Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.13.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08366	0.812
27DAP/17DAP	0.81346	0.72
39DAP/27DAP	0.73382	0.482
41DAP/39DAP	0.97198	0.911
42DAP/41DAP	2.186	0.556
43DAP/42DAP	1.03964	0.94
47DAP/43DAP	1.12634	0.926
52DAP/47DAP	1.34505	0.984
57DAP/52DAP	0.76082	0.726

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79288	0.03
17DAP/reference	0.78624	0.011
27DAP/reference	0.79411	0.013
39DAP/reference	1.01654	0.874
41DAP/reference	0.97109	0.434
42DAP/reference	0.78946	0.013
43DAP/reference	0.98997	0.805
47DAP/reference	0.81894	0.007
52DAP/reference	0.75375	0.041
57DAP/reference	0.89698	0.118

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.75944	0.065
27DAP/17DAP	1.32965	0.593
39DAP/27DAP	0.98646	0.925
41DAP/39DAP	1.00216	1
42DAP/41DAP	0.9327	0.708
43DAP/42DAP	1.15937	1
47DAP/43DAP	0.95408	0.796
52DAP/47DAP	0.93408	0.837
57DAP/52DAP	0.99436	0.869
57DAP/7DAP	0.95035	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80231	0.1
17DAP/reference	0.99884	0.693
27DAP/reference	1.03191	0.974
39DAP/reference	0.78684	0.056
41DAP/reference	0.86984	0.103
42DAP/reference	0.90532	0.2
43DAP/reference	1.03635	1
47DAP/reference	0.71029	0.057
52DAP/reference	0.87899	0.213
57DAP/reference	0.91406	0.162

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90249	0.318
17DAP/reference	0.59339	0.003
27DAP/reference	0.67011	0.015
39DAP/reference	0.55513	0.01
41DAP/reference	0.67207	0.038
42DAP/reference	0.87185	0.237
43DAP/reference	0.85141	0.147
47DAP/reference	0.92286	0.232
52DAP/reference	0.54189	0.003
57DAP/reference	0.60228	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82692	0.112
17DAP/reference	0.85708	0.262
27DAP/reference	1.30318	0.072
39DAP/reference	0.97084	0.544
41DAP/reference	0.98318	0.682
42DAP/reference	1.28727	0.373
43DAP/reference	0.80773	0.137
47DAP/reference	0.57929	0.004
52DAP/reference	0.9839	0.675
57DAP/reference	0.83617	0.138

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98173	1
26DAP/20DAP	1.29735	0.826
34DAP/26DAP	0.96762	0.94
51DAP/34DAP	1.11156	0.692
52DAP/51DAP	0.9159	1
53DAP/52DAP	1.15688	0.697
55DAP/53DAP	1.09378	0.608
57DAP/55DAP	0.90392	0.587
62DAP/57DAP	1.32	0.185
68DAP/62DAP	1.00636	0.885
68DAP/14DAP	1.56534	0.558

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.93809	0.422

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.94986
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.91532
1-1-2/M82	1.08782
12-2/M82	N/A	N/A
12-4/M82	0.88949	1
1-3/M82	0.74291
2-1-1/M82	0.82074
2-1/M82	N/A	N/A
2-6/M82	0.9634	1
3-2/M82	N/A	N/A
4-1-1/M82	0.65912
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.84968
5-3/M82	0.95548	1
6-2/M82	N/A	N/A
6-3/M82	0.93818	0.982
7-1/M82	0.91942
7-2/M82	0.93613	0.796
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	0.7015	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.29806	0.362
IL12-4/WTpooled	1.22061	0.525
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	0.98005	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	0.7982	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98133	1
DC3000/delta hrp 6h	1.21208	1
DC3000/delta hrp 12h	0.56134	1
DC3000/delta hrp 24h	1.00391	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.64144
DC3000 delta B/DC3000 delta AB	1.09139	0.558

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
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	1.07257	1
Var 0h	0.6865	0.374
Var 12h I row2-row1	1.11088	0.209
Var 12h NI row2-row1	0.91918	0.82
Var 36h I row2-row1	0.79311	0.805
Var 36h NI row2-row1	0.66927	1
Var 60h I row2-row1	1.17274	0.288
Var 60h NI row2-row1	0.78165	1
Time course 0hI-0hNI	1.00232	1
Time course 12hI-12hNI	1.01734	1
Time course 36hI-36hNI	1.01546	1
Time course 60hI-60hNI	1.08588	1

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)	0.77722	0.324
transgenic ySAMdc/azygous control (breaker)	1.25272	0.248
transgenic ySAMdc/azygous control (red)	1.35894	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01104	0.495

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.43803	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.75462	1
Manapal/WT (break)	0.73028	0.333
Manapal/WT (red)	0.7556	0.181