Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.10.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11597	0.739
27DAP/17DAP	1.15249	0.845
39DAP/27DAP	0.80971	0.495
41DAP/39DAP	1.20071	0.638
42DAP/41DAP	1.03272	1
43DAP/42DAP	1.03179	1
47DAP/43DAP	1.43925	0.349
52DAP/47DAP	0.86643	0.63
57DAP/52DAP	1.01956	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98404	0.589
17DAP/reference	1.02009	0.492
27DAP/reference	1.04093	0.299
39DAP/reference	1.0439	0.174
41DAP/reference	1.00449	1
42DAP/reference	0.96907	0.129
43DAP/reference	0.99073	0.805
47DAP/reference	1.04085	0.306
52DAP/reference	0.92763	0.3
57DAP/reference	1.00687	0.736

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83498	0.336
27DAP/17DAP	0.85922	0.363
39DAP/27DAP	1.09094	0.728
41DAP/39DAP	0.93555	0.861
42DAP/41DAP	1.01878	1
43DAP/42DAP	1.01246	1
47DAP/43DAP	1.03262	0.914
52DAP/47DAP	1.09447	0.799
57DAP/52DAP	1.00348	1
57DAP/7DAP	1.12397	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12499	0.461
17DAP/reference	1.38363	0.077
27DAP/reference	1.03111	1
39DAP/reference	0.88872	0.198
41DAP/reference	1.00234	0.709
42DAP/reference	0.92451	0.289
43DAP/reference	1.32194	0.099
47DAP/reference	0.85404	0.222
52DAP/reference	1.06623	0.401
57DAP/reference	1.33432	0.057

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94494	0.386
17DAP/reference	0.9541	0.066
27DAP/reference	0.92935	0.282
39DAP/reference	0.88978	0.243
41DAP/reference	0.89663	0.064
42DAP/reference	1.05044	0.879
43DAP/reference	0.89853	0.144
47DAP/reference	1.03248	0.795
52DAP/reference	0.93548	0.143
57DAP/reference	1.00296	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1801	0.185
17DAP/reference	1.06314	0.887
27DAP/reference	1.19494	0.325
39DAP/reference	1.90483	0.296
41DAP/reference	1.32999	0.069
42DAP/reference	1.15785	0.54
43DAP/reference	1.33577	0.209
47DAP/reference	0.96248	0.357
52DAP/reference	1.38747	0.138
57DAP/reference	1.00485	0.593

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03609	0.966
26DAP/20DAP	0.86926	0.512
34DAP/26DAP	1.08406	1
51DAP/34DAP	1.0042	0.927
52DAP/51DAP	1.0283	0.888
53DAP/52DAP	0.93497	0.572
55DAP/53DAP	1.05316	0.634
57DAP/55DAP	1.03844	0.793
62DAP/57DAP	0.99902	1
68DAP/62DAP	1.00908	1
68DAP/14DAP	1.33578	0.311

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.84008	0.145

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.03638	1
Mature Green Tomato/Ripe Tomato	1.11928	0.523
Immature Eggplant/Mature Eggplant	1.27718	0.15
Ripe Pepper/Ripe Tomato	1.04712	1
Mature Eggplant/Ripe Tomato	1.2174	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95532	0.536
1-1-2/M82	0.92589	0.958
12-2/M82	1.15911	1
12-4/M82	0.91591	0.619
1-3/M82	0.91673	0.378
2-1-1/M82	1.03225
2-1/M82	1.09513
2-6/M82	0.98992	1
3-2/M82	0.94074
4-1-1/M82	1.12051	1
4-1/M82	0.8184	1
4-3-2/M82	0.91716	1
4-3/M82	1.04245	0.268
5-3/M82	0.87204	0.642
6-2/M82	1.04153	1
6-3/M82	1.00498	1
7-1/M82	0.84485	0.44
7-2/M82	0.98458	0.796
9-3-2/M82	0.75704	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.95506	0.247
IL2-6/WTpooled	0.95857	1
IL7-5/WTpooled	0.64526
IL7-3/WTpooled	0.76983	0.418
IL12-4/WTpooled	1.07341	0.695
IL1-4/WTpooled	0.80404	0.444
WT/WTpooled	1.03238	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	0.6932	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94927	1
DC3000/delta hrp 6h	1.19928	0.95
DC3000/delta hrp 12h	0.98763	1
DC3000/delta hrp 24h	1.03621	0.62

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.05871
DC3000 delta B/DC3000 delta AB	0.93782	0.511

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.64121	0.188
Exp 36h	0.58685	0.449
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	0.97693	1
Var 0h	1.02855	1
Var 12h I row2-row1	1.09124	0.348
Var 12h NI row2-row1	0.72278	0.546
Var 36h I row2-row1	0.91915	1
Var 36h NI row2-row1	1.10205	1
Var 60h I row2-row1	1.50456	0.562
Var 60h NI row2-row1	1.27149	0.904
Time course 0hI-0hNI	1.01456	1
Time course 12hI-12hNI	0.95806	0.65
Time course 36hI-36hNI	0.76621	0.032
Time course 60hI-60hNI	0.76984	0.047

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)	0.98548	0.862
transgenic ySAMdc/azygous control (breaker)	1.72212	0.248
transgenic ySAMdc/azygous control (red)	1.62266	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93724	0.054

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.77596	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.96067	1
Manapal/WT (break)	0.89284	1
Manapal/WT (red)	0.67082	0.181