	0.409
17DAP/reference	1.11181	0.525
27DAP/reference	1.0268	0.974
39DAP/reference	0.92552	0.307
41DAP/reference	1.03543	0.637
42DAP/reference	1.04009	0.828
43DAP/reference	0.96846	0.44
47DAP/reference	1.02091	1
52DAP/reference	1.19827	0.086
57DAP/reference	1.08821	0.158

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9971	0.951
17DAP/reference	0.96203	0.378
27DAP/reference	0.96306	0.352
39DAP/reference	0.96523	0.265
41DAP/reference	1.01814	0.91
42DAP/reference	0.98373	0.534
43DAP/reference	1.01358	0.846
47DAP/reference	0.95947	0.149
52DAP/reference	0.9965	0.713
57DAP/reference	0.95263	0.338

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00028	0.75
17DAP/reference	0.92005	0.407
27DAP/reference	0.94335	0.357
39DAP/reference	0.98386	0.693
41DAP/reference	1.07937	0.554
42DAP/reference	1.0802	0.716
43DAP/reference	1.1062	0.547
47DAP/reference	0.95379	0.357
52DAP/reference	1.04446	0.917
57DAP/reference	0.84464	0.029

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00621	1
26DAP/20DAP	0.84046	0.512
34DAP/26DAP	1.00669	1
51DAP/34DAP	1.0281	0.925
52DAP/51DAP	1.00395	0.965
53DAP/52DAP	1.01404	1
55DAP/53DAP	1.01688	0.994
57DAP/55DAP	1.13897	0.214
62DAP/57DAP	0.48571
68DAP/62DAP	1.00333	1
68DAP/14DAP	1.06308	0.826

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.95613	0.466

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.97526	0.66
Immature Eggplant/Mature Eggplant	3.50047	0.043
Ripe Pepper/Ripe Tomato	0.96135	1
Mature Eggplant/Ripe Tomato	1.31552	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0383	1
1-1-2/M82	0.91395	0.804
12-2/M82	1.16837	1
12-4/M82	0.97256	1
1-3/M82	1.01503	1
2-1-1/M82	1.02867	1
2-1/M82	1.0186
2-6/M82	1.03973	1
3-2/M82	0.85282
4-1-1/M82	0.89307	1
4-1/M82	1.07902	0.466
4-3-2/M82	0.85194	0.487
4-3/M82	1.07017	1
5-3/M82	0.96259	1
6-2/M82	1.12055	1
6-3/M82	0.94184	1
7-1/M82	1.03278	1
7-2/M82	0.96141	1
9-3-2/M82	0.9789

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.411	0.277
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.70975	0.298
IL12-4/WTpooled	0.99028	1
IL1-4/WTpooled	0.87691	0.415
WT/WTpooled	0.8676	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	1.17676	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00626	1
DC3000/delta hrp 6h	1.07449	0.95
DC3000/delta hrp 12h	0.95362	1
DC3000/delta hrp 24h	0.99091	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.9984	1
DC3000 delta B/DC3000 delta AB	0.97283	0.674

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96161	1
Exp 36h	1.3453	0.693
Exp 60h	1.23669	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00742	1
Var 0h	1.0957	1
Var 12h I row2-row1	1.12488	0.283
Var 12h NI row2-row1	1.0378	1
Var 36h I row2-row1	1.01528	1
Var 36h NI row2-row1	1.07545	1
Var 60h I row2-row1	1.02603	1
Var 60h NI row2-row1	1.02453	1
Time course 0hI-0hNI	0.96996	0.827
Time course 12hI-12hNI	0.96711	0.65
Time course 36hI-36hNI	0.91164	0.072
Time course 60hI-60hNI	0.95995	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)	0.94001	0.314
transgenic ySAMdc/azygous control (breaker)	1.16288	1
transgenic ySAMdc/azygous control (red)	1.10487	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97689	0.172

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)	0.99664	1
Manapal/WT (break)	0.8713	0.299
Manapal/WT (red)	0.82834	0.274