Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.1.13.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.3839	0.015
27DAP/17DAP	1.24917	0.872
39DAP/27DAP	1.5198	0.223
41DAP/39DAP	0.95876	0.798
42DAP/41DAP	0.81082	1
43DAP/42DAP	0.65576	0.483
47DAP/43DAP	0.87426	0.58
52DAP/47DAP	1.70568	0.31
57DAP/52DAP	1.08798	0.992

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.34432	0.045
17DAP/reference	0.97054	0.503
27DAP/reference	0.94423	0.444
39DAP/reference	0.88357	0.058
41DAP/reference	0.91352	0.114
42DAP/reference	0.93105	0.085
43DAP/reference	0.87414	0.346
47DAP/reference	0.89405	0.027
52DAP/reference	0.91156	0.162
57DAP/reference	0.9479	0.395

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.37894	0.043
27DAP/17DAP	1.15606	0.842
39DAP/27DAP	1.77844	0.045
41DAP/39DAP	1.33959	0.042
42DAP/41DAP	1.01944	0.825
43DAP/42DAP	1.3327	0.056
47DAP/43DAP	1.05835	0.956
52DAP/47DAP	1.21419	0.494
57DAP/52DAP	1.92485	0.03
57DAP/7DAP	0.93064	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.43889	0.04
17DAP/reference	1.1985	0.026
27DAP/reference	1.01746	1
39DAP/reference	1.13982	0.166
41DAP/reference	1.06944	0.655
42DAP/reference	1.00636	1
43DAP/reference	1.1313	0.124
47DAP/reference	1.12923	0.395
52DAP/reference	1.00384	1
57DAP/reference	1.2195	0.018

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.35248	0.33
17DAP/reference	1.06734	0.708
27DAP/reference	0.90928	0.173
39DAP/reference	0.98517	0.554
41DAP/reference	0.96651	0.331
42DAP/reference	0.85434	0.098
43DAP/reference	1.13104	0.617
47DAP/reference	1.0058	0.965
52DAP/reference	0.87202	0.016
57DAP/reference	1.09585	0.409

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30571	0.75
17DAP/reference	1.04778	0.784
27DAP/reference	1.45377	0.016
39DAP/reference	1.24732	0.081
41DAP/reference	1.02029	0.961
42DAP/reference	0.94547	0.287
43DAP/reference	0.88498	0.188
47DAP/reference	0.85556	0.027
52DAP/reference	0.89506	0.433
57DAP/reference	1.11569	0.648

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06003	1
26DAP/20DAP	0.9795	1
34DAP/26DAP	0.7601	0.186
51DAP/34DAP	0.89024	0.522
52DAP/51DAP	1.56608	0.053
53DAP/52DAP	1.44503	0.179
55DAP/53DAP	0.74165	0.273
57DAP/55DAP	1.08601	0.975
62DAP/57DAP	1.10717	0.833
68DAP/62DAP	1.33215	0.707
68DAP/14DAP	0.63595	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.94654	0.024

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.26355	0.017
Immature Eggplant/Mature Eggplant	3.88537	0.05
Ripe Pepper/Ripe Tomato	0.05814	0.224
Mature Eggplant/Ripe Tomato	0.35237	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06429	0.877
1-1-2/M82	1.02905	0.977
12-2/M82	1.17807
12-4/M82	0.99441	1
1-3/M82	1.96936	0.255
2-1-1/M82	1.33371	1
2-1/M82	N/A	N/A
2-6/M82	1.25296	0.351
3-2/M82	1.11612
4-1-1/M82	1.02432
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.21904	1
5-3/M82	1.14094	1
6-2/M82	3.55453	0.253
6-3/M82	1.24016	1
7-1/M82	1.64385
7-2/M82	1.39275	0.299
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.87102	0.321
IL2-6/WTpooled	0.76421	0.348
IL7-5/WTpooled	0.69667	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.08664	0.553
IL1-4/WTpooled	0.93829	0.834
WT/WTpooled	0.9478	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	1.24166	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98629	1
DC3000/delta hrp 6h	1.04362	1
DC3000/delta hrp 12h	1.0406	1
DC3000/delta hrp 24h	2.38906	0.03

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.2568	0.042
DC3000 delta B/DC3000 delta AB	1.11021	0.477

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.39208	1
Exp 36h	1.51647	0.371
Exp 60h	1.23846	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96854	1
Var 0h	0.9148	0.933
Var 12h I row2-row1	1.15471	0.348
Var 12h NI row2-row1	0.95916	0.82
Var 36h I row2-row1	0.79732	0.805
Var 36h NI row2-row1	1.17877	0.482
Var 60h I row2-row1	0.61698	0.285
Var 60h NI row2-row1	1.21801	0.904
Time course 0hI-0hNI	1.04373	0.852
Time course 12hI-12hNI	1.18951	0.067
Time course 36hI-36hNI	1.18068	0.035
Time course 60hI-60hNI	1.09014	0.673

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)	1.91412	0.431
transgenic ySAMdc/azygous control (breaker)	0.47116	0.129
transgenic ySAMdc/azygous control (red)	1.37488	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.12799	0.213

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.70339	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.74373	1
Manapal/WT (break)	0.49618	0.333
Manapal/WT (red)	0.53426	0.187