Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.19.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82985	0.166
27DAP/17DAP	1.0393	1
39DAP/27DAP	1.45521	0.59
41DAP/39DAP	0.88796	0.545
42DAP/41DAP	1.15839	0.916
43DAP/42DAP	0.84241	0.776
47DAP/43DAP	0.9332	0.618
52DAP/47DAP	0.93891	0.8
57DAP/52DAP	1.0387	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88581	0.103
17DAP/reference	0.91874	0.278
27DAP/reference	0.95069	0.514
39DAP/reference	0.90244	0.292
41DAP/reference	0.87605	0.065
42DAP/reference	0.86083	0.01
43DAP/reference	0.87424	0.103
47DAP/reference	0.9485	0.207
52DAP/reference	1.15454	0.121
57DAP/reference	1.03782	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.53528	0.389
27DAP/17DAP	0.99009	0.943
39DAP/27DAP	0.9761	0.859
41DAP/39DAP	1.29682	0.382
42DAP/41DAP	0.5165	0.007
43DAP/42DAP	1.00269	0.875
47DAP/43DAP	1.68689	0.3
52DAP/47DAP	0.7558	0.338
57DAP/52DAP	1.06548	0.871
57DAP/7DAP	1.46163	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91339	0.183
17DAP/reference	0.79986	0.094
27DAP/reference	1.13413	0.804
39DAP/reference	0.8248	0.095
41DAP/reference	0.91664	0.259
42DAP/reference	0.83908	0.073
43DAP/reference	0.79703	0.029
47DAP/reference	0.90652	0.383
52DAP/reference	0.93118	0.254
57DAP/reference	1.02529	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.71864	0.038
17DAP/reference	0.73717	0.009
27DAP/reference	0.78816	0.058
39DAP/reference	1.00106	0.569
41DAP/reference	1.06454	0.513
42DAP/reference	1.01556	1
43DAP/reference	0.97264	0.552
47DAP/reference	0.88029	0.097
52DAP/reference	0.99866	0.666
57DAP/reference	0.91096	0.318

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05945	0.723
17DAP/reference	0.94279	0.477
27DAP/reference	0.88992	0.206
39DAP/reference	0.86815	0.046
41DAP/reference	0.99014	0.618
42DAP/reference	1.14479	0.382
43DAP/reference	1.06094	0.608
47DAP/reference	0.95495	0.383
52DAP/reference	0.73065	0.167
57DAP/reference	1.26008	0.268

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.32115	0.945
26DAP/20DAP	1.04529	1
34DAP/26DAP	1.06909	1
51DAP/34DAP	1.55199	0.654
52DAP/51DAP	1.27766	0.446
53DAP/52DAP	1.12387	0.552
55DAP/53DAP	0.87124	0.544
57DAP/55DAP	0.89108	0.527
62DAP/57DAP	1.15011	0.723
68DAP/62DAP	1.37292	0.285
68DAP/14DAP	1.47124	0.044

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.14258	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.40351	0.075
Mature Green Tomato/Ripe Tomato	0.21767
Immature Eggplant/Mature Eggplant	12.9824	0.05
Ripe Pepper/Ripe Tomato	0.84312	0.293
Mature Eggplant/Ripe Tomato	0.32476	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97772	0.944
1-1-2/M82	1.03631	1
12-2/M82	0.91655
12-4/M82	0.78969
1-3/M82	1.13897
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.22023	0.505
3-2/M82	0.77701	0.752
4-1-1/M82	N/A	N/A
4-1/M82	0.81962
4-3-2/M82	N/A	N/A
4-3/M82	1.75735	1
5-3/M82	1.05276	1
6-2/M82	1.3932
6-3/M82	0.76188
7-1/M82	0.99144	1
7-2/M82	1.36356
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	2.21771	0.277
IL2-6/WTpooled	1.10893
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.5813	0.362
IL12-4/WTpooled	1.31585	0.48
IL1-4/WTpooled	2.38771	1
WT/WTpooled	0.98596	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	1.31827	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.12204	0.774
DC3000/delta hrp 6h	1.94383	1
DC3000/delta hrp 12h	1.26474	1
DC3000/delta hrp 24h	0.95644	0.711

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	2.31802	1
Exp 36h	1.64818	0.693
Exp 60h	1.51952	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01938	1
Var 0h	0.98284	1
Var 12h I row2-row1	1.24833	0.222
Var 12h NI row2-row1	0.68948	1
Var 36h I row2-row1	1.3056	0.601
Var 36h NI row2-row1	0.69638	0.743
Var 60h I row2-row1	1.20053	0.487
Var 60h NI row2-row1	0.55509	0.63
Time course 0hI-0hNI	1.28913	0.852
Time course 12hI-12hNI	1.98968	0.01
Time course 36hI-36hNI	5.61621	0.005
Time course 60hI-60hNI	12.7396	0.008

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)	1.77451	0.571
transgenic ySAMdc/azygous control (breaker)	0.71988	0.251
transgenic ySAMdc/azygous control (red)	0.7704	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.25263	0.17

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.22498	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.97806	1
Manapal/WT (break)	1.24033	0.381
Manapal/WT (red)	0.25175	0.184