Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.3.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01119	0.919
27DAP/17DAP	1.02253	0.92
39DAP/27DAP	1.13787	1
41DAP/39DAP	0.77542	0.337
42DAP/41DAP	1.26157	0.644
43DAP/42DAP	1.24458	0.736
47DAP/43DAP	1.09197	0.856
52DAP/47DAP	1.08589	0.969
57DAP/52DAP	1.03474	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08264	0.544
17DAP/reference	0.8438	0.18
27DAP/reference	1.05569	0.457
39DAP/reference	1.5843	0.335
41DAP/reference	0.85026	0.201
42DAP/reference	0.82373	0.169
43DAP/reference	0.55593
47DAP/reference	1.82374	0.081
52DAP/reference	1.16307	0.048
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92278	0.454
27DAP/17DAP	0.99799	0.969
39DAP/27DAP	0.97732	0.887
41DAP/39DAP	0.98651	0.997
42DAP/41DAP	0.99271	0.841
43DAP/42DAP	1.102	0.25
47DAP/43DAP	1.06948	0.788
52DAP/47DAP	0.92352	0.624
57DAP/52DAP	0.93977	0.587
57DAP/7DAP	1.10921	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89291	0.246
17DAP/reference	0.79787	0.012
27DAP/reference	0.76431	0.01
39DAP/reference	0.87829	0.011
41DAP/reference	0.87424	0.05
42DAP/reference	0.85007	0.033
43DAP/reference	0.80878	0.012
47DAP/reference	0.88164	0.222
52DAP/reference	0.79072	0.013
57DAP/reference	0.80961	0.018

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1234	0.35
17DAP/reference	1.11871	0.236
27DAP/reference	1.14639	0.367
39DAP/reference	1.1107	0.316
41DAP/reference	0.98348	0.493
42DAP/reference	1.02387	0.951
43DAP/reference	1.24665	0.104
47DAP/reference	1.05624	0.544
52DAP/reference	1.10749	0.322
57DAP/reference	1.07556	0.306

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78642	0.03
17DAP/reference	0.9584	0.389
27DAP/reference	0.83946	0.048
39DAP/reference	0.89299	0.147
41DAP/reference	0.97374	0.56
42DAP/reference	0.84605	0.172
43DAP/reference	1.02996	1
47DAP/reference	1.47481	0.011
52DAP/reference	0.87932	0.424
57DAP/reference	1.27186	0.098

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	2.00842	0.916
26DAP/20DAP	0.73297	0.228
34DAP/26DAP	0.96971	0.945
51DAP/34DAP	1.05617	0.925
52DAP/51DAP	1.05908	0.704
53DAP/52DAP	1.06416	0.819
55DAP/53DAP	0.98576	0.876
57DAP/55DAP	1.15424	0.474
62DAP/57DAP	1.0602	0.515
68DAP/62DAP	0.93844	0.769
68DAP/14DAP	1.21695	0.541

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.90753	0.358

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.17151	0.176
Mature Green Tomato/Ripe Tomato	2.27849	0.166
Immature Eggplant/Mature Eggplant	0.67836	0.096
Ripe Pepper/Ripe Tomato	1.70018	0.258
Mature Eggplant/Ripe Tomato	0.74578	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05778	0.877
1-1-2/M82	1.06259
12-2/M82	0.94825
12-4/M82	1.29636
1-3/M82	0.80147	0.441
2-1-1/M82	0.98295	1
2-1/M82	N/A	N/A
2-6/M82	1.13501	0.452
3-2/M82	N/A	N/A
4-1-1/M82	1.12964	1
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.8878	1
5-3/M82	0.94143	1
6-2/M82	0.83753
6-3/M82	1.2886
7-1/M82	N/A	N/A
7-2/M82	0.97208	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.93751	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.0734	0.792
IL7-3/WTpooled	1.36992
IL12-4/WTpooled	0.8731	0.543
IL1-4/WTpooled	1.18736	1
WT/WTpooled	1.30351	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	0.83995	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98039	1
DC3000/delta hrp 6h	1.04847	1
DC3000/delta hrp 12h	1.01251	1
DC3000/delta hrp 24h	0.7683	0.044

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.53671	0.045
DC3000 delta B/DC3000 delta AB	1.32125	0.141

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00357	1
Exp 36h	0.77632	0.449
Exp 60h	0.80636	0.29

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0008	1
Var 0h	0.47408	1
Var 12h I row2-row1	0.83873	0.467
Var 12h NI row2-row1	1.10477	1
Var 36h I row2-row1	0.94329	0.805
Var 36h NI row2-row1	1.08447	1
Var 60h I row2-row1	1.12323	0.562
Var 60h NI row2-row1	1.04108	0.904
Time course 0hI-0hNI	1.03146	0.867
Time course 12hI-12hNI	0.94452	0.526
Time course 36hI-36hNI	0.86467	0.023
Time course 60hI-60hNI	0.55112	0.007

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)	0.94419	0.314
transgenic ySAMdc/azygous control (breaker)	0.94022	0.173
transgenic ySAMdc/azygous control (red)	0.82397	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03316	0.073

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.06718	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.10388	1
Manapal/WT (break)	1.08298	1
Manapal/WT (red)	1.75171	0.137