Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.11.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96663	0.713
27DAP/17DAP	0.86851	0.677
39DAP/27DAP	0.74244	0.286
41DAP/39DAP	1.41397	0.293
42DAP/41DAP	0.98244	1
43DAP/42DAP	0.9639	0.887
47DAP/43DAP	0.8911	0.634
52DAP/47DAP	1.29477	0.401
57DAP/52DAP	1.01677	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19821	0.567
17DAP/reference	1.07111	0.528
27DAP/reference	1.15894	0.696
39DAP/reference	0.94646	0.554
41DAP/reference	1.00947	0.814
42DAP/reference	0.94018	0.099
43DAP/reference	0.98786	0.84
47DAP/reference	0.87168	0.046
52DAP/reference	0.80788	0.223
57DAP/reference	0.86221	0.027

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99549	0.847
27DAP/17DAP	1.0041	1
39DAP/27DAP	1.0642	0.615
41DAP/39DAP	1.02902	0.921
42DAP/41DAP	1.03939	0.893
43DAP/42DAP	1.03087	0.627
47DAP/43DAP	1.02779	0.805
52DAP/47DAP	1.03692	0.883
57DAP/52DAP	1.02334	0.891
57DAP/7DAP	1.03874

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99574	0.613
17DAP/reference	1.00035	1
27DAP/reference	0.97555	0.215
39DAP/reference	1.01089	0.601
41DAP/reference	0.9809	0.341
42DAP/reference	0.9736	0.09
43DAP/reference	1.01774	0.241
47DAP/reference	0.91743	0.101
52DAP/reference	0.96735	0.398
57DAP/reference	0.96888	0.367

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00975	0.863
17DAP/reference	0.87866	0.208
27DAP/reference	1.00066	0.79
39DAP/reference	0.9137	0.144
41DAP/reference	1.02223	1
42DAP/reference	0.96407	0.594
43DAP/reference	0.98987	0.721
47DAP/reference	0.96332	0.097
52DAP/reference	0.94317	0.078
57DAP/reference	0.99428	0.789

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95371	0.135
17DAP/reference	0.95757	0.243
27DAP/reference	0.94916	0.049
39DAP/reference	0.96575	0.058
41DAP/reference	0.9719	0.293
42DAP/reference	0.90458	0.049
43DAP/reference	0.93022	0.11
47DAP/reference	0.91478	0.049
52DAP/reference	0.9203	0.16
57DAP/reference	0.89675	0.069

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95252	0.841
26DAP/20DAP	0.96193	1
34DAP/26DAP	0.98224	0.98
51DAP/34DAP	1.03067	0.814
52DAP/51DAP	1.05947	0.439
53DAP/52DAP	0.68965
55DAP/53DAP	0.96144
57DAP/55DAP	1.00407	0.96
62DAP/57DAP	1.23882	0.445
68DAP/62DAP	1.14981	0.616
68DAP/14DAP	0.95541	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.9637	0.466

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.38939	0.068
Mature Green Tomato/Ripe Tomato	0.96185	0.66
Immature Eggplant/Mature Eggplant	0.79999	0.223
Ripe Pepper/Ripe Tomato	1.10243	1
Mature Eggplant/Ripe Tomato	4.33953

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95582	0.944
1-1-2/M82	0.97393	0.958
12-2/M82	0.97015	0.955
12-4/M82	0.97791	0.619
1-3/M82	0.92488	0.441
2-1-1/M82	1.0614	0.764
2-1/M82	N/A	N/A
2-6/M82	0.95999	1
3-2/M82	1.01472	1
4-1-1/M82	1.01674	1
4-1/M82	0.90768	1
4-3-2/M82	0.88377	0.698
4-3/M82	0.9729	0.611
5-3/M82	1.0096	1
6-2/M82	1.00539	1
6-3/M82	0.99662	1
7-1/M82	0.96235	0.443
7-2/M82	0.96786	0.881
9-3-2/M82	0.93894	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.8293	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.00276	1
IL12-4/WTpooled	1.14878	0.532
IL1-4/WTpooled	1.09164	1
WT/WTpooled	1.02907	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	0.92364	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94311	1
DC3000/delta hrp 6h	1.06484	1
DC3000/delta hrp 12h	1.06949	1
DC3000/delta hrp 24h	0.95996	0.7

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.07218	0.313
DC3000 delta B/DC3000 delta AB	1.00286	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.06122	1
Exp 36h	1.57757	0.349
Exp 60h	1.49996	0.205

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9856	1
Var 0h	0.46602	0.332
Var 12h I row2-row1	1.07987	0.406
Var 12h NI row2-row1	1.12465	1
Var 36h I row2-row1	0.87457	0.805
Var 36h NI row2-row1	0.92585	0.522
Var 60h I row2-row1	1.36111	1
Var 60h NI row2-row1	1.08921	0.904
Time course 0hI-0hNI	1.06374	0.852
Time course 12hI-12hNI	1.04472	0.738
Time course 36hI-36hNI	0.94237	0.33
Time course 60hI-60hNI	0.97404	0.646

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)	1.23993	0.297
transgenic ySAMdc/azygous control (breaker)	0.96492	1
transgenic ySAMdc/azygous control (red)	0.84363	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.34419	0.083
Manapal/WT (break)	1.11706	1
Manapal/WT (red)	0.83879	0.242