Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.14.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96725	0.76
27DAP/17DAP	1.10022	0.859
39DAP/27DAP	1.09005	0.873
41DAP/39DAP	1.19049	0.797
42DAP/41DAP	0.86903	1
43DAP/42DAP	0.9646	0.909
47DAP/43DAP	1.1292	0.746
52DAP/47DAP	0.96817	0.851
57DAP/52DAP	0.94991	0.947

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.64932	0.044
17DAP/reference	0.47458	0.008
27DAP/reference	0.78111	0.092
39DAP/reference	0.60134	0.021
41DAP/reference	0.44121	0.009
42DAP/reference	0.80948	0.026
43DAP/reference	0.75079	0.017
47DAP/reference	0.96145	0.366
52DAP/reference	1.49583	0.05
57DAP/reference	1.40715	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82425	0.323
27DAP/17DAP	0.96958	0.878
39DAP/27DAP	1.13338	0.758
41DAP/39DAP	1.07425	0.849
42DAP/41DAP	1.17042	0.571
43DAP/42DAP	0.8896	0.351
47DAP/43DAP	1.03562	0.897
52DAP/47DAP	0.85323	0.345
57DAP/52DAP	0.97715	0.768
57DAP/7DAP	0.85631	0.143

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86194	0.115
17DAP/reference	1.17773	0.049
27DAP/reference	1.0993	0.049
39DAP/reference	0.97376	0.474
41DAP/reference	0.98568	0.538
42DAP/reference	1.05423	0.686
43DAP/reference	1.13764	0.035
47DAP/reference	1.0062	1
52DAP/reference	0.98778	0.621
57DAP/reference	1.0004	0.648

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.50223	0.009
17DAP/reference	0.4203	0.003
27DAP/reference	0.90856	0.304
39DAP/reference	0.97561	0.455
41DAP/reference	1.11845	0.335
42DAP/reference	0.99265	0.655
43DAP/reference	0.68901	0.082
47DAP/reference	0.67983	0.012
52DAP/reference	0.75938	0.007
57DAP/reference	0.40325	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87529	0.197
17DAP/reference	0.95886	0.579
27DAP/reference	1.45306	0.025
39DAP/reference	1.19249	0.151
41DAP/reference	1.23178	0.043
42DAP/reference	1.44928	0.076
43DAP/reference	1.34026	0.28
47DAP/reference	0.89206	0.269
52DAP/reference	1.02322	0.908
57DAP/reference	2.87793	0.009

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96128	1
26DAP/20DAP	1.02407	1
34DAP/26DAP	0.61497	0.093
51DAP/34DAP	0.93941	0.77
52DAP/51DAP	1.07215	0.836
53DAP/52DAP	0.99694	0.951
55DAP/53DAP	1.32487	0.375
57DAP/55DAP	0.9346	0.694
62DAP/57DAP	2.0785	0.303
68DAP/62DAP	14.0593	0.013
68DAP/14DAP	12.1656	0.019

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.72879	0.166

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.21414	0.073
Mature Green Tomato/Ripe Tomato	0.55412	0.019
Immature Eggplant/Mature Eggplant	2.93655	0.05
Ripe Pepper/Ripe Tomato	5.64891	0.258
Mature Eggplant/Ripe Tomato	6.02982

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.12223	1
1-1-2/M82	0.88622	1
12-2/M82	1.29425	1
12-4/M82	0.84913	1
1-3/M82	1.09665	1
2-1-1/M82	1.0626	0.457
2-1/M82	2.23641	0.312
2-6/M82	0.97067	1
3-2/M82	0.94408
4-1-1/M82	0.91553	1
4-1/M82	0.74267	1
4-3-2/M82	0.90783	1
4-3/M82	0.35048	0.475
5-3/M82	1.02248	1
6-2/M82	0.66874	0.481
6-3/M82	0.96126	1
7-1/M82	0.61324
7-2/M82	0.9056	0.796
9-3-2/M82	0.63229

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.01557	1
IL2-6/WTpooled	1.02258	1
IL7-5/WTpooled	1.01639	1
IL7-3/WTpooled	1.07661	0.362
IL12-4/WTpooled	0.93218	0.71
IL1-4/WTpooled	1.0532	1
WT/WTpooled	1.02086	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	1.01643	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.10121	0.921
DC3000/delta hrp 6h	1.15887	1
DC3000/delta hrp 12h	0.89758	1
DC3000/delta hrp 24h	0.99705	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.50157
DC3000 delta B/DC3000 delta AB	1.18823

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.82506	1
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	0.93154	1
Var 0h	0.92802	0.261
Var 12h I row2-row1	1.4648	0.473
Var 12h NI row2-row1	0.92541	0.546
Var 36h I row2-row1	0.8839	0.805
Var 36h NI row2-row1	1.3067	1
Var 60h I row2-row1	0.89763	0.306
Var 60h NI row2-row1	1.20084	0.904
Time course 0hI-0hNI	1.13964	0.413
Time course 12hI-12hNI	0.9749	0.889
Time course 36hI-36hNI	0.87462	0.054
Time course 60hI-60hNI	2.64902	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)	0.98656	0.862
transgenic ySAMdc/azygous control (breaker)	0.98169	1
transgenic ySAMdc/azygous control (red)	0.88159	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94802	0.237

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.65459	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.0517	1
Manapal/WT (break)	0.69467	1
Manapal/WT (red)	0.20282	0.181