Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.10.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08763	0.964
27DAP/17DAP	1.12117	0.902
39DAP/27DAP	1.19214	0.885
41DAP/39DAP	1.06189	0.929
42DAP/41DAP	1.26945	0.82
43DAP/42DAP	0.94703	0.888
47DAP/43DAP	0.99098	0.884
52DAP/47DAP	1.00563	0.916
57DAP/52DAP	0.87743	0.85

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.7939	0.159
17DAP/reference	0.49548	0.009
27DAP/reference	0.47395	0.013
39DAP/reference	0.4858	0.021
41DAP/reference	0.28084	0.008
42DAP/reference	0.3805	0.001
43DAP/reference	0.29673	0.012
47DAP/reference	0.24939	0.001
52DAP/reference	0.24584	0.012
57DAP/reference	0.36743	0.006

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.76045	0.041
27DAP/17DAP	1.00738	1
39DAP/27DAP	1.15425	0.262
41DAP/39DAP	1.2597	0.035
42DAP/41DAP	0.8221	0.116
43DAP/42DAP	0.93357	0.415
47DAP/43DAP	0.99559	0.954
52DAP/47DAP	1.00727	0.97
57DAP/52DAP	0.78369	0.299
57DAP/7DAP	0.94526	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97149	0.55
17DAP/reference	0.82592	0.044
27DAP/reference	0.56071	0.01
39DAP/reference	0.34469	0.011
41DAP/reference	0.27847	0.009
42DAP/reference	0.26224	0.01
43DAP/reference	0.22456	0.009
47DAP/reference	0.23039	0.033
52DAP/reference	0.28102	0.01
57DAP/reference	0.29288	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.44244	0.007
17DAP/reference	0.51691	0.01
27DAP/reference	0.54634	0.016
39DAP/reference	0.37042	0.009
41DAP/reference	0.37323	0.005
42DAP/reference	0.35925	0.011
43DAP/reference	0.20595	0.001
47DAP/reference	0.28766	0.007
52DAP/reference	0.21423	0.003
57DAP/reference	0.16709	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.12346	0.02
17DAP/reference	2.04348	0.037
27DAP/reference	1.28032	0.056
39DAP/reference	0.9866	0.643
41DAP/reference	0.70167	0.03
42DAP/reference	0.49023	0.016
43DAP/reference	0.51665	0.019
47DAP/reference	0.28707	0.004
52DAP/reference	0.2984	0.05
57DAP/reference	1.4191	0.436

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98593	1
26DAP/20DAP	0.72728	0.317
34DAP/26DAP	0.94354	0.898
51DAP/34DAP	1.10384	0.898
52DAP/51DAP	0.99605	1
53DAP/52DAP	0.85725	0.489
55DAP/53DAP	0.90565	0.563
57DAP/55DAP	1.20455	0.71
62DAP/57DAP	1.34144	0.018
68DAP/62DAP	0.8012	0.543
68DAP/14DAP	0.44519	0.09

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.99499	0.665

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.26533	0.058
Mature Green Tomato/Ripe Tomato	0.86939	0.522
Immature Eggplant/Mature Eggplant	0.44745	0.062
Ripe Pepper/Ripe Tomato	14.3566	0.256
Mature Eggplant/Ripe Tomato	64.5275	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92566	0.944
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.18942	0.611
1-3/M82	0.75406
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.01865
3-2/M82	N/A	N/A
4-1-1/M82	1.02252	1
4-1/M82	N/A	N/A
4-3-2/M82	1.64763
4-3/M82	0.91406	1
5-3/M82	1.3217	0.455
6-2/M82	0.86756
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.96543
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.10217	0.493
IL2-6/WTpooled	1.82835	0.395
IL7-5/WTpooled	1.0071	0.792
IL7-3/WTpooled	1.11839	1
IL12-4/WTpooled	0.96021	1
IL1-4/WTpooled	1.14157	1
WT/WTpooled	0.78305	0.764

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	1.14811	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95614	0.571
DC3000/delta hrp 6h	0.97582	0.95
DC3000/delta hrp 12h	1.04399	1
DC3000/delta hrp 24h	1.01303	0.821

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.10209	0.313
DC3000 delta B/DC3000 delta AB	2.19398	0.061

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96635	1
Exp 36h	0.8721	0.699
Exp 60h	0.74073	0.29

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0463	1
Var 0h	0.99113	1
Var 12h I row2-row1	0.72129	0.514
Var 12h NI row2-row1	1.36021	0.649
Var 36h I row2-row1	1.04045	1
Var 36h NI row2-row1	0.61045	0.522
Var 60h I row2-row1	0.77641	0.439
Var 60h NI row2-row1	0.78633	0.335
Time course 0hI-0hNI	1.24863	0.413
Time course 12hI-12hNI	1.08478	0.698
Time course 36hI-36hNI	2.21054	0.005
Time course 60hI-60hNI	4.73213	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)	1.21139	0.654
transgenic ySAMdc/azygous control (breaker)	3.13888	0.162
transgenic ySAMdc/azygous control (red)	1.10119	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.51783	0.072

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.34628	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	22.2627	0.083
Manapal/WT (break)	12.0795	0.123
Manapal/WT (red)	3.32124	0.413