Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.20.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16902	0.838
27DAP/17DAP	0.84499	0.72
39DAP/27DAP	1.58798	0.049
41DAP/39DAP	0.87979	0.602
42DAP/41DAP	1.19382	0.938
43DAP/42DAP	1.13215	0.968
47DAP/43DAP	1.23875	0.618
52DAP/47DAP	1.19729	0.991
57DAP/52DAP	1.6071	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09281	0.544
17DAP/reference	1.25676	0.014
27DAP/reference	0.90259	0.304
39DAP/reference	1.04798	0.581
41DAP/reference	1.01994	0.759
42DAP/reference	0.9437	0.163
43DAP/reference	0.98442	0.745
47DAP/reference	1.08586	0.685
52DAP/reference	0.87229	0.152
57DAP/reference	0.73458	0.023

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.2426	0.422
27DAP/17DAP	1.07821	0.842
39DAP/27DAP	1.02531	1
41DAP/39DAP	1.1417	0.849
42DAP/41DAP	0.85615	0.298
43DAP/42DAP	1.00267	1
47DAP/43DAP	1.12809	0.724
52DAP/47DAP	1.09834	0.749
57DAP/52DAP	1.21074	0.308
57DAP/7DAP	1.22019	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15337	0.435
17DAP/reference	0.99544	0.518
27DAP/reference	0.86834	0.088
39DAP/reference	0.87596	0.056
41DAP/reference	0.8909	0.082
42DAP/reference	0.77359	0.012
43DAP/reference	0.71664	0.012
47DAP/reference	0.92747	0.383
52DAP/reference	1.00125	0.679
57DAP/reference	0.93728	0.28

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14451	0.477
17DAP/reference	1.1103	0.531
27DAP/reference	1.08584	0.618
39DAP/reference	0.92833	0.257
41DAP/reference	0.85244	0.081
42DAP/reference	0.71909	0.012
43DAP/reference	1.03134	0.846
47DAP/reference	0.92315	0.24
52DAP/reference	0.9421	0.171
57DAP/reference	1.12628	0.229

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00435	0.804
17DAP/reference	1.04273	0.728
27DAP/reference	0.86764	0.092
39DAP/reference	0.92117	0.179
41DAP/reference	1.02432	0.826
42DAP/reference	1.02226	0.816
43DAP/reference	1.29927	0.396
47DAP/reference	0.99659	0.626
52DAP/reference	0.94217	0.551
57DAP/reference	0.87826	0.203

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.28675	0.678
26DAP/20DAP	1.24587	0.464
34DAP/26DAP	0.865	0.741
51DAP/34DAP	1.31303	0.111
52DAP/51DAP	1.2027	0.288
53DAP/52DAP	0.79098	0.336
55DAP/53DAP	0.72098	0.07
57DAP/55DAP	1.22963	0.167
62DAP/57DAP	1.09863	0.868
68DAP/62DAP	0.91206	0.609
68DAP/14DAP	0.69994	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.91926	0.591

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.75941	0.223
Mature Green Tomato/Ripe Tomato	0.74016
Immature Eggplant/Mature Eggplant	1.31986	0.13
Ripe Pepper/Ripe Tomato	1.18232	1
Mature Eggplant/Ripe Tomato	0.80071	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.88957	0.907
1-1-2/M82	1.08952	1
12-2/M82	0.88337
12-4/M82	0.74888	0.358
1-3/M82	1.44332
2-1-1/M82	0.79223	0.784
2-1/M82	1.12586	0.345
2-6/M82	0.98585	1
3-2/M82	1.09935
4-1-1/M82	0.77033
4-1/M82	N/A	N/A
4-3-2/M82	0.97769
4-3/M82	0.95005	1
5-3/M82	0.98586	1
6-2/M82	0.86536
6-3/M82	1.19832	1
7-1/M82	1.21927
7-2/M82	1.03003	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.67236	0.321
IL2-6/WTpooled	2.0749	0.46
IL7-5/WTpooled	0.82395	1
IL7-3/WTpooled	1.05674	1
IL12-4/WTpooled	1.19841	0.557
IL1-4/WTpooled	1.25707	1
WT/WTpooled	0.93332	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	1.63573	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06996	0.921
DC3000/delta hrp 6h	1.02568	0.95
DC3000/delta hrp 12h	1.16599	1
DC3000/delta hrp 24h	1.03709	0.604

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.37596	0.042
DC3000 delta B/DC3000 delta AB	1.41886	0.128

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.16277	0.228
Exp 36h	1.59022	0.489
Exp 60h	1.65794	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0237	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.09289	0.544
Var 12h NI row2-row1	1.37873	0.266
Var 36h I row2-row1	1.11526	1
Var 36h NI row2-row1	0.73354	0.45
Var 60h I row2-row1	0.67548	0.287
Var 60h NI row2-row1	0.82884	0.69
Time course 0hI-0hNI	0.92533	0.522
Time course 12hI-12hNI	1.11541	0.603
Time course 36hI-36hNI	1.91085	0.004
Time course 60hI-60hNI	4.36166	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)	1.16775	0.261
transgenic ySAMdc/azygous control (breaker)	1.40968	0.172
transgenic ySAMdc/azygous control (red)	0.92489	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03898	0.261

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.65783	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89136	1
Manapal/WT (break)	0.86329	0.333
Manapal/WT (red)	0.69049	0.216