Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.20.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14074	0.755
27DAP/17DAP	1.47049	0.809
39DAP/27DAP	0.97564	0.749
41DAP/39DAP	0.6266	0.294
42DAP/41DAP	1.14783	1
43DAP/42DAP	1.57147	0.505
47DAP/43DAP	1.31605	0.702
52DAP/47DAP	1.12287	0.946
57DAP/52DAP	0.93562	0.956

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95255	0.432
17DAP/reference	1.01029	0.653
27DAP/reference	1.00656	1
39DAP/reference	1.0295	0.534
41DAP/reference	0.9124	0.267
42DAP/reference	0.9413	0.075
43DAP/reference	1.00659	0.942
47DAP/reference	0.96707	0.3
52DAP/reference	0.95901	0.405
57DAP/reference	0.94612	0.176

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96819	0.629
27DAP/17DAP	0.98549	0.887
39DAP/27DAP	1.03941	0.643
41DAP/39DAP	1.02182	0.921
42DAP/41DAP	1.02928	0.872
43DAP/42DAP	0.99379	0.991
47DAP/43DAP	1.01419	0.93
52DAP/47DAP	1.03737	0.835
57DAP/52DAP	1.05529	0.638
57DAP/7DAP	1.11108	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90076	0.27
17DAP/reference	0.89554	0.031
27DAP/reference	0.84402	0.012
39DAP/reference	1.00766	0.96
41DAP/reference	1.0613	0.475
42DAP/reference	1.03733	0.308
43DAP/reference	0.94538	0.145
47DAP/reference	0.94285	0.168
52DAP/reference	0.94715	0.278
57DAP/reference	0.93772	0.215

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95961	0.548
17DAP/reference	0.8692	0.016
27DAP/reference	0.86897	0.119
39DAP/reference	0.8286	0.147
41DAP/reference	0.85223	0.091
42DAP/reference	0.89385	0.032
43DAP/reference	0.87553	0.084
47DAP/reference	0.98376	0.338
52DAP/reference	0.92476	0.043
57DAP/reference	0.9053	0.079

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90462	0.104
17DAP/reference	0.98365	0.739
27DAP/reference	0.94827	0.195
39DAP/reference	0.89434	0.018
41DAP/reference	0.9089	0.264
42DAP/reference	0.83244	0.049
43DAP/reference	0.78758	0.098
47DAP/reference	0.96687	0.434
52DAP/reference	0.78892	0.132
57DAP/reference	0.73237	0.033

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01165	1
26DAP/20DAP	0.93803	0.512
34DAP/26DAP	0.99662	1
51DAP/34DAP	0.93784	0.571
52DAP/51DAP	0.95282	1
53DAP/52DAP	0.91062	0.426
55DAP/53DAP	0.90313	0.417
57DAP/55DAP	1.15099	0.584
62DAP/57DAP	0.95128	0.871
68DAP/62DAP	1.05422	0.991
68DAP/14DAP	1.10223	0.694

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.93564	0.322

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.62476	0.193
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	0.90063	0.912
Ripe Pepper/Ripe Tomato	1.4233	0.258
Mature Eggplant/Ripe Tomato	0.45935	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99668	1
1-1-2/M82	0.9092	1
12-2/M82	1.13651
12-4/M82	0.91999
1-3/M82	0.87025
2-1-1/M82	1.09569
2-1/M82	N/A	N/A
2-6/M82	1.10179	0.695
3-2/M82	N/A	N/A
4-1-1/M82	0.97	1
4-1/M82	1.06597
4-3-2/M82	1.23801
4-3/M82	0.86347
5-3/M82	0.98768	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.95274	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.06836	0.493
IL2-6/WTpooled	0.98779	1
IL7-5/WTpooled	1.28691	1
IL7-3/WTpooled	1.30816	1
IL12-4/WTpooled	1.08336	0.673
IL1-4/WTpooled	0.9058	0.834
WT/WTpooled	1.01976	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	1.03093	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05025	0.75
DC3000/delta hrp 6h	1.03018	0.95
DC3000/delta hrp 12h	1.18449	1
DC3000/delta hrp 24h	1.04543	0.516

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.11748	0.094
DC3000 delta B/DC3000 delta AB	1.08377	0.429

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.11096	0.228
Exp 36h	1.2958	0.693
Exp 60h	1.25117	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96542	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.11877	0.208
Var 12h NI row2-row1	0.96092	0.906
Var 36h I row2-row1	0.983	1
Var 36h NI row2-row1	0.876	0.584
Var 60h I row2-row1	1.33079	0.562
Var 60h NI row2-row1	0.93418	0.932
Time course 0hI-0hNI	1.06075	0.852
Time course 12hI-12hNI	1.06412	0.698
Time course 36hI-36hNI	1.04111	0.513
Time course 60hI-60hNI	1.32282	0.019

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)	1.03756	0.748
transgenic ySAMdc/azygous control (breaker)	0.94169	0.49
transgenic ySAMdc/azygous control (red)	0.96939	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98288	0.471

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.04849	0.277

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)	0.96982	1
Manapal/WT (red)	0.98034	0.863