Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.13.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98692	0.779
27DAP/17DAP	1.24958	0.833
39DAP/27DAP	0.7654	0.443
41DAP/39DAP	1.59455	0.372
42DAP/41DAP	1.29592	0.852
43DAP/42DAP	0.9373	0.883
47DAP/43DAP	0.88509	0.609
52DAP/47DAP	1.29053	0.745
57DAP/52DAP	0.86847	0.878

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94611	0.336
17DAP/reference	1.002	1
27DAP/reference	0.96528	0.385
39DAP/reference	0.99062	0.841
41DAP/reference	0.93958	0.341
42DAP/reference	0.83898	0.002
43DAP/reference	0.95154	0.576
47DAP/reference	0.84883	0.001
52DAP/reference	0.8707	0.131
57DAP/reference	0.78897	0.023

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96709	0.663
27DAP/17DAP	1.05707	0.945
39DAP/27DAP	1.08912	0.534
41DAP/39DAP	1.02195	1
42DAP/41DAP	0.97178	0.797
43DAP/42DAP	1.12581	0.478
47DAP/43DAP	1.11128	0.788
52DAP/47DAP	0.94461	0.801
57DAP/52DAP	0.95383	0.608
57DAP/7DAP	1.28309	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74242	0.072
17DAP/reference	0.83908	0.019
27DAP/reference	0.79891	0.01
39DAP/reference	0.83133	0.011
41DAP/reference	0.83879	0.017
42DAP/reference	0.81846	0.01
43DAP/reference	0.75132	0.011
47DAP/reference	0.85073	0.101
52DAP/reference	0.74201	0.011
57DAP/reference	0.77599	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02027	0.863
17DAP/reference	0.99476	0.728
27DAP/reference	0.93539	0.352
39DAP/reference	0.83201	0.11
41DAP/reference	0.83897	0.051
42DAP/reference	0.85839	0.098
43DAP/reference	1.08948	0.485
47DAP/reference	0.89477	0.123
52DAP/reference	0.98785	0.576
57DAP/reference	1.17916	0.538

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87253	0.077
17DAP/reference	0.98329	0.696
27DAP/reference	0.82621	0.036
39DAP/reference	0.82644	0.025
41DAP/reference	0.80897	0.02
42DAP/reference	0.76922	0.016
43DAP/reference	0.73415	0.043
47DAP/reference	0.91886	0.335
52DAP/reference	0.73557	0.073
57DAP/reference	0.60222	0.02

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01851	1
26DAP/20DAP	0.89396	0.512
34DAP/26DAP	1.08797	0.819
51DAP/34DAP	1.01293	0.962
52DAP/51DAP	1.00817	0.954
53DAP/52DAP	1.12735	0.608
55DAP/53DAP	1.0858	0.634
57DAP/55DAP	1.09796	0.793
62DAP/57DAP	1.14542	0.723
68DAP/62DAP	0.83731	0.195
68DAP/14DAP	0.63377	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.73752	0.145

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.87401	0.411
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	2.80982	1
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.94214	0.944
1-1-2/M82	0.65929	0.958
12-2/M82	1.06143	1
12-4/M82	1.20156
1-3/M82	0.83804	0.378
2-1-1/M82	1.49458
2-1/M82	N/A	N/A
2-6/M82	1.03042	0.695
3-2/M82	N/A	N/A
4-1-1/M82	0.92959	1
4-1/M82	0.50255
4-3-2/M82	N/A	N/A
4-3/M82	0.87662
5-3/M82	0.97217	1
6-2/M82	0.92988
6-3/M82	0.97597	1
7-1/M82	0.84065
7-2/M82	0.98769	1
9-3-2/M82	0.63861	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.1409	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.25485	1
IL12-4/WTpooled	1.14365	0.52
IL1-4/WTpooled	1.28799
WT/WTpooled	0.96994	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	0.90471	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03584	0.921
DC3000/delta hrp 6h	0.97877	0.95
DC3000/delta hrp 12h	1.28503	1
DC3000/delta hrp 24h	1.10003	0.347

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.79004
DC3000 delta B/DC3000 delta AB	0.94721	0.693

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	1.9086	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01562	1
Var 0h	0.48813	1
Var 12h I row2-row1	1.04003	0.613
Var 12h NI row2-row1	0.94578	0.906
Var 36h I row2-row1	0.78338	0.805
Var 36h NI row2-row1	1.0014	1
Var 60h I row2-row1	1.42263	0.562
Var 60h NI row2-row1	1.2008	0.904
Time course 0hI-0hNI	1.11702	0.719
Time course 12hI-12hNI	1.05288	0.785
Time course 36hI-36hNI	1.02505	0.722
Time course 60hI-60hNI	1.10929	0.16

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)	1.03403	0.921
transgenic ySAMdc/azygous control (breaker)	1.29891	0.178
transgenic ySAMdc/azygous control (red)	0.94725	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98781	0.568

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.21917	0.227

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.88324	1
Manapal/WT (break)	0.75159	0.333
Manapal/WT (red)	0.98493	0.863