Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.2.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97034	0.76
27DAP/17DAP	1.08846	1
39DAP/27DAP	0.76733	0.399
41DAP/39DAP	0.93159	0.727
42DAP/41DAP	0.71308	1
43DAP/42DAP	0.93476	0.865
47DAP/43DAP	0.71138	0.225
52DAP/47DAP	1.20818	0.615
57DAP/52DAP	0.92325	0.85

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98933	0.661
17DAP/reference	0.98596	0.737
27DAP/reference	0.97862	0.61
39DAP/reference	0.89215	0.088
41DAP/reference	0.86088	0.039
42DAP/reference	0.87705	0.072
43DAP/reference	0.9265	0.107
47DAP/reference	0.9324	0.174
52DAP/reference	1.08257	0.371
57DAP/reference	1.07343	0.496

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.20365	0.051
27DAP/17DAP	0.80497	0.418
39DAP/27DAP	0.63127	0.034
41DAP/39DAP	1.57122	0.025
42DAP/41DAP	0.83121	0.156
43DAP/42DAP	0.92315	0.558
47DAP/43DAP	1.16623	0.529
52DAP/47DAP	0.89345	0.491
57DAP/52DAP	0.92076	0.545
57DAP/7DAP	1.03772	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.3471	0.027
17DAP/reference	1.55339	0.014
27DAP/reference	1.30791	0.008
39DAP/reference	1.56818	0.008
41DAP/reference	1.36228	0.891
42DAP/reference	1.52364	0.014
43DAP/reference	1.39555	0.024
47DAP/reference	1.19864	0.079
52DAP/reference	1.36236	0.052
57DAP/reference	1.31901	0.017

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09575	0.605
17DAP/reference	1.00162	0.747
27DAP/reference	0.94362	0.22
39DAP/reference	0.98552	0.526
41DAP/reference	1.07908	0.642
42DAP/reference	0.87723	0.05
43DAP/reference	1.03665	0.969
47DAP/reference	0.87935	0.025
52DAP/reference	1.01194	1
57DAP/reference	0.88307	0.169

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23984	0.051
17DAP/reference	1.09258	0.887
27DAP/reference	1.2435	0.042
39DAP/reference	1.41201	0.018
41DAP/reference	1.28807	0.02
42DAP/reference	1.31175	0.209
43DAP/reference	1.24599	0.19
47DAP/reference	0.97777	0.558
52DAP/reference	1.068	0.952
57DAP/reference	1.05467	0.614

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09887	0.966
26DAP/20DAP	0.84206	0.512
34DAP/26DAP	0.79903	0.261
51DAP/34DAP	1.24025	0.962
52DAP/51DAP	1.0814	0.821
53DAP/52DAP	1.02954	0.91
55DAP/53DAP	0.79048	0.445
57DAP/55DAP	0.83525	0.37
62DAP/57DAP	0.81018
68DAP/62DAP	1.54173	0.035
68DAP/14DAP	0.96755	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.8244	0.016

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.34666	0.058
Mature Green Tomato/Ripe Tomato	2.04651	0.077
Immature Eggplant/Mature Eggplant	1.32444	0.053
Ripe Pepper/Ripe Tomato	0.57021	0.293
Mature Eggplant/Ripe Tomato	0.73008	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.31277	0.877
1-1-2/M82	1.07458
12-2/M82	1.1904	1
12-4/M82	1.01615	1
1-3/M82	0.97436	1
2-1-1/M82	1.11102
2-1/M82	0.99989	1
2-6/M82	0.83304	1
3-2/M82	1.23366
4-1-1/M82	0.74025	1
4-1/M82	0.70409	0.706
4-3-2/M82	0.98873	1
4-3/M82	1.10597	1
5-3/M82	1.23815	0.572
6-2/M82	0.79516
6-3/M82	0.93479	1
7-1/M82	1.09139	1
7-2/M82	0.9532	1
9-3-2/M82	1.4445

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.79101	0.321
IL2-6/WTpooled	0.88529	1
IL7-5/WTpooled	1.01597	1
IL7-3/WTpooled	1.33439	1
IL12-4/WTpooled	1.12472	0.695
IL1-4/WTpooled	1.0015	1
WT/WTpooled	1.04492	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	0.84731	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06307	0.75
DC3000/delta hrp 6h	0.96541	0.95
DC3000/delta hrp 12h	0.88569	1
DC3000/delta hrp 24h	1.04499	0.535

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.25867	0.183
DC3000 delta B/DC3000 delta AB	0.8482	0.288

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98078	1
Exp 36h	1.29371	0.409
Exp 60h	1.24454	1

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.97409	1
Var 12h I row2-row1	1.35335	0.506
Var 12h NI row2-row1	1.24394	0.649
Var 36h I row2-row1	1.02717	1
Var 36h NI row2-row1	1.15704	1
Var 60h I row2-row1	0.84064	0.285
Var 60h NI row2-row1	0.93807	0.932
Time course 0hI-0hNI	0.95732	0.881
Time course 12hI-12hNI	1.04613	0.762
Time course 36hI-36hNI	1.09156	0.19
Time course 60hI-60hNI	1.36608	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)	0.90502	0.428
transgenic ySAMdc/azygous control (breaker)	1.09761	1
transgenic ySAMdc/azygous control (red)	1.01929	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95792	0.256

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.93158	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.43725	0.307
Manapal/WT (break)	0.85765	0.333
Manapal/WT (red)	0.8758	0.424