Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.16.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.54807	0.101
27DAP/17DAP	1.61413	0.532
39DAP/27DAP	1.50696	0.378
41DAP/39DAP	0.58273	0.046
42DAP/41DAP	1.74036	0.126
43DAP/42DAP	1.94477	0.595
47DAP/43DAP	2.31395	0.188
52DAP/47DAP	1.46673	0.472
57DAP/52DAP	1.51866	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08378	0.093
17DAP/reference	0.92336	0.278
27DAP/reference	1.04888	0.139
39DAP/reference	1.04652	0.106
41DAP/reference	0.92086	0.341
42DAP/reference	1.02856	0.352
43DAP/reference	1.09089	0.05
47DAP/reference	1.48709	0.002
52DAP/reference	1.24506	0.05
57DAP/reference	1.16859	0.039

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04467	0.65
27DAP/17DAP	1.02689	0.938
39DAP/27DAP	0.95396	0.507
41DAP/39DAP	0.94406	0.849
42DAP/41DAP	1.06562	0.615
43DAP/42DAP	0.99228	0.928
47DAP/43DAP	1.01164	0.914
52DAP/47DAP	0.97833	0.905
57DAP/52DAP	1.00626	1
57DAP/7DAP	1.02445	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88167
17DAP/reference	0.93073	0.031
27DAP/reference	0.97139	0.375
39DAP/reference	1.00923	0.538
41DAP/reference	1.00671	1
42DAP/reference	1.14689	0.012
43DAP/reference	1.01965	0.603
47DAP/reference	0.90993	0.079
52DAP/reference	1.04384	0.941
57DAP/reference	1.02074	0.746

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02222	0.724
17DAP/reference	0.99458	0.747
27DAP/reference	1.0666	0.704
39DAP/reference	0.94881	0.178
41DAP/reference	0.9601	0.384
42DAP/reference	0.95776	0.089
43DAP/reference	1.00974	0.957
47DAP/reference	0.97089	0.41
52DAP/reference	0.8933	0.005
57DAP/reference	1.03404	0.737

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94166	0.05
17DAP/reference	0.933	0.071
27DAP/reference	0.92312	0.031
39DAP/reference	0.91888	0.122
41DAP/reference	0.98004	0.417
42DAP/reference	1.02179	0.863
43DAP/reference	0.98868	0.639
47DAP/reference	1.13085	0.104
52DAP/reference	1.23552	0.116
57DAP/reference	1.34141	0.018

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97595	1
26DAP/20DAP	1.00727	1
34DAP/26DAP	0.97474	0.936
51DAP/34DAP	0.98062	0.883
52DAP/51DAP	1.07782	0.534
53DAP/52DAP	1.15834	0.37
55DAP/53DAP	0.99913	0.939
57DAP/55DAP	1.0642	0.881
62DAP/57DAP	1.65319	0.8
68DAP/62DAP	0.95556	0.747
68DAP/14DAP	1.33784	0.17

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.64535	0.064

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.57835	0.193
Mature Green Tomato/Ripe Tomato	0.28215	0.017
Immature Eggplant/Mature Eggplant	1.32602	0.239
Ripe Pepper/Ripe Tomato	0.09298	0.224
Mature Eggplant/Ripe Tomato	0.08954	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92214	0.907
1-1-2/M82	0.95811	0.754
12-2/M82	0.95605	0.955
12-4/M82	1.00911	1
1-3/M82	1.10172	1
2-1-1/M82	0.88532	0.465
2-1/M82	0.95266	1
2-6/M82	0.95271	1
3-2/M82	1.03747	0.967
4-1-1/M82	1.00755	1
4-1/M82	1.47113	0.853
4-3-2/M82	0.94868	1
4-3/M82	0.96183	1
5-3/M82	0.98882	1
6-2/M82	0.9254	1
6-3/M82	1.02137	1
7-1/M82	0.96169	1
7-2/M82	0.93106	0.796
9-3-2/M82	1.32474	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	1.0947
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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00758	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.98253	1
DC3000/delta hrp 24h	0.98833	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.1951	0.042
DC3000 delta B/DC3000 delta AB	1.17945	0.206

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.87803	1
Exp 36h	N/A	N/A
Exp 60h	0.82249	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01697	1
Var 0h	1.27456	0.98
Var 12h I row2-row1	1.24654	0.215
Var 12h NI row2-row1	1.20116	1
Var 36h I row2-row1	1.01361	1
Var 36h NI row2-row1	0.83544	0.469
Var 60h I row2-row1	1.09915	1
Var 60h NI row2-row1	0.98825	1
Time course 0hI-0hNI	1.07731	0.867
Time course 12hI-12hNI	1.13655	0.43
Time course 36hI-36hNI	1.02378	0.975
Time course 60hI-60hNI	2.18611	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)	1.0693	0.798
transgenic ySAMdc/azygous control (breaker)	1.26823	0.178
transgenic ySAMdc/azygous control (red)	1.21847	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97704	0.27

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.10253	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.99518	0.14
Manapal/WT (break)	0.82527	1
Manapal/WT (red)	0.26784	0.181