Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-2.1.9.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.12518	0.932
27DAP/17DAP	1.43125	0.854
39DAP/27DAP	0.83091	0.529
41DAP/39DAP	1.22164	0.619
42DAP/41DAP	1.23846	0.647
43DAP/42DAP	1.20285	0.918
47DAP/43DAP	1.31087	0.474
52DAP/47DAP	1.20486	0.757
57DAP/52DAP	0.96134	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82693	0.035
17DAP/reference	1.11663	0.282
27DAP/reference	0.92469	0.457
39DAP/reference	0.95317	0.587
41DAP/reference	0.933	0.434
42DAP/reference	0.81275	0.02
43DAP/reference	0.98962	0.785
47DAP/reference	0.88779	0.06
52DAP/reference	0.88227	0.215
57DAP/reference	0.82602	0.106

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09055	0.774
27DAP/17DAP	1.08842	0.794
39DAP/27DAP	0.85751	0.377
41DAP/39DAP	0.926	0.875
42DAP/41DAP	1.09981	0.961
43DAP/42DAP	1.06204	0.83
47DAP/43DAP	1.34632	0.848
52DAP/47DAP	0.68417	0.05
57DAP/52DAP	0.97503	0.768
57DAP/7DAP	1.30421	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05451	0.691
17DAP/reference	0.978	0.192
27DAP/reference	0.89059	0.01
39DAP/reference	0.97653	0.307
41DAP/reference	0.93249	0.259
42DAP/reference	0.98952	0.554
43DAP/reference	0.9619	0.368
47DAP/reference	0.97829	0.671
52DAP/reference	0.94504	0.09
57DAP/reference	0.95885	0.083

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11722	0.495
17DAP/reference	1.37542	0.303
27DAP/reference	1.55176	0.016
39DAP/reference	0.84873	0.14
41DAP/reference	0.98659	0.519
42DAP/reference	0.80316	0.261
43DAP/reference	1.01923	0.929
47DAP/reference	1.07169	0.377
52DAP/reference	0.85584	0.302
57DAP/reference	0.94038	0.488

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93056	0.05
17DAP/reference	0.98698	0.647
27DAP/reference	1.0085	0.903
39DAP/reference	0.91107	0.063
41DAP/reference	0.98139	0.237
42DAP/reference	0.88338	0.22
43DAP/reference	0.98887	0.685
47DAP/reference	0.75508	0.097
52DAP/reference	0.86999	0.184
57DAP/reference	0.83773	0.171

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.074	0.966
26DAP/20DAP	1.03483	0.941
34DAP/26DAP	1.53273	0.304
51DAP/34DAP	1.04161	0.883
52DAP/51DAP	0.89559	1
53DAP/52DAP	0.84921	0.817
55DAP/53DAP	0.91404	0.784
57DAP/55DAP	1.07401	0.947
62DAP/57DAP	1.42113	0.833
68DAP/62DAP	1.12672	1
68DAP/14DAP	2.58126	0.384

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.09513	0.865

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	9.42379	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	5.68013	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	1.04564	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	1.18469	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	N/A	N/A
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	1.13988	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.21556	0.846
DC3000/delta hrp 6h	0.75361	0.95
DC3000/delta hrp 12h	1.06859	1
DC3000/delta hrp 24h	0.65461	0.037

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.26793	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.90345	1
Exp 36h	0.90772	0.82
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00899	1
Var 0h	0.81831	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	1.14081	1
Var 36h I row2-row1	0.98231	N/A
Var 36h NI row2-row1	0.563	0.645
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	3.46715	0.904
Time course 0hI-0hNI	1.0205	0.852
Time course 12hI-12hNI	1.0795	0.672
Time course 36hI-36hNI	0.74553	0.052
Time course 60hI-60hNI	0.50226	0.026

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)	0.98863	0.862
transgenic ySAMdc/azygous control (breaker)	0.71443	0.251
transgenic ySAMdc/azygous control (red)	0.95741	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02343	0.35

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.90778	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.09034	1
Manapal/WT (break)	1.10504	1
Manapal/WT (red)	1.35237	0.222