Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.11.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03043	0.964
27DAP/17DAP	0.85749	0.661
39DAP/27DAP	1.13446	0.732
41DAP/39DAP	0.85506	0.447
42DAP/41DAP	1.14734	0.916
43DAP/42DAP	0.92487	0.858
47DAP/43DAP	0.79064	0.334
52DAP/47DAP	0.85478	0.593
57DAP/52DAP	1.1206	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94947	0.379
17DAP/reference	1.17854	0.013
27DAP/reference	1.06961	0.277
39DAP/reference	1.01969	0.8
41DAP/reference	1.19768	0.013
42DAP/reference	0.88922	0.012
43DAP/reference	1.0278	0.73
47DAP/reference	0.88772	0.019
52DAP/reference	0.80356	0.077
57DAP/reference	0.79112	0.022

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96539	0.663
27DAP/17DAP	1.13988	0.429
39DAP/27DAP	0.97481	0.859
41DAP/39DAP	1.06468	0.887
42DAP/41DAP	1.17457	0.487
43DAP/42DAP	0.84408	0.049
47DAP/43DAP	1.0507	0.822
52DAP/47DAP	0.78213	0.1
57DAP/52DAP	0.89287	0.328
57DAP/7DAP	0.8905	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85407	0.246
17DAP/reference	0.7955	0.049
27DAP/reference	0.82553	0.026
39DAP/reference	0.85546	0.073
41DAP/reference	0.76865	0.013
42DAP/reference	0.80875	0.077
43DAP/reference	0.83279	0.015
47DAP/reference	0.80223	0.034
52DAP/reference	0.69912	0.019
57DAP/reference	0.91492	0.149

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99858	0.97
17DAP/reference	1.04342	0.941
27DAP/reference	0.83286	0.108
39DAP/reference	0.8507	0.108
41DAP/reference	0.77004	0.024
42DAP/reference	0.82193	0.046
43DAP/reference	1.031	0.949
47DAP/reference	0.95313	0.246
52DAP/reference	0.91375	0.06
57DAP/reference	1.1851	0.085

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83378	0.077
17DAP/reference	0.99451	0.792
27DAP/reference	0.90748	0.081
39DAP/reference	0.90085	0.069
41DAP/reference	0.93504	0.512
42DAP/reference	0.81001	0.22
43DAP/reference	0.74467	0.179
47DAP/reference	0.89523	0.249
52DAP/reference	1.07178	0.837
57DAP/reference	0.46882	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07793	0.966
26DAP/20DAP	1.71968	0.098
34DAP/26DAP	0.85412	0.455
51DAP/34DAP	1.07649	0.654
52DAP/51DAP	1.06846	0.467
53DAP/52DAP	0.90224	0.612
55DAP/53DAP	1.05148	1
57DAP/55DAP	0.97881	0.859
62DAP/57DAP	1.12345	0.515
68DAP/62DAP	0.96669	0.787
68DAP/14DAP	0.8986	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.28487	0.369

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.98584	0.783
Mature Green Tomato/Ripe Tomato	1.24966	0.437
Immature Eggplant/Mature Eggplant	0.61325	0.062
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	1.30027

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.35569
1-1-2/M82	1.06533	1
12-2/M82	N/A	N/A
12-4/M82	1.20755	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.93536	1
4-1-1/M82	N/A	N/A
4-1/M82	0.79988	0.665
4-3-2/M82	1.10663	1
4-3/M82	N/A	N/A
5-3/M82	0.7806	0.395
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.87329
7-2/M82	0.70833
9-3-2/M82	1.25478

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.84282	0.243
IL2-6/WTpooled	1.1217	0.456
IL7-5/WTpooled	1.33501	0.792
IL7-3/WTpooled	0.90737	1
IL12-4/WTpooled	0.99725	1
IL1-4/WTpooled	1.46429	1
WT/WTpooled	0.92292	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	1.11714	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05821	0.921
DC3000/delta hrp 6h	1.03654	1
DC3000/delta hrp 12h	1.13908	1
DC3000/delta hrp 24h	0.96626	0.782

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.13169	0.333
DC3000 delta B/DC3000 delta AB	1.17049	0.349

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.12685	1
Exp 36h	0.98018	0.943
Exp 60h	0.77733	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98458	1
Var 0h	1.15044
Var 12h I row2-row1	1.08709	0.736
Var 12h NI row2-row1	1.0685	1
Var 36h I row2-row1	1.22123	0.304
Var 36h NI row2-row1	1.0982	1
Var 60h I row2-row1	0.90572	0.832
Var 60h NI row2-row1	0.89544	0.302
Time course 0hI-0hNI	0.90316	0.111
Time course 12hI-12hNI	1.00858	0.867
Time course 36hI-36hNI	1.22485	0.044
Time course 60hI-60hNI	1.23821	0.01

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)	1.03652	0.612
transgenic ySAMdc/azygous control (breaker)	0.751	0.134
transgenic ySAMdc/azygous control (red)	0.66865	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01636	0.619

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.43033	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.76361	0.14
Manapal/WT (break)	2.14598	0.123
Manapal/WT (red)	1.52339	0.413