Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.1.16.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09473	0.725
27DAP/17DAP	1.09864	0.873
39DAP/27DAP	1.13647	0.663
41DAP/39DAP	0.89418	0.566
42DAP/41DAP	1.00367	1
43DAP/42DAP	1.02583	0.937
47DAP/43DAP	1.24624	0.555
52DAP/47DAP	0.90609	0.702
57DAP/52DAP	0.94905	0.947

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13464	0.034
17DAP/reference	0.97636	0.393
27DAP/reference	0.97369	0.406
39DAP/reference	0.98529	0.885
41DAP/reference	1.02545	0.624
42DAP/reference	1.08835	0.002
43DAP/reference	0.98982	0.745
47DAP/reference	1.01882	0.773
52DAP/reference	1.01328	1
57DAP/reference	1.03265	0.332

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94156	0.336
27DAP/17DAP	1.01082	0.98
39DAP/27DAP	0.97154	0.703
41DAP/39DAP	1.08369	0.531
42DAP/41DAP	0.93927	0.429
43DAP/42DAP	0.92012
47DAP/43DAP	0.98884	0.947
52DAP/47DAP	0.92618	0.439
57DAP/52DAP	0.97496	0.665
57DAP/7DAP	0.91678	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05741
17DAP/reference	0.95338	0.056
27DAP/reference	0.91545	0.01
39DAP/reference	1.00767	0.909
41DAP/reference	1.08204	0.086
42DAP/reference	1.08623	0.037
43DAP/reference	1.07134	0.307
47DAP/reference	0.99819	1
52DAP/reference	1.02542	0.636
57DAP/reference	1.22964	0.571

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00887	0.874
17DAP/reference	1.06188	0.311
27DAP/reference	0.99917	0.79
39DAP/reference	1.00845	1
41DAP/reference	0.95741	0.373
42DAP/reference	1.0817	0.309
43DAP/reference	0.9861	0.67
47DAP/reference	1.08636	0.041
52DAP/reference	1.04008	0.053
57DAP/reference	1.05167	0.387

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.37122
17DAP/reference	1.03243	0.792
27DAP/reference	0.88979	0.025
39DAP/reference	0.93987	0.101
41DAP/reference	0.95492	0.237
42DAP/reference	0.95311	0.361
43DAP/reference	0.95276	0.294
47DAP/reference	1.03482	0.63
52DAP/reference	1.00946	1
57DAP/reference	1.01268	0.971

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93963	0.981
26DAP/20DAP	0.97231	1
34DAP/26DAP	1.05983	1
51DAP/34DAP	1.00163	0.967
52DAP/51DAP	1.00761	0.965
53DAP/52DAP	1.11686	0.334
55DAP/53DAP	0.98861	0.886
57DAP/55DAP	1.45534	0.492
62DAP/57DAP	0.97556	0.871
68DAP/62DAP	0.84878	0.429
68DAP/14DAP	0.92762	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.01304	0.954

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.98003	0.692
Mature Green Tomato/Ripe Tomato	1.06988	0.881
Immature Eggplant/Mature Eggplant	0.94858	0.72
Ripe Pepper/Ripe Tomato	0.2077
Mature Eggplant/Ripe Tomato	2.10364	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03665	1
1-1-2/M82	1.05166	1
12-2/M82	0.94078	0.955
12-4/M82	0.98162	0.619
1-3/M82	0.88838	0.378
2-1-1/M82	N/A	N/A
2-1/M82	1.02262
2-6/M82	0.91334	1
3-2/M82	0.96448	1
4-1-1/M82	1.02157	1
4-1/M82	1.09993	1
4-3-2/M82	0.97137	1
4-3/M82	0.9201	0.72
5-3/M82	0.95109	0.642
6-2/M82	1.01182	1
6-3/M82	1.03772	1
7-1/M82	1.15588	1
7-2/M82	1.00278	1
9-3-2/M82	1.01287	1

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	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	1.02971	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00109	1
DC3000/delta hrp 6h	1.0759	1
DC3000/delta hrp 12h	0.99431	1
DC3000/delta hrp 24h	1.05715	0.422

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.09201	0.25
DC3000 delta B/DC3000 delta AB	1.06182	0.524

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88469	1
Exp 36h	0.91453	0.539
Exp 60h	0.99521	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.90839	1
Var 0h	0.59462	0.782
Var 12h I row2-row1	1.06163	0.406
Var 12h NI row2-row1	0.9066	0.488
Var 36h I row2-row1	1.03809	1
Var 36h NI row2-row1	0.95085	0.791
Var 60h I row2-row1	1.05508	0.562
Var 60h NI row2-row1	1.24467	0.904
Time course 0hI-0hNI	1.01202	1
Time course 12hI-12hNI	1.03396	0.754
Time course 36hI-36hNI	0.91987	0.274
Time course 60hI-60hNI	1.08331	0.137

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)	0.89069	0.377
transgenic ySAMdc/azygous control (breaker)	1.39046	0.248
transgenic ySAMdc/azygous control (red)	1.41326	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98112	0.404

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.45618	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.04837	1
Manapal/WT (break)	1.09298	0.381
Manapal/WT (red)	1.42837	0.222