Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.20.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02231	0.823
27DAP/17DAP	1.15604	0.91
39DAP/27DAP	1.09695	0.857
41DAP/39DAP	0.92942	0.766
42DAP/41DAP	1.06642	1
43DAP/42DAP	1.53696	1
47DAP/43DAP	0.75518	0.298
52DAP/47DAP	1.02528	0.994
57DAP/52DAP	1.10213	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00533	1
17DAP/reference	0.95761	0.278
27DAP/reference	0.93496	0.208
39DAP/reference	0.97157	0.6
41DAP/reference	0.94987	0.341
42DAP/reference	1.00298	1
43DAP/reference	0.94	0.17
47DAP/reference	1.01801	0.862
52DAP/reference	0.91446	0.108
57DAP/reference	0.96612	0.221

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98363	0.732
27DAP/17DAP	1.04599	0.811
39DAP/27DAP	1.04275	0.623
41DAP/39DAP	1.0273	0.849
42DAP/41DAP	0.99924	0.932
43DAP/42DAP	0.96451	0.466
47DAP/43DAP	0.97698	0.833
52DAP/47DAP	0.98147	0.902
57DAP/52DAP	1.03161	0.818
57DAP/7DAP	0.96116	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.32865	0.093
17DAP/reference	1.67951	0.006
27DAP/reference	1.5684	0.006
39DAP/reference	1.83679	0.006
41DAP/reference	1.5706	0.018
42DAP/reference	1.82434	0.008
43DAP/reference	2.19594	0.007
47DAP/reference	1.17396	0.604
52DAP/reference	1.832	0.007
57DAP/reference	1.88862	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02601	0.933
17DAP/reference	0.92862	0.039
27DAP/reference	0.94196	0.229
39DAP/reference	0.94361	0.129
41DAP/reference	0.91467	0.148
42DAP/reference	0.86177	0.022
43DAP/reference	0.94866	0.43
47DAP/reference	0.92889	0.12
52DAP/reference	0.92772	0.013
57DAP/reference	1.0242	0.771

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.46891	0.027
17DAP/reference	1.14549	0.558
27DAP/reference	1.50336	0.032
39DAP/reference	1.35026	0.018
41DAP/reference	1.39488	0.041
42DAP/reference	1.33479	0.117
43DAP/reference	1.44677	0.084
47DAP/reference	0.97877	0.509
52DAP/reference	1.72248	0.072
57DAP/reference	1.07346	0.801

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0281	0.966
26DAP/20DAP	1.04985	0.896
34DAP/26DAP	1.0954	0.819
51DAP/34DAP	0.9679	0.785
52DAP/51DAP	0.99961	1
53DAP/52DAP	1.05981	0.688
55DAP/53DAP	0.96068	0.675
57DAP/55DAP	1.12903	0.543
62DAP/57DAP	0.7403	0.088
68DAP/62DAP	1.10648	0.821
68DAP/14DAP	1.12429	0.802

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.02581	0.415

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.2128	0.176
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	1.10828	0.248
Ripe Pepper/Ripe Tomato	1.14854	1
Mature Eggplant/Ripe Tomato	1.27858	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97032	0.944
1-1-2/M82	0.77264	1
12-2/M82	0.9693	0.955
12-4/M82	0.97286	0.619
1-3/M82	1.00405	1
2-1-1/M82	0.88886	0.465
2-1/M82	1.30427	1
2-6/M82	0.97669	1
3-2/M82	1.00398
4-1-1/M82	0.92015	0.667
4-1/M82	0.90406
4-3-2/M82	0.66051
4-3/M82	0.9368	0.72
5-3/M82	1.08667	0.572
6-2/M82	1.01551	1
6-3/M82	1.06693	1
7-1/M82	0.90042
7-2/M82	0.86613	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.82576	0.484
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	0.98468	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00186	1
DC3000/delta hrp 6h	1.36599	1
DC3000/delta hrp 12h	0.9464	1
DC3000/delta hrp 24h	1.0491	0.467

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.1519	0.055
DC3000 delta B/DC3000 delta AB	1.09113	0.368

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.13571	1
Exp 36h	1.11934	1
Exp 60h	1.25844	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01535	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.1578	0.204
Var 12h NI row2-row1	1.02273	0.649
Var 36h I row2-row1	1.04193	1
Var 36h NI row2-row1	0.93008	0.645
Var 60h I row2-row1	1.00079	1
Var 60h NI row2-row1	1.00116	1
Time course 0hI-0hNI	1.04446	0.867
Time course 12hI-12hNI	1.0113	0.885
Time course 36hI-36hNI	1.15676	0.019
Time course 60hI-60hNI	1.4239	0.025

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)	1.02376	0.408
transgenic ySAMdc/azygous control (breaker)	1.09927	1
transgenic ySAMdc/azygous control (red)	1.15521	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96689	0.362

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87072	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.83487	1
Manapal/WT (break)	0.92223	1
Manapal/WT (red)	0.85548	0.229