Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.9.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99164	0.891
27DAP/17DAP	1.06956	0.873
39DAP/27DAP	0.70013	0.241
41DAP/39DAP	1.56291	0.303
42DAP/41DAP	0.90705	1
43DAP/42DAP	1.19082	0.867
47DAP/43DAP	1.07002	0.909
52DAP/47DAP	0.92135	0.758
57DAP/52DAP	1.09871	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93315	0.145
17DAP/reference	0.96862	0.503
27DAP/reference	0.99163	0.741
39DAP/reference	1.083	0.514
41DAP/reference	0.96932	0.542
42DAP/reference	0.9831	0.315
43DAP/reference	1.00077	0.924
47DAP/reference	0.99552	0.636
52DAP/reference	0.85238	0.035
57DAP/reference	0.94929	0.21

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13658	0.662
27DAP/17DAP	1.00059	1
39DAP/27DAP	0.98795	0.943
41DAP/39DAP	1.05591	0.65
42DAP/41DAP	1.017	0.999
43DAP/42DAP	1.00767	1
47DAP/43DAP	0.99783	0.998
52DAP/47DAP	0.99642	0.975
57DAP/52DAP	0.9366	0.436
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92636	0.224
17DAP/reference	1.00561	1
27DAP/reference	0.82838	0.013
39DAP/reference	0.93622	0.016
41DAP/reference	0.92963	0.166
42DAP/reference	0.89219	0.117
43DAP/reference	0.94625	0.22
47DAP/reference	0.89918	0.079
52DAP/reference	0.92746	0.115
57DAP/reference	1.00062	0.804

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03146	0.495
17DAP/reference	1.08481	0.338
27DAP/reference	0.97709	0.519
39DAP/reference	0.94226	0.392
41DAP/reference	0.97787	0.441
42DAP/reference	0.91208	0.089
43DAP/reference	0.92989	0.292
47DAP/reference	0.93684	0.094
52DAP/reference	1.04013	0.559
57DAP/reference	1.12528	0.06

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8305	0.049
17DAP/reference	0.98421	0.636
27DAP/reference	0.98016	0.539
39DAP/reference	0.90964	0.092
41DAP/reference	0.88941	0.119
42DAP/reference	0.77721	0.019
43DAP/reference	0.77529	0.029
47DAP/reference	0.97234	0.409
52DAP/reference	0.82328	0.177
57DAP/reference	0.76334	0.025

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99596	1
26DAP/20DAP	0.92599	1
34DAP/26DAP	1.06362	1
51DAP/34DAP	1.01038	0.978
52DAP/51DAP	0.97009	1
53DAP/52DAP	0.98904	0.978
55DAP/53DAP	1.08718	0.671
57DAP/55DAP	1.13102	0.274
62DAP/57DAP	0.98935	1
68DAP/62DAP	1.22768	0.589
68DAP/14DAP	0.83219	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.99118	0.737

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.86043	0.371
Mature Green Tomato/Ripe Tomato	1.00968	0.898
Immature Eggplant/Mature Eggplant	1.1133	0.088
Ripe Pepper/Ripe Tomato	1.21463	1
Mature Eggplant/Ripe Tomato	1.33005	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96678	0.961
1-1-2/M82	1.02753	1
12-2/M82	0.99745	1
12-4/M82	0.96213	1
1-3/M82	0.91546	0.501
2-1-1/M82	1.0769	0.764
2-1/M82	1.20908	0.335
2-6/M82	0.92592	1
3-2/M82	0.92509	1
4-1-1/M82	1.02453	0.968
4-1/M82	0.85554	1
4-3-2/M82	0.87909	1
4-3/M82	1.08617	1
5-3/M82	0.98923	1
6-2/M82	1.06489	1
6-3/M82	0.93168	0.916
7-1/M82	0.9956	1
7-2/M82	0.95678	0.519
9-3-2/M82	0.9027	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.87858	1
IL2-6/WTpooled	1.13582	0.584
IL7-5/WTpooled	0.5967	1
IL7-3/WTpooled	0.85076	0.418
IL12-4/WTpooled	0.92736	0.71
IL1-4/WTpooled	1.58617	1
WT/WTpooled	1.04693	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	1.08896	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97894	1
DC3000/delta hrp 6h	0.95058	0.95
DC3000/delta hrp 12h	0.98271	1
DC3000/delta hrp 24h	0.97569	0.897

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.96992	0.724
DC3000 delta B/DC3000 delta AB	1.04974	0.484

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0167	1
Exp 36h	1.07974	1
Exp 60h	1.29039	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02872	1
Var 0h	1.07685	1
Var 12h I row2-row1	1.08558	0.199
Var 12h NI row2-row1	1.00123	1
Var 36h I row2-row1	0.96272	1
Var 36h NI row2-row1	0.91721	0.45
Var 60h I row2-row1	1.02751	0.562
Var 60h NI row2-row1	1.05455	0.904
Time course 0hI-0hNI	1.07282	0.764
Time course 12hI-12hNI	1.03042	0.762
Time course 36hI-36hNI	1.02224	0.799
Time course 60hI-60hNI	1.00713	1

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)	0.99571	0.722
transgenic ySAMdc/azygous control (breaker)	0.78253	0.132
transgenic ySAMdc/azygous control (red)	0.95446	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9839	0.323

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.76608	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.01916	1
Manapal/WT (break)	0.89011	0.333
Manapal/WT (red)	0.70181	0.181