Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.7.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.51489	0.09
27DAP/17DAP	0.884	0.725
39DAP/27DAP	1.6359	0.206
41DAP/39DAP	0.56513	0.045
42DAP/41DAP	0.97373	1
43DAP/42DAP	1.13622	0.968
47DAP/43DAP	0.73681	0.242
52DAP/47DAP	1.04264	1
57DAP/52DAP	1.24694	0.746

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.70762	0.047
17DAP/reference	0.59226	0.015
27DAP/reference	0.79192	0.098
39DAP/reference	0.59412	0.012
41DAP/reference	0.54124	0.008
42DAP/reference	0.7729	0.004
43DAP/reference	0.59538	0.013
47DAP/reference	1.00783	0.636
52DAP/reference	1.08145	0.663
57DAP/reference	0.93239	0.294

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.61934	0.036
27DAP/17DAP	0.81803	0.363
39DAP/27DAP	0.74611	0.113
41DAP/39DAP	1.10662	0.883
42DAP/41DAP	1.0429	0.902
43DAP/42DAP	0.87964	0.181
47DAP/43DAP	0.97201	0.896
52DAP/47DAP	0.9498	0.893
57DAP/52DAP	0.9154	0.221
57DAP/7DAP	0.54883	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85286	0.168
17DAP/reference	0.67803	0.012
27DAP/reference	0.56483	0.011
39DAP/reference	0.44532	0.011
41DAP/reference	0.41537	0.009
42DAP/reference	0.55826	0.01
43DAP/reference	0.38304	0.009
47DAP/reference	0.65567	0.079
52DAP/reference	0.47319	0.01
57DAP/reference	0.54584	0.01

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.44927	0.007
17DAP/reference	0.79497	0.095
27DAP/reference	1.02204	0.79
39DAP/reference	0.83658	0.147
41DAP/reference	0.75388	0.027
42DAP/reference	0.83346	0.035
43DAP/reference	0.53873	0.007
47DAP/reference	0.7981	0.038
52DAP/reference	0.45876	0.003
57DAP/reference	0.56985	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.40216	0.017
17DAP/reference	1.40107	0.169
27DAP/reference	0.93787	0.397
39DAP/reference	0.79159	0.016
41DAP/reference	0.55276	0.021
42DAP/reference	0.61659	0.036
43DAP/reference	0.74706	0.098
47DAP/reference	0.76226	0.097
52DAP/reference	0.6984	0.145
57DAP/reference	2.16034	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00266	1
26DAP/20DAP	1.04215	1
34DAP/26DAP	0.92314	0.771
51DAP/34DAP	0.80415	0.104
52DAP/51DAP	0.87324	1
53DAP/52DAP	0.78902	0.179
55DAP/53DAP	0.85127	0.091
57DAP/55DAP	1.03263	1
62DAP/57DAP	1.08583	0.8
68DAP/62DAP	1.43533	0.019
68DAP/14DAP	1.06887	0.889

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.35481	0.212

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.05885	0.058
Mature Green Tomato/Ripe Tomato	1.88415	0.267
Immature Eggplant/Mature Eggplant	0.82607	0.071
Ripe Pepper/Ripe Tomato	0.7887	0.224
Mature Eggplant/Ripe Tomato	5.91558	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.32376	0.591
1-1-2/M82	1.07523	0.977
12-2/M82	0.59492	0.678
12-4/M82	1.09756	1
1-3/M82	0.95051	0.441
2-1-1/M82	0.67156	0.465
2-1/M82	N/A	N/A
2-6/M82	0.95535	1
3-2/M82	1.04043	0.426
4-1-1/M82	0.93985
4-1/M82	1.90632	0.853
4-3-2/M82	1.26281	0.284
4-3/M82	0.90477	0.551
5-3/M82	1.62125	0.572
6-2/M82	N/A	N/A
6-3/M82	1.09383
7-1/M82	0.8858
7-2/M82	1.14633
9-3-2/M82	0.89262	0.449

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	0.9564	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99683	1
DC3000/delta hrp 6h	1.0636	1
DC3000/delta hrp 12h	1.08723	1
DC3000/delta hrp 24h	0.95608	0.607

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.7838
DC3000 delta B/DC3000 delta AB	0.42695	0.02

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	0.978	1
Var 0h	0.76085	1
Var 12h I row2-row1	0.82486	0.39
Var 12h NI row2-row1	0.94226	0.713
Var 36h I row2-row1	0.86549	0.805
Var 36h NI row2-row1	1.14226	1
Var 60h I row2-row1	1.27971	0.543
Var 60h NI row2-row1	1.09371	0.904
Time course 0hI-0hNI	0.99407	1
Time course 12hI-12hNI	1.00918	0.868
Time course 36hI-36hNI	0.98267	0.569
Time course 60hI-60hNI	0.2868	0.006

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)	1.04138	0.798
transgenic ySAMdc/azygous control (breaker)	0.86666	0.49
transgenic ySAMdc/azygous control (red)	0.83656	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.72413	0.163

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.11921	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	4.88653	0.096
Manapal/WT (break)	1.26332	0.381
Manapal/WT (red)	1.4619	1