Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.4.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17127	0.365
27DAP/17DAP	0.7922	0.373
39DAP/27DAP	1.37647	0.735
41DAP/39DAP	1.29264	0.691
42DAP/41DAP	0.94769	1
43DAP/42DAP	0.97381	0.925
47DAP/43DAP	0.91325	0.634
52DAP/47DAP	1.06367	0.848
57DAP/52DAP	1.08047	0.982

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92202	0.326
17DAP/reference	1.00753	1
27DAP/reference	0.98308	0.763
39DAP/reference	1.2543	0.077
41DAP/reference	0.9438	0.667
42DAP/reference	1.82345	0.002
43DAP/reference	N/A	N/A
47DAP/reference	1.40612	0.096
52DAP/reference	1.02178	1
57DAP/reference	0.80017	0.479

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1935	0.278
27DAP/17DAP	0.85078	0.508
39DAP/27DAP	1.06392	0.874
41DAP/39DAP	1.07755	0.883
42DAP/41DAP	0.92166	0.508
43DAP/42DAP	0.83965	0.132
47DAP/43DAP	0.96671	0.843
52DAP/47DAP	1.11469	0.742
57DAP/52DAP	0.78203	0.201
57DAP/7DAP	0.87675	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81076	0.168
17DAP/reference	0.91697	0.22
27DAP/reference	1.56693	0.008
39DAP/reference	0.76013	0.031
41DAP/reference	0.99733	0.646
42DAP/reference	1.16701	0.308
43DAP/reference	0.64569	0.015
47DAP/reference	0.83721	0.293
52DAP/reference	0.73971	0.021
57DAP/reference	0.56707	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.37892	0.213
17DAP/reference	1.86626	0.018
27DAP/reference	2.59718	0.013
39DAP/reference	1.71192	0.027
41DAP/reference	1.94954	0.009
42DAP/reference	1.93272	0.009
43DAP/reference	3.3703	0.009
47DAP/reference	1.936	0.008
52DAP/reference	1.35347	0.145
57DAP/reference	1.43413	0.277

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19496	0.23
17DAP/reference	1.14699	0.638
27DAP/reference	0.9338	0.302
39DAP/reference	0.95768	0.43
41DAP/reference	1.59806	0.044
42DAP/reference	2.13324	0.007
43DAP/reference	1.57632	0.107
47DAP/reference	1.39464	0.007
52DAP/reference	1.33829	0.088
57DAP/reference	2.17272	0.013

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.92533	1
26DAP/20DAP	1.00938	1
34DAP/26DAP	1.40175	1
51DAP/34DAP	1.45786	0.281
52DAP/51DAP	1.15163	0.313
53DAP/52DAP	1.10683	0.502
55DAP/53DAP	1.20519	0.312
57DAP/55DAP	0.91116	0.698
62DAP/57DAP	2.16206
68DAP/62DAP	0.91549	0.641
68DAP/14DAP	0.81208	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.59499	0.061

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.36156	0.108
Mature Green Tomato/Ripe Tomato	3.06128	0.026
Immature Eggplant/Mature Eggplant	1.33787
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99954	1
1-1-2/M82	1.30203
12-2/M82	N/A	N/A
12-4/M82	1.03388	1
1-3/M82	0.90518	0.501
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.79861	1
3-2/M82	1.02446
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.72351	0.698
4-3/M82	N/A	N/A
5-3/M82	0.97435	1
6-2/M82	0.73752
6-3/M82	N/A	N/A
7-1/M82	0.70885
7-2/M82	0.9016	0.417
9-3-2/M82	0.57155	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.13452	0.277
IL2-6/WTpooled	0.8488	0.473
IL7-5/WTpooled	0.95785	1
IL7-3/WTpooled	1.15236	1
IL12-4/WTpooled	1.03534	1
IL1-4/WTpooled	1.03322	1
WT/WTpooled	1.03096	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	0.82141	0.256

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96874	1
DC3000/delta hrp 6h	0.97396	0.95
DC3000/delta hrp 12h	0.88387	1
DC3000/delta hrp 24h	0.85185	0.241

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.12059	1
Exp 36h	0.76892	0.749
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.16544
Var 0h	0.46872	1
Var 12h I row2-row1	1.40422
Var 12h NI row2-row1	0.64692	0.906
Var 36h I row2-row1	0.8305	0.805
Var 36h NI row2-row1	1.23512
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	1.04134	1
Time course 0hI-0hNI	0.8936	0.233
Time course 12hI-12hNI	1.0985	0.122
Time course 36hI-36hNI	1.11119	0.513
Time course 60hI-60hNI	1.09843	0.254

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)	0.79598	0.3
transgenic ySAMdc/azygous control (breaker)	1.78599	0.248
transgenic ySAMdc/azygous control (red)	1.41757	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01259	0.723

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.28856	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.86618	0.088
Manapal/WT (break)	1.59366	1
Manapal/WT (red)	2.54932	0.137