Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.6.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.73527	0.148
27DAP/17DAP	1.04006	1
39DAP/27DAP	1.10277	1
41DAP/39DAP	0.85941	0.47
42DAP/41DAP	1.23365	0.647
43DAP/42DAP	1.02305	1
47DAP/43DAP	0.99696	0.904
52DAP/47DAP	1.02798	0.875
57DAP/52DAP	0.8435	0.759

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76502	0.039
17DAP/reference	0.99812	1
27DAP/reference	0.9211	0.047
39DAP/reference	1.02051	0.889
41DAP/reference	0.978	0.667
42DAP/reference	1.12367	0.093
43DAP/reference	1.53778	0.006
47DAP/reference	1.70387	0.001
52DAP/reference	1.16794	0.021
57DAP/reference	1.1274	0.239

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1939	0.515
27DAP/17DAP	1.13801	0.836
39DAP/27DAP	1.06091	0.596
41DAP/39DAP	0.96348	0.959
42DAP/41DAP	1.14471	0.947
43DAP/42DAP	1.03373	1
47DAP/43DAP	0.98408	0.93
52DAP/47DAP	0.97239	0.886
57DAP/52DAP	1.04407	0.997
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.32463	0.351
17DAP/reference	0.70868	0.017
27DAP/reference	1.17105	0.551
39DAP/reference	1.12013	0.314
41DAP/reference	0.92459	0.284
42DAP/reference	0.97236	0.482
43DAP/reference	1.29052	0.148
47DAP/reference	1.01569	1
52DAP/reference	1.24755	0.066
57DAP/reference	1.24529	0.147

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83971	0.046
17DAP/reference	0.76824	0.006
27DAP/reference	0.8748	0.076
39DAP/reference	0.72007	0.012
41DAP/reference	0.91696	0.231
42DAP/reference	0.88763	0.035
43DAP/reference	0.86725	0.128
47DAP/reference	1.03128	0.675
52DAP/reference	0.80227	0.021
57DAP/reference	0.95692	0.408

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.65591	0.048
17DAP/reference	0.80337	0.342
27DAP/reference	0.74538
39DAP/reference	0.79398	0.011
41DAP/reference	1.55386	0.019
42DAP/reference	1.32212	0.021
43DAP/reference	1.70145	0.007
47DAP/reference	2.56434	0.005
52DAP/reference	2.74655	0.044
57DAP/reference	1.14624	0.706

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93862	1
26DAP/20DAP	0.98119	1
34DAP/26DAP	0.97877	0.988
51DAP/34DAP	0.93751	0.785
52DAP/51DAP	1.17193	0.492
53DAP/52DAP	1.29499	0.783
55DAP/53DAP	1.3508	0.842
57DAP/55DAP	1.42627	0.311
62DAP/57DAP	0.44755	0.003
68DAP/62DAP	0.79251	0.314
68DAP/14DAP	0.86856	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.46214	0.105

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.69913	0.187
Mature Green Tomato/Ripe Tomato	0.9518	0.66
Immature Eggplant/Mature Eggplant	0.75201	0.074
Ripe Pepper/Ripe Tomato	0.20556	0.224
Mature Eggplant/Ripe Tomato	6.37631	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.91061	1
12-2/M82	N/A	N/A
12-4/M82	1.43215
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.99178
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.01364	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.90338
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.88399
IL12-4/WTpooled	0.69984
IL1-4/WTpooled	0.75097
WT/WTpooled	1.05154	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	0.78223	0.163

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02881	0.921
DC3000/delta hrp 6h	1.13354	1
DC3000/delta hrp 12h	0.92388	1
DC3000/delta hrp 24h	1.21855	0.192

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	0.93989	1
Exp 36h	1.15439	1
Exp 60h	1.18891	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95577	1
Var 0h	0.90837	0.198
Var 12h I row2-row1	1.06045	0.692
Var 12h NI row2-row1	0.96685	0.82
Var 36h I row2-row1	1.06829	1
Var 36h NI row2-row1	0.93215	0.706
Var 60h I row2-row1	0.82106	0.582
Var 60h NI row2-row1	0.78425	0.904
Time course 0hI-0hNI	1.01713	0.867
Time course 12hI-12hNI	0.98183	0.897
Time course 36hI-36hNI	1.07218	0.401
Time course 60hI-60hNI	1.52302	0.009

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)	0.81166	0.409
transgenic ySAMdc/azygous control (breaker)	0.73579	0.251
transgenic ySAMdc/azygous control (red)	1.02568	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01339	0.587

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.11573	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.67297	0.105
Manapal/WT (break)	1.19734	0.381
Manapal/WT (red)	1.22949	0.222