Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.11.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88738	0.169
27DAP/17DAP	1.02326	0.92
39DAP/27DAP	1.3338	0.165
41DAP/39DAP	0.8461	0.412
42DAP/41DAP	0.9589	1
43DAP/42DAP	0.95282	0.877
47DAP/43DAP	1.00963	0.926
52DAP/47DAP	1.07382	0.906
57DAP/52DAP	0.99077	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0921	0.303
17DAP/reference	1.07289	0.066
27DAP/reference	1.05118	0.587
39DAP/reference	1.04437
41DAP/reference	0.98592	0.667
42DAP/reference	0.99515	0.567
43DAP/reference	1.0125	0.812
47DAP/reference	1.00609	0.963
52DAP/reference	0.98417	0.618
57DAP/reference	0.97516	0.358

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1168	0.179
27DAP/17DAP	0.99459	0.969
39DAP/27DAP	0.96548	0.628
41DAP/39DAP	1.02136	0.909
42DAP/41DAP	1.03333	0.783
43DAP/42DAP	0.96689	0.558
47DAP/43DAP	1.01926	0.857
52DAP/47DAP	0.98948	0.93
57DAP/52DAP	1.05328	0.662
57DAP/7DAP	1.06692	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07839	0.344
17DAP/reference	1.08898	0.399
27DAP/reference	1.03172	0.06
39DAP/reference	1.04293	0.114
41DAP/reference	1.01096	0.864
42DAP/reference	0.99747	0.675
43DAP/reference	1.02279	0.256
47DAP/reference	1.06177	0.468
52DAP/reference	0.98344	0.435
57DAP/reference	1.04271	0.356

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01254	0.802
17DAP/reference	1.0584	0.229
27DAP/reference	1.00212	0.735
39DAP/reference	1.03868	0.67
41DAP/reference	0.95047	0.256
42DAP/reference	0.96956	0.392
43DAP/reference	1.01819	0.688
47DAP/reference	0.92332	0.129
52DAP/reference	1.01877	0.988
57DAP/reference	1.03238	0.593

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04417	0.303
17DAP/reference	0.98653	0.658
27DAP/reference	0.99641	0.727
39DAP/reference	1.04177	0.084
41DAP/reference	1.005	0.939
42DAP/reference	1.06141	0.45
43DAP/reference	1.04817	0.445
47DAP/reference	1.0344	0.68
52DAP/reference	1.06628	0.443
57DAP/reference	1.06721	0.228

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91985	1
26DAP/20DAP	1.14401	0.449
34DAP/26DAP	0.99162	1
51DAP/34DAP	0.93964	0.714
52DAP/51DAP	1.0013	1
53DAP/52DAP	0.98407	0.924
55DAP/53DAP	0.98823	0.886
57DAP/55DAP	0.95115	0.819
62DAP/57DAP	0.94919	0.871
68DAP/62DAP	1.12562	0.507
68DAP/14DAP	0.87667	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.12902	0.022

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.13956	0.176
Mature Green Tomato/Ripe Tomato	1.36018	0.04
Immature Eggplant/Mature Eggplant	1.13545	0.222
Ripe Pepper/Ripe Tomato	0.88378	0.224
Mature Eggplant/Ripe Tomato	1.27217	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98435	0.961
1-1-2/M82	0.89275	1
12-2/M82	0.8991	0.955
12-4/M82	1.00045	1
1-3/M82	1.13277	0.479
2-1-1/M82	0.95772	1
2-1/M82	1.3431	1
2-6/M82	0.97244	1
3-2/M82	1.02634	0.84
4-1-1/M82	0.96373	1
4-1/M82	1.07531	1
4-3-2/M82	N/A	N/A
4-3/M82	1.04507	1
5-3/M82	1.06079	1
6-2/M82	1.01686	1
6-3/M82	1.04657	1
7-1/M82	0.98084	1
7-2/M82	1.03266	1
9-3-2/M82	1.15958

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.94221	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.21008	1
IL12-4/WTpooled	0.94696	0.71
IL1-4/WTpooled	1.10018
WT/WTpooled	0.95959	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	1.08843	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04443	0.921
DC3000/delta hrp 6h	0.96824	0.95
DC3000/delta hrp 12h	0.96547	1
DC3000/delta hrp 24h	1.06106	0.673

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.11852	0.081
DC3000 delta B/DC3000 delta AB	1.09537	0.406

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.80841	1
Exp 36h	1.55997	0.489
Exp 60h	1.37208	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97163	1
Var 0h	0.84334	0.255
Var 12h I row2-row1	1.31326	0.324
Var 12h NI row2-row1	1.09588	0.649
Var 36h I row2-row1	1.06354	1
Var 36h NI row2-row1	0.90275	0.584
Var 60h I row2-row1	1.02948	0.562
Var 60h NI row2-row1	1.04467	1
Time course 0hI-0hNI	1.04948	0.662
Time course 12hI-12hNI	1.0536	0.55
Time course 36hI-36hNI	1.32867	0.005
Time course 60hI-60hNI	1.48906	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)	1.06714	0.798
transgenic ySAMdc/azygous control (breaker)	1.05723	1
transgenic ySAMdc/azygous control (red)	1.22598	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04646	0.177

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95047	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.07501	0.14
Manapal/WT (break)	1.31878	0.381
Manapal/WT (red)	0.96203	0.728