Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.17.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14226	0.851
27DAP/17DAP	1.2179	0.839
39DAP/27DAP	3.23487	0.027
41DAP/39DAP	2.57057	0.18
42DAP/41DAP	4.36128	0.022
43DAP/42DAP	2.98085	0.655
47DAP/43DAP	1.03257	0.879
52DAP/47DAP	0.51703	0.071
57DAP/52DAP	1.54769	0.894

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12351	0.5
17DAP/reference	1.3709	0.014
27DAP/reference	1.29663	0.061
39DAP/reference	1.45001	0.054
41DAP/reference	1.70361	0.016
42DAP/reference	1.72806	0.001
43DAP/reference	1.75737	0.007
47DAP/reference	1.72516	0.007
52DAP/reference	1.16209	0.242
57DAP/reference	1.42707	0.056

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.21765	0.241
27DAP/17DAP	0.85859	0.279
39DAP/27DAP	7.97887	0.016
41DAP/39DAP	0.2238	0.013
42DAP/41DAP	3.90751	0.002
43DAP/42DAP	4.7492	0.013
47DAP/43DAP	0.85124	0.325
52DAP/47DAP	1.0208	0.925
57DAP/52DAP	1.38431	0.153
57DAP/7DAP	7.73678	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.36568	0.082
17DAP/reference	0.25663	0.012
27DAP/reference	0.15378	0.01
39DAP/reference	0.81736	0.146
41DAP/reference	0.32907	0.02
42DAP/reference	0.98036	0.415
43DAP/reference	2.15464	0.013
47DAP/reference	2.36971	0.035
52DAP/reference	0.77323	0.061
57DAP/reference	0.70456	0.024

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02578	0.623
17DAP/reference	1.62005	0.012
27DAP/reference	1.36027	0.055
39DAP/reference	1.19412	0.182
41DAP/reference	1.07081	0.536
42DAP/reference	1.2641	0.039
43DAP/reference	1.02151	0.298
47DAP/reference	1.21553	0.008
52DAP/reference	1.25711	0.24
57DAP/reference	1.33841	0.409

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.2559	0.034
17DAP/reference	1.15586	0.348
27DAP/reference	0.1453	0.02
39DAP/reference	0.49243	0.025
41DAP/reference	0.60693	0.043
42DAP/reference	4.43297	0.008
43DAP/reference	4.11252	0.008
47DAP/reference	1.75636	0.006
52DAP/reference	3.78659	0.03
57DAP/reference	0.82222	0.089

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.69803	0.672
26DAP/20DAP	0.91039	1
34DAP/26DAP	0.98764	0.898
51DAP/34DAP	0.87808	0.667
52DAP/51DAP	0.93796	1
53DAP/52DAP	0.80485	0.621
55DAP/53DAP	0.91546	0.761
57DAP/55DAP	1.24174	0.975
62DAP/57DAP	1.21245	0.515
68DAP/62DAP	0.82675	0.7
68DAP/14DAP	0.89376	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	52.9931	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.13749	0.016
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.04985
Mature Eggplant/Ripe Tomato	0.03094	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.10857	0.591
1-1-2/M82	1.31926	1
12-2/M82	1.06391	1
12-4/M82	1.32974	1
1-3/M82	2.43136	0.479
2-1-1/M82	0.92814	0.683
2-1/M82	0.91182	1
2-6/M82	0.98723	1
3-2/M82	1.19753	0.717
4-1-1/M82	0.7539	1
4-1/M82	2.45215	0.853
4-3-2/M82	0.97478	1
4-3/M82	0.95726	1
5-3/M82	1.02877	1
6-2/M82	0.98567	1
6-3/M82	0.90784	1
7-1/M82	1.01383	1
7-2/M82	0.99619	1
9-3-2/M82	0.73896	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.87815	0.247
IL2-6/WTpooled	1.04328	0.46
IL7-5/WTpooled	0.24032
IL7-3/WTpooled	0.89459	1
IL12-4/WTpooled	0.99052	1
IL1-4/WTpooled	0.92844	0.834
WT/WTpooled	1.117	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	1.08071	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.17193	0.875
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.30313	1
DC3000/delta hrp 24h	0.62869	0.036

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.54933	0.081
DC3000 delta B/DC3000 delta AB	1.01744	0.677

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
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	0.95826
Var 0h	1.06542	1
Var 12h I row2-row1	0.98404	1
Var 12h NI row2-row1	0.90204	0.82
Var 36h I row2-row1	1.10069	1
Var 36h NI row2-row1	1.00737	1
Var 60h I row2-row1	1.01436	1
Var 60h NI row2-row1	1.14837	0.904
Time course 0hI-0hNI	0.93604	0.639
Time course 12hI-12hNI	0.79527	0.111
Time course 36hI-36hNI	0.9753	0.533
Time course 60hI-60hNI	0.56926	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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	0.94119	1
transgenic ySAMdc/azygous control (red)	0.91763	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.96137	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.5708	1
Manapal/WT (red)	0.74878	0.188