Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.10.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.7525	0.107
27DAP/17DAP	1.52144	0.521
39DAP/27DAP	0.79685	0.241
41DAP/39DAP	1.01098	0.935
42DAP/41DAP	0.88056	1
43DAP/42DAP	1.23284	0.507
47DAP/43DAP	3.29624	0.201
52DAP/47DAP	1.66718	0.12
57DAP/52DAP	1.06823	0.992

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1426	0.522
17DAP/reference	0.6897	0.01
27DAP/reference	0.64338	0.015
39DAP/reference	0.85227	0.2
41DAP/reference	0.63558	0.009
42DAP/reference	1.21564	0.003
43DAP/reference	1.45355	0.009
47DAP/reference	3.38401	0.001
52DAP/reference	2.50526	0.007
57DAP/reference	1.60524	0.01

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9272	0.442
27DAP/17DAP	1.01738	1
39DAP/27DAP	1.27811	0.067
41DAP/39DAP	1.00923	1
42DAP/41DAP	0.85188	0.143
43DAP/42DAP	1.21878	0.103
47DAP/43DAP	1.03786	0.897
52DAP/47DAP	1.60005	0.106
57DAP/52DAP	2.3109	0.035
57DAP/7DAP	1.99764	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07098	0.576
17DAP/reference	0.70734	0.015
27DAP/reference	0.5403	0.019
39DAP/reference	0.95467	0.411
41DAP/reference	1.13155	0.475
42DAP/reference	1.04178	0.889
43DAP/reference	1.06417	0.83
47DAP/reference	0.92262	0.293
52DAP/reference	1.15521	0.092
57DAP/reference	1.04832	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90224	0.204
17DAP/reference	0.81232	0.019
27DAP/reference	1.2214	0.297
39DAP/reference	0.91513	0.25
41DAP/reference	0.81246	0.041
42DAP/reference	1.11578	0.302
43DAP/reference	0.87697	0.17
47DAP/reference	0.89645	0.173
52DAP/reference	0.65781	0.004
57DAP/reference	0.71156	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08255	0.296
17DAP/reference	0.82683	0.231
27DAP/reference	1.00019	0.843
39DAP/reference	0.75119	0.069
41DAP/reference	1.10484	0.889
42DAP/reference	1.0781	0.907
43DAP/reference	1.33473	0.076
47DAP/reference	2.04048	0.006
52DAP/reference	1.74648	0.158
57DAP/reference	2.51636	0.005

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10896	0.966
26DAP/20DAP	0.96021	1
34DAP/26DAP	0.97034	0.972
51DAP/34DAP	1.03334	0.936
52DAP/51DAP	1.22015	0.579
53DAP/52DAP	1.02721	0.944
55DAP/53DAP	1.07035	0.922
57DAP/55DAP	0.85726	0.318
62DAP/57DAP	1.35533	0.021
68DAP/62DAP	0.67038	0.048
68DAP/14DAP	0.90657	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.14573	0.162

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.73363
Mature Green Tomato/Ripe Tomato	0.04874	0.014
Immature Eggplant/Mature Eggplant	1.05017	0.683
Ripe Pepper/Ripe Tomato	0.11941	0.224
Mature Eggplant/Ripe Tomato	0.05064	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	2.44773	0.551
1-1-2/M82	0.99667	1
12-2/M82	0.6457	0.862
12-4/M82	0.99267
1-3/M82	2.12722	0.479
2-1-1/M82	1.79369	0.422
2-1/M82	1.00661
2-6/M82	2.85705	0.452
3-2/M82	1.03281	1
4-1-1/M82	3.00535	0.876
4-1/M82	1.65311
4-3-2/M82	3.94077
4-3/M82	5.64355	0.268
5-3/M82	0.27819	0.374
6-2/M82	3.32698
6-3/M82	0.903	1
7-1/M82	1.24432	0.992
7-2/M82	2.16816	0.282
9-3-2/M82	2.30556	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.60028	0.243
IL2-6/WTpooled	1.11774	0.427
IL7-5/WTpooled	1.12584	1
IL7-3/WTpooled	0.56181	0.31
IL12-4/WTpooled	0.8299	0.71
IL1-4/WTpooled	0.88148	0.699
WT/WTpooled	0.99084	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	1.22252	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06111	0.692
DC3000/delta hrp 6h	0.96563	0.95
DC3000/delta hrp 12h	0.91904	1
DC3000/delta hrp 24h	1.9619	0.023

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.14409
DC3000 delta B/DC3000 delta AB	0.98985	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.18569	1
Exp 36h	1.59189	0.371
Exp 60h	1.23072	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05018	1
Var 0h	0.91784	1
Var 12h I row2-row1	1.13745	0.379
Var 12h NI row2-row1	0.89162	0.82
Var 36h I row2-row1	1.13783	0.309
Var 36h NI row2-row1	1.04766	1
Var 60h I row2-row1	0.99068	1
Var 60h NI row2-row1	1.68961	0.904
Time course 0hI-0hNI	1.06056	0.799
Time course 12hI-12hNI	1.10778	0.287
Time course 36hI-36hNI	1.32242	0.004
Time course 60hI-60hNI	2.9873	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)	1.55959	0.318
transgenic ySAMdc/azygous control (breaker)	0.5257	0.131
transgenic ySAMdc/azygous control (red)	0.62488	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00027	0.967

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.61305	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.90521	1
Manapal/WT (break)	0.93238	1
Manapal/WT (red)	1.88204	0.164