Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.11.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99719	0.938
27DAP/17DAP	1.00016	1
39DAP/27DAP	1.00171	0.899
41DAP/39DAP	0.96542	0.854
42DAP/41DAP	0.95853	1
43DAP/42DAP	1.09149	0.923
47DAP/43DAP	1.07389	0.438
52DAP/47DAP	0.92284	0.758
57DAP/52DAP	1.08724	0.908

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96347	0.371
17DAP/reference	0.93892	0.24
27DAP/reference	0.93733	0.114
39DAP/reference	0.94008	0.333
41DAP/reference	0.96287	0.341
42DAP/reference	1.0024	0.731
43DAP/reference	0.9816	0.728
47DAP/reference	1.0069	1
52DAP/reference	0.98095	0.515
57DAP/reference	1.05014	0.321

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00271	1
27DAP/17DAP	1.06129	0.859
39DAP/27DAP	1.01381	0.758
41DAP/39DAP	1.01182	0.868
42DAP/41DAP	0.99133	0.882
43DAP/42DAP	0.95889	0.149
47DAP/43DAP	1.02943	0.779
52DAP/47DAP	1.00211	1
57DAP/52DAP	0.98749	0.763
57DAP/7DAP	0.96506	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83871	0.246
17DAP/reference	0.76163	0.012
27DAP/reference	0.67503	0.01
39DAP/reference	0.75906	0.011
41DAP/reference	0.73095	0.016
42DAP/reference	0.66197	0.01
43DAP/reference	0.66923	0.012
47DAP/reference	0.8537	0.222
52DAP/reference	0.76144	0.014
57DAP/reference	0.77184	0.02

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00459	0.915
17DAP/reference	1.03649	0.459
27DAP/reference	1.00546	1
39DAP/reference	0.98019	0.392
41DAP/reference	0.96521	0.277
42DAP/reference	0.99785	0.723
43DAP/reference	1.07321	0.547
47DAP/reference	1.00393	1
52DAP/reference	0.95966	0.131
57DAP/reference	1.066	0.161

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80782	0.077
17DAP/reference	0.89926	0.348
27DAP/reference	0.854	0.206
39DAP/reference	0.67301	0.016
41DAP/reference	0.80305	0.019
42DAP/reference	0.73734	0.019
43DAP/reference	0.87129	0.034
47DAP/reference	0.97908	0.494
52DAP/reference	0.80494	0.25
57DAP/reference	0.96031	0.491

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97025	1
26DAP/20DAP	0.96819	1
34DAP/26DAP	1.00701	1
51DAP/34DAP	0.96849
52DAP/51DAP	0.93965	1
53DAP/52DAP	0.96303	0.848
55DAP/53DAP	1.2673
57DAP/55DAP	1.11012	0.71
62DAP/57DAP	1.04575	0.902
68DAP/62DAP	1.15247	0.653
68DAP/14DAP	1.2289	0.036

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.01011	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.19014	0.417
Mature Green Tomato/Ripe Tomato	1.63551	0.017
Immature Eggplant/Mature Eggplant	1.16528	0.363
Ripe Pepper/Ripe Tomato	1.27629	1
Mature Eggplant/Ripe Tomato	2.1913	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.86696	0.944
1-1-2/M82	0.94184	1
12-2/M82	0.97042	1
12-4/M82	0.98851	1
1-3/M82	0.97191	0.501
2-1-1/M82	0.89401	0.784
2-1/M82	0.91988	1
2-6/M82	0.88567	1
3-2/M82	0.92389	1
4-1-1/M82	0.99224	1
4-1/M82	1.08992	1
4-3-2/M82	0.92767	1
4-3/M82	0.92087	1
5-3/M82	0.99414	1
6-2/M82	0.98648	1
6-3/M82	1.05656	1
7-1/M82	1.00674	0.598
7-2/M82	0.9033	0.881
9-3-2/M82	0.9594	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.7916	0.321
IL2-6/WTpooled	0.7038	0.337
IL7-5/WTpooled	1.06542
IL7-3/WTpooled	1.50265	1
IL12-4/WTpooled	1.67613	0.516
IL1-4/WTpooled	0.98698	1
WT/WTpooled	0.94952	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	1.8459	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0085	1
DC3000/delta hrp 6h	1.29778	1
DC3000/delta hrp 12h	1.01794	1
DC3000/delta hrp 24h	1.0308	0.62

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.27645	0.042
DC3000 delta B/DC3000 delta AB	1.08531	0.484

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97598	1
Exp 36h	1.69544	0.489
Exp 60h	1.32466	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98373	1
Var 0h	2.09033	0.782
Var 12h I row2-row1	1.11143	0.196
Var 12h NI row2-row1	0.92979	0.466
Var 36h I row2-row1	1.07686	1
Var 36h NI row2-row1	0.98199	0.791
Var 60h I row2-row1	1.43006	1
Var 60h NI row2-row1	1.04853	1
Time course 0hI-0hNI	1.07228	0.799
Time course 12hI-12hNI	1.02354	0.816
Time course 36hI-36hNI	1.06732	0.355
Time course 60hI-60hNI	1.11757	0.047

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)	0.91941	0.454
transgenic ySAMdc/azygous control (breaker)	1.30617	0.248
transgenic ySAMdc/azygous control (red)	1.24813	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95942	0.067

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.97053	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.87886	1
Manapal/WT (break)	0.92629	1
Manapal/WT (red)	1.01222	1