Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.12.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94745	0.671
27DAP/17DAP	0.57557	0.037
39DAP/27DAP	0.79229	0.39
41DAP/39DAP	0.60102	0.05
42DAP/41DAP	1.05751	1
43DAP/42DAP	1.30654	0.682
47DAP/43DAP	0.5665	0.08
52DAP/47DAP	1.24102	0.76
57DAP/52DAP	1.07921	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13978	0.685
17DAP/reference	0.83656	0.079
27DAP/reference	0.83359	0.083
39DAP/reference	1.02488	0.855
41DAP/reference	0.87826	0.114
42DAP/reference	1.9205	0.001
43DAP/reference	3.357	0.009
47DAP/reference	4.24399	0.002
52DAP/reference	1.41527	0.079
57DAP/reference	1.55308	0.039

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.57148	0.036
27DAP/17DAP	0.84478	0.279
39DAP/27DAP	0.40489	0.031
41DAP/39DAP	1.43625	0.355
42DAP/41DAP	0.86337	0.149
43DAP/42DAP	0.56653	0.022
47DAP/43DAP	0.95801	0.677
52DAP/47DAP	1.01774	0.939
57DAP/52DAP	1.11947	0.335
57DAP/7DAP	0.4681	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97001	0.495
17DAP/reference	0.96767	0.447
27DAP/reference	1.02285	0.974
39DAP/reference	0.82906	0.095
41DAP/reference	1.08521	0.767
42DAP/reference	1.10015	0.889
43DAP/reference	1.12839	0.226
47DAP/reference	0.96344	0.671
52DAP/reference	0.83475	0.043
57DAP/reference	1.03378	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16661	0.495
17DAP/reference	1.33793	0.385
27DAP/reference	0.8955	0.304
39DAP/reference	1.21041	0.848
41DAP/reference	0.87724	0.284
42DAP/reference	1.02125	1
43DAP/reference	1.3688	0.058
47DAP/reference	0.99358	0.574
52DAP/reference	0.94903	0.302
57DAP/reference	1.20353

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10475	0.984
17DAP/reference	1.13015	0.578
27DAP/reference	0.9111	0.243
39DAP/reference	0.99175	0.693
41DAP/reference	0.88848	0.167
42DAP/reference	1.29474	0.097
43DAP/reference	1.45449	0.445
47DAP/reference	1.11001	0.519
52DAP/reference	1.04421	0.946
57DAP/reference	0.95712	0.516

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	N/A	N/A
26DAP/20DAP	0.97677	1
34DAP/26DAP	0.97247	0.945
51DAP/34DAP	0.86609	0.292
52DAP/51DAP	1.37026	0.035
53DAP/52DAP	0.93726	0.649
55DAP/53DAP	1.19274	0.066
57DAP/55DAP	0.92962	0.718
62DAP/57DAP	0.85116	0.871
68DAP/62DAP	1.28416	0.682
68DAP/14DAP	1.47404

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.04402	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.13926
Mature Green Tomato/Ripe Tomato	6.32776	0.015
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.4228
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	1.07025
12-2/M82	N/A	N/A
12-4/M82	0.97944
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	0.9635
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.18234	0.508
4-3/M82	1.35499
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.04609
7-2/M82	N/A	N/A
9-3-2/M82	1.28612	0.191

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	0.84472
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	0.8866	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.24187	0.758
DC3000/delta hrp 6h	1.2432	1
DC3000/delta hrp 12h	1.00388	1
DC3000/delta hrp 24h	2.01097	0.028

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.718	0.028
DC3000 delta B/DC3000 delta AB	0.52862	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.22529	1
Exp 36h	1.15964	1
Exp 60h	1.19351	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.92311	1
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.70895	0.315
transgenic ySAMdc/azygous control (breaker)	0.93689	1
transgenic ySAMdc/azygous control (red)	0.88929	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9331	0.052

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.28968	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.36121	0.14
Manapal/WT (break)	1.29953	0.183
Manapal/WT (red)	1.34607	1