Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.8.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.72887	0.211
27DAP/17DAP	1.80957	0.395
39DAP/27DAP	4.83022	0.02
41DAP/39DAP	2.20268	0.212
42DAP/41DAP	2.39129	0.023
43DAP/42DAP	2.48287	0.682
47DAP/43DAP	0.97139	0.847
52DAP/47DAP	0.61916	0.13
57DAP/52DAP	1.49197	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94307	0.3
17DAP/reference	1.29151	0.201
27DAP/reference	1.04429	1
39DAP/reference	1.18885	0.174
41DAP/reference	1.18547	0.085
42DAP/reference	1.2378	0.007
43DAP/reference	1.19423	0.021
47DAP/reference	1.10246	0.433
52DAP/reference	0.89043	0.079
57DAP/reference	0.96271	0.435

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.24708	0.492
27DAP/17DAP	0.9458	0.854
39DAP/27DAP	3.64628	0.035
41DAP/39DAP	0.40119	0.013
42DAP/41DAP	2.81039	0.008
43DAP/42DAP	4.0017	0.014
47DAP/43DAP	0.80135	0.145
52DAP/47DAP	1.0467	0.987
57DAP/52DAP	1.1088	0.708
57DAP/7DAP	3.52476	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99782	0.682
17DAP/reference	0.77004	0.22
27DAP/reference	1.05426	0.698
39DAP/reference	1.30358	0.077
41DAP/reference	1.11699	0.416
42DAP/reference	1.14519	0.686
43DAP/reference	1.43483	0.02
47DAP/reference	1.82175	0.014
52DAP/reference	1.30805	0.048
57DAP/reference	1.18108	0.087

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17214	0.384
17DAP/reference	1.35553	0.014
27DAP/reference	1.10675	0.292
39DAP/reference	1.00633	0.586
41DAP/reference	0.8687	0.315
42DAP/reference	1.29791	0.046
43DAP/reference	1.33229	0.144
47DAP/reference	1.12287	0.013
52DAP/reference	0.99045	0.619
57DAP/reference	1.24908	0.166

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1367	0.303
17DAP/reference	1.21092	0.354
27DAP/reference	0.88111
39DAP/reference	0.86695	0.199
41DAP/reference	0.87906	0.459
42DAP/reference	1.10834	0.775
43DAP/reference	1.18505	0.505
47DAP/reference	0.98887	0.61
52DAP/reference	0.94256	0.663
57DAP/reference	0.94187	0.43

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.24604	0.966
26DAP/20DAP	1.19135	0.442
34DAP/26DAP	1.31706	0.819
51DAP/34DAP	0.61281	0.197
52DAP/51DAP	1.20156	0.792
53DAP/52DAP	1.2503	0.901
55DAP/53DAP	0.94956	0.761
57DAP/55DAP	1.08303	0.61
62DAP/57DAP	1.2153	0.902
68DAP/62DAP	1.01563	0.834
68DAP/14DAP	1.18268	0.384

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	78.7917	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	7.48247
Mature Green Tomato/Ripe Tomato	0.09446	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.17396
Mature Eggplant/Ripe Tomato	0.48407

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.89787
1-1-2/M82	1.26516	0.977
12-2/M82	N/A	N/A
12-4/M82	1.26306	1
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	1.11337	0.967
4-1-1/M82	N/A	N/A
4-1/M82	1.85821	1
4-3-2/M82	0.92138	0.698
4-3/M82	N/A	N/A
5-3/M82	0.99864
6-2/M82	N/A	N/A
6-3/M82	0.82326
7-1/M82	0.99805
7-2/M82	1.08297
9-3-2/M82	0.60011	0.355

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	0.33446	0.581
IL1-4/WTpooled	2.13328
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	1.03725	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01679	0.921
DC3000/delta hrp 6h	1.20733	1
DC3000/delta hrp 12h	1.01021	1
DC3000/delta hrp 24h	0.93108	0.794

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
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	0.8277	0.24
Exp 36h	1.11093	1
Exp 60h	1.02461	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02883	1
Var 0h	1.30426	0.339
Var 12h I row2-row1	1.15163	0.283
Var 12h NI row2-row1	0.77711	1
Var 36h I row2-row1	1.42541	0.908
Var 36h NI row2-row1	0.82047	0.743
Var 60h I row2-row1	0.79571	0.582
Var 60h NI row2-row1	0.93308	1
Time course 0hI-0hNI	0.94171	0.738
Time course 12hI-12hNI	0.98864	0.964
Time course 36hI-36hNI	0.88767	0.169
Time course 60hI-60hNI	0.7095	0.006

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)	0.98384	0.314
transgenic ySAMdc/azygous control (breaker)	0.58148	0.131
transgenic ySAMdc/azygous control (red)	0.90634	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98102	0.237

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.55658	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.85695	0.172
Manapal/WT (break)	0.67714	0.299
Manapal/WT (red)	1.08096	0.413