Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.9.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.51025	0.037
27DAP/17DAP	1.16361	0.833
39DAP/27DAP	1.06002	0.888
41DAP/39DAP	1.14202	0.58
42DAP/41DAP	1.17567	0.752
43DAP/42DAP	1.0673	1
47DAP/43DAP	1.12118	0.369
52DAP/47DAP	1.05938	0.956
57DAP/52DAP	1.19131	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.64744	0.062
17DAP/reference	1.41774	0.012
27DAP/reference	1.78301	0.007
39DAP/reference	1.61876	0.012
41DAP/reference	1.62769	0.014
42DAP/reference	2.78489	0.001
43DAP/reference	1.66004	0.008
47DAP/reference	2.71397	0.001
52DAP/reference	1.52844	0.008
57DAP/reference	1.35543	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04679	0.762
27DAP/17DAP	0.9376	0.782
39DAP/27DAP	1.05581	0.677
41DAP/39DAP	1.19347	0.362
42DAP/41DAP	0.97062	0.776
43DAP/42DAP	0.95931	0.665
47DAP/43DAP	1.01727	0.92
52DAP/47DAP	1.10467	0.713
57DAP/52DAP	1.06962	0.666
57DAP/7DAP	1.00942

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78488	0.077
17DAP/reference	1.11158	0.269
27DAP/reference	1.07336	0.453
39DAP/reference	1.30223	0.029
41DAP/reference	1.24425	0.097
42DAP/reference	1.48743	0.008
43DAP/reference	2.10331	0.006
47DAP/reference	2.3471	0.018
52DAP/reference	2.01328	0.017
57DAP/reference	1.95054	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.55027	0.005
17DAP/reference	1.5627	0.12
27DAP/reference	1.89368	0.126
39DAP/reference	1.59615	0.038
41DAP/reference	1.97578	0.166
42DAP/reference	1.75653	0.01
43DAP/reference	1.02268	0.787
47DAP/reference	1.28681	0.032
52DAP/reference	1.51652	0.004
57DAP/reference	1.1417	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.39215	0.026
17DAP/reference	0.87995	0.3
27DAP/reference	0.89015	0.206
39DAP/reference	1.0527	0.733
41DAP/reference	0.85674	0.119
42DAP/reference	1.20239	0.459
43DAP/reference	1.3848	0.073
47DAP/reference	1.41967	0.077
52DAP/reference	1.31103	0.073
57DAP/reference	2.12006	0.135

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05228	0.966
26DAP/20DAP	1.11848	0.567
34DAP/26DAP	1.02657	1
51DAP/34DAP	0.8292	0.143
52DAP/51DAP	0.97053	0.151
53DAP/52DAP	N/A	N/A
55DAP/53DAP	N/A	N/A
57DAP/55DAP	0.94154	0.736
62DAP/57DAP	0.96771	0.871
68DAP/62DAP	1.03655	0.897
68DAP/14DAP	0.98271	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.8082	0.092

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.2477	0.075
Mature Green Tomato/Ripe Tomato	1.39876	0.185
Immature Eggplant/Mature Eggplant	0.57957	0.063
Ripe Pepper/Ripe Tomato	0.44395	0.293
Mature Eggplant/Ripe Tomato	0.22763	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95835	0.944
1-1-2/M82	1.03773	1
12-2/M82	0.9345	0.955
12-4/M82	1.0121	1
1-3/M82	1.12964	1
2-1-1/M82	0.7849	0.565
2-1/M82	1.01204	1
2-6/M82	0.94964	0.501
3-2/M82	1.07586	0.967
4-1-1/M82	1.22239	1
4-1/M82	1.47979	1
4-3-2/M82	0.70098	0.698
4-3/M82	0.89157	1
5-3/M82	0.98768	1
6-2/M82	0.95383	1
6-3/M82	1.04086	1
7-1/M82	0.98606	1
7-2/M82	0.95273	1
9-3-2/M82	0.98904

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.11273	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.70157	0.294
IL12-4/WTpooled	1.10815	0.737
IL1-4/WTpooled	0.86882
WT/WTpooled	0.96848	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	0.7365	0.197

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93148	0.849
DC3000/delta hrp 6h	1.12412	1
DC3000/delta hrp 12h	1.08124	1
DC3000/delta hrp 24h	0.99186	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.11923
DC3000 delta B/DC3000 delta AB	1.0989	0.353

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00901	1
Exp 36h	1.23426	1
Exp 60h	0.97702	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00913	1
Var 0h	1.0731	0.339
Var 12h I row2-row1	1.20706	0.222
Var 12h NI row2-row1	1.00649	1
Var 36h I row2-row1	0.93072	1
Var 36h NI row2-row1	0.81099	0.645
Var 60h I row2-row1	1.12887	0.562
Var 60h NI row2-row1	1.17079	0.904
Time course 0hI-0hNI	1.05453	0.833
Time course 12hI-12hNI	0.96663	0.739
Time course 36hI-36hNI	0.99487	0.73
Time course 60hI-60hNI	1.86543	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)	1.04195	0.748
transgenic ySAMdc/azygous control (breaker)	1.20361	0.178
transgenic ySAMdc/azygous control (red)	0.92056	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02274	0.204

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.73381	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.01158	1
Manapal/WT (break)	1.04255	1
Manapal/WT (red)	0.89461	0.315