Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.13.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19362	0.575
27DAP/17DAP	1.16428	0.849
39DAP/27DAP	1.1081	0.789
41DAP/39DAP	1.06382	0.728
42DAP/41DAP	1.1266	0.852
43DAP/42DAP	0.93539	0.827
47DAP/43DAP	0.87535	0.591
52DAP/47DAP	1.27006	0.553
57DAP/52DAP	0.98029	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97426	0.465
17DAP/reference	0.96313	0.448
27DAP/reference	0.99482	0.822
39DAP/reference	1.00452	1
41DAP/reference	0.96013	0.341
42DAP/reference	0.9893	0.413
43DAP/reference	1.02678	0.445
47DAP/reference	0.9015	0.014
52DAP/reference	0.93145	0.121
57DAP/reference	0.93337	0.015

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99813	0.847
27DAP/17DAP	1.0512	0.867
39DAP/27DAP	1.07478	0.534
41DAP/39DAP	0.8683	0.158
42DAP/41DAP	1.14159	0.029
43DAP/42DAP	0.99763	1
47DAP/43DAP	1.01206	0.969
52DAP/47DAP	0.96856	0.899
57DAP/52DAP	0.93432	0.384
57DAP/7DAP	1.00874	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90907	0.069
17DAP/reference	0.84636	0.02
27DAP/reference	0.9829	0.348
39DAP/reference	0.92775	0.018
41DAP/reference	0.9467	0.203
42DAP/reference	1.00234	1
43DAP/reference	1.07726	0.087
47DAP/reference	1.17405	0.038
52DAP/reference	1.19558	0.015
57DAP/reference	1.05882	0.907

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99508	0.907
17DAP/reference	0.99208	0.711
27DAP/reference	0.97696	0.537
39DAP/reference	0.95214	0.33
41DAP/reference	0.97558	0.459
42DAP/reference	0.96461	0.392
43DAP/reference	1.15215	0.026
47DAP/reference	0.96858	0.188
52DAP/reference	0.9432	0.156
57DAP/reference	1.04186	0.581

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01416	0.827
17DAP/reference	0.99767	0.855
27DAP/reference	0.93588	0.067
39DAP/reference	1.04315	0.33
41DAP/reference	1.02638	0.502
42DAP/reference	1.12013	0.3
43DAP/reference	1.02087	0.803
47DAP/reference	0.95229	0.335
52DAP/reference	0.91763	0.472
57DAP/reference	0.80896	0.045

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04688	0.966
26DAP/20DAP	0.96727	1
34DAP/26DAP	0.93491	0.763
51DAP/34DAP	1.20138	0.064
52DAP/51DAP	0.93949	1
53DAP/52DAP	0.97135	0.797
55DAP/53DAP	1.0814	0.434
57DAP/55DAP	0.93928	0.718
62DAP/57DAP	1.08899	0.723
68DAP/62DAP	0.81984	0.263
68DAP/14DAP	0.84057	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.18414	0.041

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.13905	0.417
Mature Green Tomato/Ripe Tomato	1.22546	0.064
Immature Eggplant/Mature Eggplant	1.48789	0.05
Ripe Pepper/Ripe Tomato	0.97307	1
Mature Eggplant/Ripe Tomato	0.88446	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04932	1
1-1-2/M82	1.02979	1
12-2/M82	0.94912	0.955
12-4/M82	0.98253	1
1-3/M82	1.27662
2-1-1/M82	0.95199	0.92
2-1/M82	1.18388
2-6/M82	1.01656	1
3-2/M82	1.00896	1
4-1-1/M82	1.1527	0.977
4-1/M82	0.7964	1
4-3-2/M82	0.99763	1
4-3/M82	1.23437	1
5-3/M82	1.13509	1
6-2/M82	1.02832	1
6-3/M82	1.14212	1
7-1/M82	0.9971	1
7-2/M82	1.10585	1
9-3-2/M82	1.17974	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.00227	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.0261	1
IL12-4/WTpooled	1.06548	0.737
IL1-4/WTpooled	1.01964
WT/WTpooled	0.97641	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	1.05809	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02004	0.914
DC3000/delta hrp 6h	1.01841	1
DC3000/delta hrp 12h	1.12177	1
DC3000/delta hrp 24h	1.11008	0.123

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.41125	0.121
DC3000 delta B/DC3000 delta AB	1.08211	0.42

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.22655	1
Exp 36h	1.18489	1
Exp 60h	1.00989	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00928	1
Var 0h	2.35053	0.936
Var 12h I row2-row1	1.09375	0.379
Var 12h NI row2-row1	0.92507	0.713
Var 36h I row2-row1	0.93067	1
Var 36h NI row2-row1	0.87587	0.584
Var 60h I row2-row1	1.0239	0.543
Var 60h NI row2-row1	0.95672	1
Time course 0hI-0hNI	1.08192	0.603
Time course 12hI-12hNI	1.03959	0.754
Time course 36hI-36hNI	1.03867	0.316
Time course 60hI-60hNI	1.36009	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)	0.86168	0.278
transgenic ySAMdc/azygous control (breaker)	0.87919	0.49
transgenic ySAMdc/azygous control (red)	1.20172	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08954	0.044

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.02513	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.06621	0.307
Manapal/WT (break)	0.84669	0.333
Manapal/WT (red)	1.07151	0.413