Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.15.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.76148	0.324
27DAP/17DAP	1.19004	0.857
39DAP/27DAP	0.99022	0.798
41DAP/39DAP	1.20414	0.67
42DAP/41DAP	1.17975	0.931
43DAP/42DAP	0.9136	0.865
47DAP/43DAP	1.21094	0.715
52DAP/47DAP	0.7734	0.461
57DAP/52DAP	1.30511	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8385	0.038
17DAP/reference	1.02135	0.717
27DAP/reference	1.01774	0.831
39DAP/reference	1.04466	0.149
41DAP/reference	0.97302	0.667
42DAP/reference	0.82502	0.007
43DAP/reference	0.91004	0.222
47DAP/reference	0.91732	0.083
52DAP/reference	1.00447	0.668
57DAP/reference	1.01917	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90738	0.323
27DAP/17DAP	1.33676	0.471
39DAP/27DAP	1.14428	0.436
41DAP/39DAP	1.18408	0.807
42DAP/41DAP	0.85088	0.213
43DAP/42DAP	1.07313	0.585
47DAP/43DAP	0.90836	0.395
52DAP/47DAP	0.9914	0.917
57DAP/52DAP	0.93049	0.532
57DAP/7DAP	1.05173	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13879	0.311
17DAP/reference	1.37688	0.017
27DAP/reference	1.05056	0.664
39DAP/reference	1.35298	0.062
41DAP/reference	1.3629	0.093
42DAP/reference	1.17257	0.889
43DAP/reference	1.37362	0.012
47DAP/reference	1.13256	0.822
52DAP/reference	1.24661	0.081
57DAP/reference	1.21906	0.053

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9423	0.487
17DAP/reference	0.84145	0.016
27DAP/reference	0.78267	0.069
39DAP/reference	0.88731	0.156
41DAP/reference	0.77721	0.035
42DAP/reference	0.89017	0.15
43DAP/reference	0.79709	0.09
47DAP/reference	0.89564	0.046
52DAP/reference	0.9348	0.093
57DAP/reference	0.99058	0.72

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14939	0.142
17DAP/reference	0.96574	0.55
27DAP/reference	1.16318	0.061
39DAP/reference	1.07011	0.422
41DAP/reference	0.93574	0.371
42DAP/reference	1.01745	1
43DAP/reference	0.95655	0.484
47DAP/reference	0.92229	0.357
52DAP/reference	1.08629	0.601
57DAP/reference	0.85777	0.092

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95345	1
26DAP/20DAP	0.83541	0.512
34DAP/26DAP	0.88523	0.771
51DAP/34DAP	1.24755	0.511
52DAP/51DAP	0.8576	1
53DAP/52DAP	1.12776	0.697
55DAP/53DAP	1.12533	0.28
57DAP/55DAP	1.3193	0.955
62DAP/57DAP	1.46585	0.833
68DAP/62DAP	0.97223	0.787
68DAP/14DAP	0.50694	0.09

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.54243

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.40401	0.085
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	0.53565	0.084
Ripe Pepper/Ripe Tomato	18.4914	0.256
Mature Eggplant/Ripe Tomato	11.4378

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.93936
12-2/M82	1.14017
12-4/M82	1.90565
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	N/A	N/A
3-2/M82	0.80526
4-1-1/M82	1.09958
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	0.85965	1
6-2/M82	N/A	N/A
6-3/M82	0.88974
7-1/M82	N/A	N/A
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	0.89541	0.321
IL2-6/WTpooled	0.84293
IL7-5/WTpooled	0.59596	0.279
IL7-3/WTpooled	1.00195	1
IL12-4/WTpooled	0.65257	0.71
IL1-4/WTpooled	0.9326	0.834
WT/WTpooled	0.95807	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	0.96022	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.90922	1
DC3000/delta hrp 6h	1.1701	1
DC3000/delta hrp 12h	0.62642	1
DC3000/delta hrp 24h	6.61457	0.018

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.971	1
DC3000 delta B/DC3000 delta AB	0.76433	0.045

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.11146	1
Exp 36h	0.67706	0.406
Exp 60h	0.71156	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00497	1
Var 0h	1.03181	1
Var 12h I row2-row1	0.7523	0.363
Var 12h NI row2-row1	0.68311	0.546
Var 36h I row2-row1	0.65268	0.805
Var 36h NI row2-row1	0.95936	0.791
Var 60h I row2-row1	1.0504	1
Var 60h NI row2-row1	1.18465	0.904
Time course 0hI-0hNI	1.1386	0.833
Time course 12hI-12hNI	0.9216	0.312
Time course 36hI-36hNI	0.79258	0.03
Time course 60hI-60hNI	0.34104	0.006

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)	1.09345	0.863
transgenic ySAMdc/azygous control (breaker)	1.43285	0.165
transgenic ySAMdc/azygous control (red)	1.04742	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.89598	0.049

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.08286	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.44668	0.096
Manapal/WT (break)	1.19147	0.183
Manapal/WT (red)	1.05565	1