Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.13.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16265	0.63
27DAP/17DAP	1.10397	0.849
39DAP/27DAP	0.89243	0.549
41DAP/39DAP	1.11626	0.494
42DAP/41DAP	1.02279	1
43DAP/42DAP	1.17745	0.94
47DAP/43DAP	0.95885	0.799
52DAP/47DAP	1.02668	0.982
57DAP/52DAP	0.95633	0.952

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98563	0.601
17DAP/reference	0.97179	0.567
27DAP/reference	1.00912	0.782
39DAP/reference	0.99261	0.874
41DAP/reference	1.06247	0.022
42DAP/reference	0.9557	0.054
43DAP/reference	0.99634	0.882
47DAP/reference	1.02093	0.666
52DAP/reference	0.97586	0.475
57DAP/reference	1.05567	0.405

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0389	0.749
27DAP/17DAP	0.99567	0.943
39DAP/27DAP	1.03977	0.659
41DAP/39DAP	0.98253	0.98
42DAP/41DAP	0.97562	0.751
43DAP/42DAP	1.00522	0.746
47DAP/43DAP	1.00946	0.914
52DAP/47DAP	0.99451	0.962
57DAP/52DAP	1.01081	0.992
57DAP/7DAP	0.9918	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91016	0.058
17DAP/reference	0.8979	0.028
27DAP/reference	0.96868	0.215
39DAP/reference	0.90507	0.034
41DAP/reference	0.91657	0.027
42DAP/reference	0.89558	0.013
43DAP/reference	0.95875	0.305
47DAP/reference	0.90442	0.222
52DAP/reference	0.81871	0.02
57DAP/reference	0.85462	0.034

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95856	0.399
17DAP/reference	1.02436	0.69
27DAP/reference	0.93978	0.188
39DAP/reference	0.96973	0.359
41DAP/reference	0.9745	0.364
42DAP/reference	0.96543	0.392
43DAP/reference	1.08356	0.121
47DAP/reference	1.05373	0.095
52DAP/reference	0.98691	0.433
57DAP/reference	0.98355	0.61

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86974	0.045
17DAP/reference	0.94152	0.108
27DAP/reference	0.84311	0.034
39DAP/reference	0.96424	0.328
41DAP/reference	0.91418	0.07
42DAP/reference	0.90372	0.087
43DAP/reference	0.84416	0.023
47DAP/reference	1.00868	1
52DAP/reference	1.03862	0.657
57DAP/reference	0.92669	0.059

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03087	0.966
26DAP/20DAP	1.00502	1
34DAP/26DAP	1.01461	1
51DAP/34DAP	1.1019	0.511
52DAP/51DAP	0.98227	1
53DAP/52DAP	0.9407	0.715
55DAP/53DAP	0.94845	0.225
57DAP/55DAP	1.01646	0.898
62DAP/57DAP	1.00816	1
68DAP/62DAP	1.10156	0.285
68DAP/14DAP	1.17042	0.311

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.96183	0.239

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.8407	0.329
Mature Green Tomato/Ripe Tomato	0.415
Immature Eggplant/Mature Eggplant	0.96576	0.72
Ripe Pepper/Ripe Tomato	0.41766	0.224
Mature Eggplant/Ripe Tomato	0.22868	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.93934	0.944
1-1-2/M82	1.00126	1
12-2/M82	0.90936	0.955
12-4/M82	0.86798	1
1-3/M82	1.01118	1
2-1-1/M82	0.88718	0.784
2-1/M82	1.0346	1
2-6/M82	0.95854	1
3-2/M82	0.97053	1
4-1-1/M82	1.03885	1
4-1/M82	0.86166	0.737
4-3-2/M82	1.09718	1
4-3/M82	0.92985	0.72
5-3/M82	0.98693	1
6-2/M82	0.90319	1
6-3/M82	1.00905	1
7-1/M82	0.82087	1
7-2/M82	0.95579	0.796
9-3-2/M82	1.03163	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.16263	0.277
IL2-6/WTpooled	0.96466	1
IL7-5/WTpooled	1.05371	1
IL7-3/WTpooled	1.05657	1
IL12-4/WTpooled	1.0201	1
IL1-4/WTpooled	1.27612	1
WT/WTpooled	0.98236	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	0.97004	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.15809	0.692
DC3000/delta hrp 6h	1.26089	1
DC3000/delta hrp 12h	0.97261	1
DC3000/delta hrp 24h	1.02909	0.728

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.044	0.515
DC3000 delta B/DC3000 delta AB	0.97356	0.693

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03635	1
Exp 36h	1.17315	1
Exp 60h	1.30452	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96925	1
Var 0h	1.21436	0.594
Var 12h I row2-row1	1.14798	0.211
Var 12h NI row2-row1	0.94613	0.82
Var 36h I row2-row1	0.95333	1
Var 36h NI row2-row1	1.02366	1
Var 60h I row2-row1	1.34732	0.562
Var 60h NI row2-row1	1.06109	1
Time course 0hI-0hNI	1.08091	0.852
Time course 12hI-12hNI	1.03311	0.854
Time course 36hI-36hNI	0.85073	0.142
Time course 60hI-60hNI	0.92465	0.319

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)	0.96613	0.614
transgenic ySAMdc/azygous control (breaker)	0.69141	0.142
transgenic ySAMdc/azygous control (red)	1.13681	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97103	0.077

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.7993	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.74933	0.172
Manapal/WT (break)	0.57982	0.299
Manapal/WT (red)	0.81172	0.181