Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-1.1.8.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13157	0.904
27DAP/17DAP	0.94058	0.899
39DAP/27DAP	0.85549	0.458
41DAP/39DAP	1.53318	0.372
42DAP/41DAP	1.2754	0.871
43DAP/42DAP	0.85331	0.709
47DAP/43DAP	0.9121	0.618
52DAP/47DAP	1.64419	0.52
57DAP/52DAP	0.77422	0.687

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91053	0.132
17DAP/reference	1.01959	0.355
27DAP/reference	0.91865	0.065
39DAP/reference	0.9479	0.35
41DAP/reference	1.15539	0.054
42DAP/reference	0.97396	0.25
43DAP/reference	1.0524	0.445
47DAP/reference	0.96281	0.191
52DAP/reference	0.90312	0.135
57DAP/reference	0.82258	0.012

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10275	0.114
27DAP/17DAP	1.01177	0.969
39DAP/27DAP	0.89445	0.156
41DAP/39DAP	0.9727	0.959
42DAP/41DAP	1.12794	0.436
43DAP/42DAP	1.08679	0.513
47DAP/43DAP	0.93727	0.402
52DAP/47DAP	1.06059	0.835
57DAP/52DAP	1.0754	0.895
57DAP/7DAP	0.55887	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81302	0.071
17DAP/reference	0.87214	0.028
27DAP/reference	0.83324	0.01
39DAP/reference	0.80641	0.012
41DAP/reference	0.75661	0.02
42DAP/reference	0.8077	0.016
43DAP/reference	0.8122	0.032
47DAP/reference	0.86297	0.293
52DAP/reference	0.74884	0.012
57DAP/reference	0.77913	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05601	0.704
17DAP/reference	1.0271	0.739
27DAP/reference	0.92967	0.438
39DAP/reference	0.88602	0.029
41DAP/reference	0.99728	0.735
42DAP/reference	0.94676	0.189
43DAP/reference	1.5128	0.009
47DAP/reference	1.00524	1
52DAP/reference	1.03071	0.667
57DAP/reference	1.29523	0.104

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84549	0.046
17DAP/reference	0.93726	0.281
27DAP/reference	0.81871	0.047
39DAP/reference	0.85792	0.133
41DAP/reference	0.93468	0.371
42DAP/reference	0.87588	0.134
43DAP/reference	0.88195	0.042
47DAP/reference	0.98102	0.538
52DAP/reference	0.88451	0.232
57DAP/reference	0.7718	0.026

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95127	1
26DAP/20DAP	0.83557	0.317
34DAP/26DAP	1.03766	1
51DAP/34DAP	0.92978	0.674
52DAP/51DAP	1.29394	0.058
53DAP/52DAP	0.91823	0.649
55DAP/53DAP	1.33712	0.071
57DAP/55DAP	0.92882	0.677
62DAP/57DAP	1.06384	0.35
68DAP/62DAP	0.68953	N/A
68DAP/14DAP	0.72053	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.70837	0.041

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.88475	0.21
Mature Green Tomato/Ripe Tomato	0.67336	0.02
Immature Eggplant/Mature Eggplant	4.49632	0.05
Ripe Pepper/Ripe Tomato	1.29436	1
Mature Eggplant/Ripe Tomato	1.09941	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06053	0.877
1-1-2/M82	0.95454	1
12-2/M82	1.11463	1
12-4/M82	0.90321	1
1-3/M82	0.90909	0.441
2-1-1/M82	0.97448	1
2-1/M82	0.6883	N/A
2-6/M82	0.9875	1
3-2/M82	0.97093	N/A
4-1-1/M82	0.89432	1
4-1/M82	1.15965	0.512
4-3-2/M82	0.9366	1
4-3/M82	0.91403	1
5-3/M82	0.97387	1
6-2/M82	0.931	1
6-3/M82	0.98044	1
7-1/M82	0.97083	1
7-2/M82	1.00769	1
9-3-2/M82	0.71118	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.20782	0.365
IL2-6/WTpooled	1.05804	0.788
IL7-5/WTpooled	0.45242	N/A
IL7-3/WTpooled	1.01634	1
IL12-4/WTpooled	0.84762	0.581
IL1-4/WTpooled	1.08391	1
WT/WTpooled	0.90441	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	0.99185	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08878	0.846
DC3000/delta hrp 6h	1.26526	0.857
DC3000/delta hrp 12h	1.25434	1
DC3000/delta hrp 24h	1.0004	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.87879	0.141
DC3000 delta B/DC3000 delta AB	0.98832	0.983

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.86385	1
Exp 36h	0.8318	0.661
Exp 60h	0.81481	0.251

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96805	1
Var 0h	1.20883	0.782
Var 12h I row2-row1	0.84666	0.316
Var 12h NI row2-row1	0.9545	0.82
Var 36h I row2-row1	0.96813	1
Var 36h NI row2-row1	1.14048	1
Var 60h I row2-row1	1.16806	1
Var 60h NI row2-row1	1.03268	0.904
Time course 0hI-0hNI	0.92445	0.376
Time course 12hI-12hNI	0.97625	0.795
Time course 36hI-36hNI	0.87434	0.023
Time course 60hI-60hNI	0.43407	0.005

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)	1.95614	0.571
transgenic ySAMdc/azygous control (breaker)	1.0734	1
transgenic ySAMdc/azygous control (red)	1.35791	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03632	0.092

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.66041	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.81285	0.13
Manapal/WT (red)	1.3545	0.222