Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.16.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99113	0.823
27DAP/17DAP	1.36827	0.732
39DAP/27DAP	0.94069	0.652
41DAP/39DAP	1.06136	0.753
42DAP/41DAP	1.14886	0.949
43DAP/42DAP	1.11887	1
47DAP/43DAP	1.15408	0.727
52DAP/47DAP	1.00032	0.991
57DAP/52DAP	1.0087	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0777	0.101
17DAP/reference	1.0281	0.508
27DAP/reference	1.07152	0.271
39DAP/reference	1.02822	0.423
41DAP/reference	1.02813	0.808
42DAP/reference	1.08332	0.004
43DAP/reference	0.96445	0.302
47DAP/reference	1.07462	0.125
52DAP/reference	1.15042	0.195
57DAP/reference	1.06054	0.682

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97494	0.697
27DAP/17DAP	1.02347	0.969
39DAP/27DAP	1.15783	0.249
41DAP/39DAP	1.07535	0.868
42DAP/41DAP	0.96723	0.715
43DAP/42DAP	1.09128	0.382
47DAP/43DAP	1.11614	0.708
52DAP/47DAP	1.00776	0.991
57DAP/52DAP	0.95729	0.366
57DAP/7DAP	1.11063	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96138	0.402
17DAP/reference	1.01651	1
27DAP/reference	0.9119	0.215
39DAP/reference	0.91127	0.025
41DAP/reference	0.96508	0.412
42DAP/reference	0.8588	0.111
43DAP/reference	0.9626	0.403
47DAP/reference	0.95362	0.383
52DAP/reference	0.92477	0.137
57DAP/reference	0.99617	0.648

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05969	0.589
17DAP/reference	1.05689	0.229
27DAP/reference	1.03844	0.86
39DAP/reference	1.21252	0.026
41DAP/reference	1.01646	1
42DAP/reference	1.03452	0.583
43DAP/reference	1.02579	0.91
47DAP/reference	0.9953	0.678
52DAP/reference	1.13437	0.011
57DAP/reference	1.15949	0.101

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94965	0.391
17DAP/reference	1.00101	0.9
27DAP/reference	0.94816	0.23
39DAP/reference	0.93767	0.222
41DAP/reference	1.082	0.174
42DAP/reference	0.98866	0.816
43DAP/reference	1.15656	0.254
47DAP/reference	0.92111	0.168
52DAP/reference	0.97423	0.675
57DAP/reference	1.0681	0.878

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91221	0.981
26DAP/20DAP	2.14155	0.107
34DAP/26DAP	1.34546	0.542
51DAP/34DAP	0.97005	0.779
52DAP/51DAP	0.97701	1
53DAP/52DAP	1.00497	1
55DAP/53DAP	0.97742	0.82
57DAP/55DAP	0.8818	0.41
62DAP/57DAP	1.14045	0.767
68DAP/62DAP	0.95429	0.769
68DAP/14DAP	0.83377	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.41128	0.027

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.15022	0.287
Mature Green Tomato/Ripe Tomato	0.62153	0.02
Immature Eggplant/Mature Eggplant	4.64333	0.05
Ripe Pepper/Ripe Tomato	0.56838	0.293
Mature Eggplant/Ripe Tomato	0.23753	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98588	0.944
1-1-2/M82	0.82877	0.958
12-2/M82	1.02061	1
12-4/M82	0.96414	1
1-3/M82	0.91859	1
2-1-1/M82	1.10597	0.689
2-1/M82	N/A	N/A
2-6/M82	1.26469
3-2/M82	1.06499
4-1-1/M82	1.13637
4-1/M82	0.89938	1
4-3-2/M82	0.91415	1
4-3/M82	0.96048
5-3/M82	1.00284	1
6-2/M82	N/A	N/A
6-3/M82	1.07541
7-1/M82	1.14307
7-2/M82	0.98686	1
9-3-2/M82	1.0127	1

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	1.3883	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98132	1
DC3000/delta hrp 6h	1.05349	1
DC3000/delta hrp 12h	1.11388	1
DC3000/delta hrp 24h	1.07136	0.582

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.15912	0.16
DC3000 delta B/DC3000 delta AB	1.21818	0.24

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0936	1
Exp 36h	1.11899	0.693
Exp 60h	1.27039	0.221

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9862	1
Var 0h	1.04715	0.98
Var 12h I row2-row1	0.72861	0.514
Var 12h NI row2-row1	1.34418	0.649
Var 36h I row2-row1	0.97064	1
Var 36h NI row2-row1	0.71028	0.549
Var 60h I row2-row1	0.67335	0.285
Var 60h NI row2-row1	0.71755	0.359
Time course 0hI-0hNI	1.00638	1
Time course 12hI-12hNI	1.12251	0.204
Time course 36hI-36hNI	2.45319	0.004
Time course 60hI-60hNI	16.3474	0.008

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)	1.12957	0.213
transgenic ySAMdc/azygous control (breaker)	0.96258	1
transgenic ySAMdc/azygous control (red)	0.94416	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99451	0.737

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.01398	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.35257	0.083
Manapal/WT (break)	1.04661	1
Manapal/WT (red)	0.87446	0.274