Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.12.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94674	0.671
27DAP/17DAP	1.09481	0.881
39DAP/27DAP	1.36032	0.745
41DAP/39DAP	0.91627	0.675
42DAP/41DAP	1.06332	0.978
43DAP/42DAP	0.99229	0.937
47DAP/43DAP	0.87656	0.595
52DAP/47DAP	1.23201	0.763
57DAP/52DAP	0.85678	0.783

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07495	0.403
17DAP/reference	0.9955	0.777
27DAP/reference	1.111	0.569
39DAP/reference	1.03657	0.747
41DAP/reference	0.92964	0.267
42DAP/reference	0.91708	0.081
43DAP/reference	0.95572	0.5
47DAP/reference	0.96795	0.345
52DAP/reference	0.99714	0.709
57DAP/reference	1.18225	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09113	0.812
27DAP/17DAP	1.03687	0.969
39DAP/27DAP	1.04196	0.824
41DAP/39DAP	0.82505	0.09
42DAP/41DAP	1.05228	0.893
43DAP/42DAP	0.89746	0.351
47DAP/43DAP	0.92207	0.447
52DAP/47DAP	0.93369	0.746
57DAP/52DAP	1.58393	0.204
57DAP/7DAP	1.22938	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27827	0.037
17DAP/reference	1.27973	0.007
27DAP/reference	1.39068	0.017
39DAP/reference	1.2139	0.025
41DAP/reference	1.14611	0.184
42DAP/reference	1.12641	0.132
43DAP/reference	1.17598	0.05
47DAP/reference	1.13585	0.241
52DAP/reference	0.99166	0.621
57DAP/reference	1.17532	0.198

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09265	0.516
17DAP/reference	0.99972	0.728
27DAP/reference	1.13111	0.271
39DAP/reference	0.95661	0.348
41DAP/reference	1.09133	0.737
42DAP/reference	1.16208	0.02
43DAP/reference	1.18962	0.15
47DAP/reference	1.11037	0.225
52DAP/reference	0.96308	0.5
57DAP/reference	1.03206	0.874

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16055	0.153
17DAP/reference	1.06555	0.72
27DAP/reference	1.23533	0.078
39DAP/reference	1.26106	0.01
41DAP/reference	1.16244	0.086
42DAP/reference	1.2229	0.08
43DAP/reference	1.00506	1
47DAP/reference	0.96044	0.396
52DAP/reference	1.5819	0.148
57DAP/reference	1.58958	0.111

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02145	1
26DAP/20DAP	1.09187	0.793
34DAP/26DAP	0.95078	0.94
51DAP/34DAP	1.16938	0.706
52DAP/51DAP	0.96979	1
53DAP/52DAP	1.3452	0.067
55DAP/53DAP	0.81398	0.149
57DAP/55DAP	1.056	1
62DAP/57DAP	0.69455	0.005
68DAP/62DAP	0.93962	0.769
68DAP/14DAP	1.06376	0.785

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.83779	0.102

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.84621	0.329
Mature Green Tomato/Ripe Tomato	1.16721	0.814
Immature Eggplant/Mature Eggplant	1.9161
Ripe Pepper/Ripe Tomato	2.62867
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.23476	0.277
IL2-6/WTpooled	0.67275	0.473
IL7-5/WTpooled	0.96731	1
IL7-3/WTpooled	1.24883	0.362
IL12-4/WTpooled	1.11105	0.785
IL1-4/WTpooled	0.81433	0.476
WT/WTpooled	1.19505	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	1.1896	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0478	0.921
DC3000/delta hrp 6h	1.09613	1
DC3000/delta hrp 12h	1.03166	1
DC3000/delta hrp 24h	1.52366	0.088

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.0235	0.648
DC3000 delta B/DC3000 delta AB	1.21396	0.274

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0026	1
Exp 36h	1.20359	0.489
Exp 60h	1.03956	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03425	1
Var 0h	1.01057	1
Var 12h I row2-row1	1.00126	1
Var 12h NI row2-row1	0.91228	0.906
Var 36h I row2-row1	1.13009	0.304
Var 36h NI row2-row1	0.78523	0.478
Var 60h I row2-row1	0.75956	0.287
Var 60h NI row2-row1	1.00868	1
Time course 0hI-0hNI	0.95501	0.699
Time course 12hI-12hNI	1.0636	0.615
Time course 36hI-36hNI	1.23273	0.005
Time course 60hI-60hNI	1.66517	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)	1.06498	0.297
transgenic ySAMdc/azygous control (breaker)	1.10651	1
transgenic ySAMdc/azygous control (red)	0.91587	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0036	0.854

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.92484	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.82815	0.172
Manapal/WT (break)	0.96959	1
Manapal/WT (red)	1.25979	0.413