Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.16.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.75143	0.226
27DAP/17DAP	0.55289	0.05
39DAP/27DAP	0.51092	0.146
41DAP/39DAP	0.74796	0.195
42DAP/41DAP	0.81148	1
43DAP/42DAP	1.32562	0.629
47DAP/43DAP	1.38664	0.293
52DAP/47DAP	0.97832	0.754
57DAP/52DAP	0.8866	0.784

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88073	0.2
17DAP/reference	0.96857	0.419
27DAP/reference	1.04878	0.232
39DAP/reference	1.04815	0.249
41DAP/reference	1.004	1
42DAP/reference	0.97753	0.326
43DAP/reference	1.01222	0.928
47DAP/reference	0.99667	0.674
52DAP/reference	0.91083	0.292
57DAP/reference	0.98139	0.58

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95314	0.542
27DAP/17DAP	1.03088	0.915
39DAP/27DAP	1.04398	0.654
41DAP/39DAP	0.93244	0.822
42DAP/41DAP	0.99085	0.841
43DAP/42DAP	1.06425	0.478
47DAP/43DAP	1.04762	0.873
52DAP/47DAP	0.97763	0.905
57DAP/52DAP	0.92684	0.424
57DAP/7DAP	0.91996	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8169	0.086
17DAP/reference	0.97785	0.338
27DAP/reference	0.91648	0.042
39DAP/reference	0.89608	0.073
41DAP/reference	0.94613	0.194
42DAP/reference	0.91291	0.048
43DAP/reference	0.96416	0.305
47DAP/reference	0.89714	0.222
52DAP/reference	0.82791	0.017
57DAP/reference	0.89833	0.061

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96405	0.58
17DAP/reference	1.06924	0.415
27DAP/reference	0.9055	0.212
39DAP/reference	0.82278	0.079
41DAP/reference	1.06485	0.781
42DAP/reference	0.93152	0.261
43DAP/reference	1.02711	0.865
47DAP/reference	0.95606	0.184
52DAP/reference	0.97021	0.327
57DAP/reference	0.94927	0.208

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84862	0.087
17DAP/reference	0.97312	0.615
27DAP/reference	0.94735	0.195
39DAP/reference	0.84661	0.021
41DAP/reference	0.92125	0.264
42DAP/reference	0.88161	0.134
43DAP/reference	0.90843	0.116
47DAP/reference	1.18581	0.06
52DAP/reference	1.00353	0.821
57DAP/reference	0.95688	0.387

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.88821	0.585
26DAP/20DAP	0.88104	0.512
34DAP/26DAP	0.93094	0.816
51DAP/34DAP	0.96371	0.77
52DAP/51DAP	0.96878	1
53DAP/52DAP	1.02385	0.935
55DAP/53DAP	1.0824	0.898
57DAP/55DAP	0.92923	0.715
62DAP/57DAP	0.88518	0.681
68DAP/62DAP	1.03978	0.984
68DAP/14DAP	0.85318	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.89194	0.253

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	3.03537	0.015
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	0.89139	0.907
1-1-2/M82	0.90772	0.958
12-2/M82	1.07169	1
12-4/M82	1.12941	0.611
1-3/M82	0.75496	0.378
2-1-1/M82	1.14013	1
2-1/M82	1.75674
2-6/M82	1.0981	0.695
3-2/M82	0.86882
4-1-1/M82	1.06753	1
4-1/M82	1.16418
4-3-2/M82	0.9748
4-3/M82	0.74336	0.611
5-3/M82	0.93522	0.642
6-2/M82	0.83074	1
6-3/M82	0.96015	1
7-1/M82	1.13892	1
7-2/M82	1.04462	1
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	1.18008	0.46
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.85929	0.31
IL12-4/WTpooled	1.08187	0.737
IL1-4/WTpooled	0.6664
WT/WTpooled	1.0057	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	3.72818	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01534	0.921
DC3000/delta hrp 6h	4.0629
DC3000/delta hrp 12h	1.24065	1
DC3000/delta hrp 24h	1.17748	0.283

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.6252	0.042
DC3000 delta B/DC3000 delta AB	1.12861	0.335

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.2439	1
Exp 36h	2.12874	0.489
Exp 60h	2.17806	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96766	1
Var 0h	0.81221	0.933
Var 12h I row2-row1	1.13323	0.222
Var 12h NI row2-row1	0.99373	1
Var 36h I row2-row1	0.96146	1
Var 36h NI row2-row1	0.94614	0.645
Var 60h I row2-row1	0.9775	0.952
Var 60h NI row2-row1	1.10718	0.904
Time course 0hI-0hNI	1.15047	0.63
Time course 12hI-12hNI	1.15548	0.347
Time course 36hI-36hNI	1.65393	0.006
Time course 60hI-60hNI	3.21124	0.008

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)	1.0561	0.789
transgenic ySAMdc/azygous control (breaker)	0.65043	0.173
transgenic ySAMdc/azygous control (red)	1.01929	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00231	0.909

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.78754	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.87723	1
Manapal/WT (break)	0.63877	0.299
Manapal/WT (red)	1.43454	0.413