Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.16.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02827	0.961
27DAP/17DAP	1.03171	1
39DAP/27DAP	1.11221	0.906
41DAP/39DAP	0.99572	0.887
42DAP/41DAP	0.93185	1
43DAP/42DAP	1.00621	0.937
47DAP/43DAP	1.23661	0.609
52DAP/47DAP	1.05066	0.96
57DAP/52DAP	1.25093	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96632	0.465
17DAP/reference	1.02368	0.492
27DAP/reference	0.98334	0.623
39DAP/reference	0.98414	0.75
41DAP/reference	0.88191	0.114
42DAP/reference	0.89551	0.002
43DAP/reference	1.01031	0.787
47DAP/reference	0.99299	0.568
52DAP/reference	0.97633	0.427
57DAP/reference	0.93139	0.308

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98567	0.75
27DAP/17DAP	1.05989	0.706
39DAP/27DAP	1.01993	0.77
41DAP/39DAP	1.03187	0.817
42DAP/41DAP	0.99755	0.884
43DAP/42DAP	0.9759	0.466
47DAP/43DAP	1.01539	0.892
52DAP/47DAP	1.0019	1
57DAP/52DAP	1.0268	0.874
57DAP/7DAP	1.03676	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99482	0.758
17DAP/reference	1.08485	0.574
27DAP/reference	1.06325	0.974
39DAP/reference	1.24387	0.314
41DAP/reference	1.13471	0.177
42DAP/reference	0.96647	0.482
43DAP/reference	1.1109	0.569
47DAP/reference	0.98809	0.671
52DAP/reference	1.03121	0.886
57DAP/reference	0.84453	0.047

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99203	0.848
17DAP/reference	0.90409	0.047
27DAP/reference	0.96656	0.381
39DAP/reference	0.90432	0.095
41DAP/reference	0.87182	0.042
42DAP/reference	0.91843	0.05
43DAP/reference	0.90892	0.196
47DAP/reference	0.99132	0.487
52DAP/reference	0.92692	0.034
57DAP/reference	0.95358	0.259

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03923	1
17DAP/reference	1.02594	0.887
27DAP/reference	0.88375	0.085
39DAP/reference	1.08563	0.422
41DAP/reference	0.93822	0.371
42DAP/reference	0.91821	0.22
43DAP/reference	1.09983	0.426
47DAP/reference	0.95912	0.335
52DAP/reference	1.13979	0.312
57DAP/reference	0.85148	0.031

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98995	1
26DAP/20DAP	0.97994	1
34DAP/26DAP	1.00145	1
51DAP/34DAP	1.05254	0.458
52DAP/51DAP	0.99898	1
53DAP/52DAP	1.02466	0.91
55DAP/53DAP	0.97116	0.746
57DAP/55DAP	1.0653	0.865
62DAP/57DAP	1.0415	1
68DAP/62DAP	0.95293	0.769
68DAP/14DAP	0.9985	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.97379	0.547

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.425	0.089
Mature Green Tomato/Ripe Tomato	0.96815	0.611
Immature Eggplant/Mature Eggplant	1.13541	0.259
Ripe Pepper/Ripe Tomato	0.77935	0.293
Mature Eggplant/Ripe Tomato	2.49993	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00407	1
1-1-2/M82	0.99053	1
12-2/M82	0.93323	0.955
12-4/M82	1.04641	1
1-3/M82	0.89835	0.33
2-1-1/M82	1.03124	0.689
2-1/M82	1.34703	1
2-6/M82	1.02053	1
3-2/M82	1.03284
4-1-1/M82	1.14716
4-1/M82	1.10296	0.418
4-3-2/M82	1.09669	1
4-3/M82	1.01989	1
5-3/M82	1.02783	1
6-2/M82	0.9982	1
6-3/M82	1.07553	1
7-1/M82	0.63409
7-2/M82	0.9397	1
9-3-2/M82	0.95276	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.0698	0.277
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.18025	0.635
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.9423	1
IL1-4/WTpooled	0.93512
WT/WTpooled	1.10953

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	0.82429	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02285	0.921
DC3000/delta hrp 6h	1.25453	1
DC3000/delta hrp 12h	0.98671	1
DC3000/delta hrp 24h	1.16892	0.085

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.21093	0.042
DC3000 delta B/DC3000 delta AB	1.17019	0.24

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.13921	1
Exp 36h	1.02949	1
Exp 60h	1.30125	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0348	1
Var 0h	1.01382	1
Var 12h I row2-row1	1.2	0.189
Var 12h NI row2-row1	1.15684	1
Var 36h I row2-row1	1.03136	1
Var 36h NI row2-row1	0.90683	0.743
Var 60h I row2-row1	1.13374	1
Var 60h NI row2-row1	1.04297	1
Time course 0hI-0hNI	1.06618	0.852
Time course 12hI-12hNI	0.99168	1
Time course 36hI-36hNI	1.0001	0.783
Time course 60hI-60hNI	1.41595	0.008

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)	0.9785	0.662
transgenic ySAMdc/azygous control (breaker)	1.30294	0.248
transgenic ySAMdc/azygous control (red)	1.20118	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03305	0.247

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.91435	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.95966	1
Manapal/WT (break)	0.8101	0.333
Manapal/WT (red)	0.89623	0.229