Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.3.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19285	0.588
27DAP/17DAP	0.49454	0.027
39DAP/27DAP	0.7961	0.414
41DAP/39DAP	0.74138	0.156
42DAP/41DAP	1.03016	1
43DAP/42DAP	1.1266	0.991
47DAP/43DAP	0.78239	0.35
52DAP/47DAP	0.75009	0.293
57DAP/52DAP	1.17205	0.735

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81427	0.08
17DAP/reference	0.79061	0.028
27DAP/reference	0.82298	0.068
39DAP/reference	0.73699	0.027
41DAP/reference	0.75681	0.085
42DAP/reference	0.61503	0.002
43DAP/reference	0.85002	0.135
47DAP/reference	0.727	0.007
52DAP/reference	0.65173	0.027
57DAP/reference	0.88147	0.078

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.62694	0.037
27DAP/17DAP	0.68666	0.172
39DAP/27DAP	0.47028	0.056
41DAP/39DAP	1.29931	0.115
42DAP/41DAP	0.92192	0.491
43DAP/42DAP	0.92057	0.351
47DAP/43DAP	0.96108	0.781
52DAP/47DAP	0.99186	0.93
57DAP/52DAP	0.88783	0.399
57DAP/7DAP	0.54988	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12927	0.235
17DAP/reference	0.82479	0.049
27DAP/reference	0.70317	0.03
39DAP/reference	0.5958	0.011
41DAP/reference	0.44774	0.012
42DAP/reference	0.51401	0.01
43DAP/reference	0.4009	0.011
47DAP/reference	0.4943	0.034
52DAP/reference	0.48645	0.01
57DAP/reference	0.46886	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.55504	0.007
17DAP/reference	0.49206	0.006
27DAP/reference	0.69041	0.047
39DAP/reference	0.51588	0.009
41DAP/reference	0.61642	0.01
42DAP/reference	0.594	0.011
43DAP/reference	0.32161	0.002
47DAP/reference	0.56476	0.007
52DAP/reference	0.47739	0.004
57DAP/reference	0.34747	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.94566	0.015
17DAP/reference	1.68733	0.111
27DAP/reference	1.17543	0.26
39DAP/reference	0.90684	0.063
41DAP/reference	0.68196	0.019
42DAP/reference	0.5377	0.016
43DAP/reference	0.55797	0.019
47DAP/reference	0.5528	0.005
52DAP/reference	0.48667	0.047
57DAP/reference	1.02438	0.991

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0999	0.966
26DAP/20DAP	1.34372	0.394
34DAP/26DAP	1.00563	1
51DAP/34DAP	0.41223	0.054
52DAP/51DAP	0.84094	1
53DAP/52DAP	0.96522	0.848
55DAP/53DAP	0.91085	0.632
57DAP/55DAP	1.00173	0.902
62DAP/57DAP	1.29244
68DAP/62DAP	1.90417	0.02
68DAP/14DAP	1.04774	0.826

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.67753	0.369

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.95318	0.058
Mature Green Tomato/Ripe Tomato	2.03676	0.026
Immature Eggplant/Mature Eggplant	0.53856	0.057
Ripe Pepper/Ripe Tomato	2.1376	0.258
Mature Eggplant/Ripe Tomato	5.23364	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.99497	1
12-2/M82	0.59356
12-4/M82	0.93071	0.619
1-3/M82	0.85998
2-1-1/M82	0.98548
2-1/M82	N/A	N/A
2-6/M82	1.27688	0.385
3-2/M82	1.44153
4-1-1/M82	0.73584
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.09474	1
5-3/M82	1.26867	1
6-2/M82	1.37277
6-3/M82	0.7643
7-1/M82	1.11153
7-2/M82	1.03461	1
9-3-2/M82	1.55731

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.36028	0.277
IL2-6/WTpooled	1.07329	0.788
IL7-5/WTpooled	0.77403	1
IL7-3/WTpooled	0.8442	0.294
IL12-4/WTpooled	0.78159	0.71
IL1-4/WTpooled	0.80354	0.444
WT/WTpooled	0.9866	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	0.87316	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97558	1
DC3000/delta hrp 6h	0.92697	0.95
DC3000/delta hrp 12h	0.63843
DC3000/delta hrp 24h	0.96592	0.794

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.56538	0.031
DC3000 delta B/DC3000 delta AB	0.36382	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0307	1
Exp 36h	0.82782	0.623
Exp 60h	0.81754	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97101	1
Var 0h	0.86643	1
Var 12h I row2-row1	0.79521	0.363
Var 12h NI row2-row1	0.99545	1
Var 36h I row2-row1	0.82081	0.805
Var 36h NI row2-row1	1.00219	1
Var 60h I row2-row1	1.27582	0.271
Var 60h NI row2-row1	1.14126	0.904
Time course 0hI-0hNI	1.05412	0.833
Time course 12hI-12hNI	0.96261	0.745
Time course 36hI-36hNI	1.01222	1
Time course 60hI-60hNI	0.12656	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)	1.10235	0.798
transgenic ySAMdc/azygous control (breaker)	1.63192	0.166
transgenic ySAMdc/azygous control (red)	1.04804	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.61808	0.085

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.5259	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	11.5817	0.086
Manapal/WT (break)	5.91887	0.123
Manapal/WT (red)	1.50334	0.413