Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.4.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10731	0.951
27DAP/17DAP	1.17433	0.845
39DAP/27DAP	1.05504	0.927
41DAP/39DAP	1.00115	0.962
42DAP/41DAP	1.08691	0.912
43DAP/42DAP	1.12183	0.954
47DAP/43DAP	1.01392	0.953
52DAP/47DAP	0.99903	0.967
57DAP/52DAP	1.38898	0.843

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.34648	0.105
17DAP/reference	0.96347	0.664
27DAP/reference	0.81148	0.187
39DAP/reference	0.87725	0.324
41DAP/reference	0.87325	0.341
42DAP/reference	0.87134	0.081
43DAP/reference	1.03435	0.787
47DAP/reference	0.89868	0.05
52DAP/reference	0.82853	0.019
57DAP/reference	0.93633	0.395

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93132	0.578
27DAP/17DAP	1.26383	0.453
39DAP/27DAP	1.42784	0.378
41DAP/39DAP	1.6056	0.407
42DAP/41DAP	0.94035	0.684
43DAP/42DAP	0.97906	0.854
47DAP/43DAP	0.87411	0.554
52DAP/47DAP	1.03482	0.986
57DAP/52DAP	1.26797	0.162
57DAP/7DAP	2.22527	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13628	0.11
17DAP/reference	1.18062	0.162
27DAP/reference	1.09998	0.301
39DAP/reference	1.3411	0.015
41DAP/reference	1.10252	0.475
42DAP/reference	1.49517	0.016
43DAP/reference	1.36835	0.048
47DAP/reference	1.26383	0.152
52DAP/reference	1.33174	0.041
57DAP/reference	1.10619	0.288

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1044	0.903
17DAP/reference	0.81056	0.025
27DAP/reference	1.35161	0.021
39DAP/reference	1.08013	0.602
41DAP/reference	1.03056	0.878
42DAP/reference	1.07844	0.466
43DAP/reference	1.04471	1
47DAP/reference	1.35988	0.084
52DAP/reference	0.76779	0.023
57DAP/reference	1.11323	0.755

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10541	0.397
17DAP/reference	0.97135	0.615
27DAP/reference	1.18052	0.216
39DAP/reference	1.22206	0.032
41DAP/reference	1.09231	0.754
42DAP/reference	1.12012	0.73
43DAP/reference	1.43949	0.034
47DAP/reference	0.99936	0.61
52DAP/reference	1.12528	0.257
57DAP/reference	1.19057	0.491

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.901	1
26DAP/20DAP	0.99587	1
34DAP/26DAP	0.77305	0.192
51DAP/34DAP	0.88116	0.442
52DAP/51DAP	0.82994	1
53DAP/52DAP	0.80277	0.106
55DAP/53DAP	0.90049	0.478
57DAP/55DAP	1.08926	0.728
62DAP/57DAP	1.01683	1
68DAP/62DAP	1.35815	0.533
68DAP/14DAP	0.96243	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.56567	0.025

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.93764	0.774
Immature Eggplant/Mature Eggplant	1.26467	0.05
Ripe Pepper/Ripe Tomato	1.43866	0.258
Mature Eggplant/Ripe Tomato	3.14151	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.83153
1-1-2/M82	0.95371
12-2/M82	N/A	N/A
12-4/M82	1.04078	1
1-3/M82	1.39233
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.73375	1
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.76453	0.551
5-3/M82	1.10838	1
6-2/M82	0.80965
6-3/M82	0.97324
7-1/M82	1.22567
7-2/M82	1.24998
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	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	0.87937
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	0.94254	0.256

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03355	0.921
DC3000/delta hrp 6h	0.705	0.706
DC3000/delta hrp 12h	0.98926	1
DC3000/delta hrp 24h	1.25184	0.054

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	4.97127
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.67915	1
Exp 60h	0.86321	0.754

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	N/A	N/A
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)	0.92287	0.348
transgenic ySAMdc/azygous control (breaker)	1.01066	1
transgenic ySAMdc/azygous control (red)	1.00258	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01235	0.619

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.15401	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.70444	0.172
Manapal/WT (break)	0.87905	1
Manapal/WT (red)	1.0164	1