Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.7.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93233	0.464
27DAP/17DAP	0.85847	0.644
39DAP/27DAP	1.27928	0.277
41DAP/39DAP	1.02499	0.893
42DAP/41DAP	1.37498	0.481
43DAP/42DAP	0.86732	0.456
47DAP/43DAP	0.82834	0.48
52DAP/47DAP	1.44187	0.474
57DAP/52DAP	0.91395	0.82

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10594	0.071
17DAP/reference	0.98106	0.701
27DAP/reference	0.96467	0.497
39DAP/reference	1.08603	0.318
41DAP/reference	1.01322	1
42DAP/reference	1.04169	0.264
43DAP/reference	0.97736	0.728
47DAP/reference	1.09711	0.284
52DAP/reference	1.04639	0.388
57DAP/reference	1.37331	0.01

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01923	0.899
27DAP/17DAP	1.0354	0.928
39DAP/27DAP	0.86072	0.092
41DAP/39DAP	1.02986	0.876
42DAP/41DAP	1.1464	0.343
43DAP/42DAP	1.02601	0.554
47DAP/43DAP	0.97384	0.877
52DAP/47DAP	0.92064	0.694
57DAP/52DAP	0.8228	0.119
57DAP/7DAP	0.81052	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93126	0.203
17DAP/reference	0.94139	0.049
27DAP/reference	0.86607	0.01
39DAP/reference	0.89826	0.011
41DAP/reference	0.91764	0.122
42DAP/reference	0.91779	0.055
43DAP/reference	0.90848	0.013
47DAP/reference	0.88465	0.101
52DAP/reference	0.92584	0.254
57DAP/reference	1.01339	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9147	0.374
17DAP/reference	0.92074	0.287
27DAP/reference	1.08859	0.781
39DAP/reference	1.19836	0.082
41DAP/reference	1.07513	0.48
42DAP/reference	1.06161	0.899
43DAP/reference	1.02574	1
47DAP/reference	0.96362	0.39
52DAP/reference	0.94347	0.143
57DAP/reference	0.90277	0.092

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88132	0.036
17DAP/reference	1.00045	0.855
27DAP/reference	0.89467	0.065
39DAP/reference	0.95299	0.069
41DAP/reference	0.9856	0.682
42DAP/reference	1.02952	1
43DAP/reference	1.1362	0.721
47DAP/reference	1.05399	0.877
52DAP/reference	1.00154	0.871
57DAP/reference	1.78125	0.029

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01327	1
26DAP/20DAP	1.12631	0.481
34DAP/26DAP	0.89505	0.682
51DAP/34DAP	1.01733	0.962
52DAP/51DAP	1.16007	0.056
53DAP/52DAP	1.07026	0.806
55DAP/53DAP	0.78239
57DAP/55DAP	1.11056	0.694
62DAP/57DAP	0.94005	0.871
68DAP/62DAP	0.96968	0.81
68DAP/14DAP	0.98762	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.9876	0.696

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.68005	0.058
Mature Green Tomato/Ripe Tomato	1.10239	0.209
Immature Eggplant/Mature Eggplant	1.12041	0.181
Ripe Pepper/Ripe Tomato	1.39799	0.258
Mature Eggplant/Ripe Tomato	1.16623	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97086	0.536
1-1-2/M82	1.01436	1
12-2/M82	1.07075	1
12-4/M82	1.01303	1
1-3/M82	1.07407	1
2-1-1/M82	1.19721
2-1/M82	N/A	N/A
2-6/M82	0.99778	1
3-2/M82	1.03748	1
4-1-1/M82	1.02019	1
4-1/M82	0.94171	1
4-3-2/M82	0.97027	1
4-3/M82	1.10534	1
5-3/M82	0.99179	1
6-2/M82	1.02861	1
6-3/M82	1.01293	1
7-1/M82	0.97698
7-2/M82	0.98597	1
9-3-2/M82	1.00949	1

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	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	1.14099	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09941	0.921
DC3000/delta hrp 6h	0.98955	0.95
DC3000/delta hrp 12h	1.17085	1
DC3000/delta hrp 24h	1.03669	0.84

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.11899	0.16
DC3000 delta B/DC3000 delta AB	1.12154	0.353

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
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	0.9652	1
Var 0h	0.87746	0.457
Var 12h I row2-row1	1.12691	0.348
Var 12h NI row2-row1	1.03796	1
Var 36h I row2-row1	1.29635	0.742
Var 36h NI row2-row1	0.97369	0.791
Var 60h I row2-row1	0.99934	1
Var 60h NI row2-row1	0.89256	0.756
Time course 0hI-0hNI	0.8866	0.136
Time course 12hI-12hNI	0.98884	0.94
Time course 36hI-36hNI	1.14795	0.101
Time course 60hI-60hNI	1.31138	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)	0.98454	0.862
transgenic ySAMdc/azygous control (breaker)	1.69244	0.165
transgenic ySAMdc/azygous control (red)	1.17659	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.06621	0.119

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.97492	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.9005	1
Manapal/WT (break)	0.92738	1
Manapal/WT (red)	2.58942	0.142