Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.8.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07863	0.786
27DAP/17DAP	1.11032	0.88
39DAP/27DAP	0.97399	0.719
41DAP/39DAP	0.95254	0.802
42DAP/41DAP	1.08311	0.949
43DAP/42DAP	1.37509	0.388
47DAP/43DAP	0.91165	0.696
52DAP/47DAP	1.05096	0.976
57DAP/52DAP	0.95097	0.94

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0675	0.265
17DAP/reference	1.10336	0.148
27DAP/reference	0.93668	0.304
39DAP/reference	1.08346	0.089
41DAP/reference	1.00977	0.759
42DAP/reference	0.86933	0.027
43DAP/reference	1.09681	0.102
47DAP/reference	0.8783	0.005
52DAP/reference	0.99286	0.668
57DAP/reference	1.066	0.447

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83271	0.096
27DAP/17DAP	1.01222	1
39DAP/27DAP	0.93303	0.456
41DAP/39DAP	1.05738	0.807
42DAP/41DAP	0.97117	0.746
43DAP/42DAP	1.06963	0.094
47DAP/43DAP	1.10436	0.827
52DAP/47DAP	0.94585	0.839
57DAP/52DAP	1.09164	0.622
57DAP/7DAP	1.1554	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30217	0.04
17DAP/reference	1.37156	0.009
27DAP/reference	1.40947	0.009
39DAP/reference	1.37952	0.044
41DAP/reference	1.39957	0.121
42DAP/reference	1.26279	0.076
43DAP/reference	1.26472	0.148
47DAP/reference	1.19092	0.318
52DAP/reference	1.42721	0.046
57DAP/reference	1.39557	0.033

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17907	0.38
17DAP/reference	1.05193	0.69
27DAP/reference	1.06001	0.543
39DAP/reference	1.11407	0.489
41DAP/reference	1.02957	0.96
42DAP/reference	1.05533	0.466
43DAP/reference	1.18905	0.279
47DAP/reference	1.01317	0.965
52DAP/reference	1.10882	0.208
57DAP/reference	0.87541	0.058

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.50878	0.017
17DAP/reference	1.13725	0.518
27DAP/reference	1.27617	0.092
39DAP/reference	1.07026	0.377
41DAP/reference	1.08753	0.397
42DAP/reference	0.96417	0.552
43DAP/reference	0.95102	0.416
47DAP/reference	0.83907	0.013
52DAP/reference	0.96709	0.611
57DAP/reference	1.08329	0.57

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98263	1
26DAP/20DAP	1.07325	0.77
34DAP/26DAP	1.01485	1
51DAP/34DAP	0.96578	0.722
52DAP/51DAP	1.08573	0.651
53DAP/52DAP	0.9742	0.862
55DAP/53DAP	1.2468	0.629
57DAP/55DAP	1.07824	0.927
62DAP/57DAP	0.72946	0.162
68DAP/62DAP	1.9446	0.336
68DAP/14DAP	0.96864	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.86626	0.211

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.47504	0.058
Mature Green Tomato/Ripe Tomato	0.90733	0.487
Immature Eggplant/Mature Eggplant	0.78257	0.448
Ripe Pepper/Ripe Tomato	1.23467	1
Mature Eggplant/Ripe Tomato	1.95926	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01532	1
1-1-2/M82	1.0724	1
12-2/M82	0.89012	0.955
12-4/M82	1.00218	1
1-3/M82	0.78058	0.378
2-1-1/M82	1.10245	0.403
2-1/M82	N/A	N/A
2-6/M82	1.06345	0.329
3-2/M82	0.77171	0.455
4-1-1/M82	0.78179	1
4-1/M82	1.09401	1
4-3-2/M82	N/A	N/A
4-3/M82	0.96228	1
5-3/M82	0.99723	1
6-2/M82	0.99756	1
6-3/M82	0.9474	0.796
7-1/M82	0.89819
7-2/M82	0.98457	1
9-3-2/M82	0.9576	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.66935	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.75542	0.581
IL1-4/WTpooled	1.07113
WT/WTpooled	0.88275	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	1.05434	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98315	1
DC3000/delta hrp 6h	0.9937	0.95
DC3000/delta hrp 12h	0.99216	1
DC3000/delta hrp 24h	1.09412	0.516

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.80751	0.065
DC3000 delta B/DC3000 delta AB	0.85854	0.326

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.81091	1
Exp 36h	1.13397	1
Exp 60h	1.04669	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01774	1
Var 0h	0.9356	1
Var 12h I row2-row1	1.05164	0.692
Var 12h NI row2-row1	1.11001	0.34
Var 36h I row2-row1	1.1325	0.298
Var 36h NI row2-row1	0.7831	0.329
Var 60h I row2-row1	0.87649	0.582
Var 60h NI row2-row1	0.94894	1
Time course 0hI-0hNI	1.00416	1
Time course 12hI-12hNI	1.08113	0.256
Time course 36hI-36hNI	1.41371	0.009
Time course 60hI-60hNI	1.43409	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)	1.08599	0.261
transgenic ySAMdc/azygous control (breaker)	0.95526	1
transgenic ySAMdc/azygous control (red)	1.01109	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00317	0.854

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.73274	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.86992	1
Manapal/WT (break)	1.24717	1
Manapal/WT (red)	1.08625	1