Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.9.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.79648	0.26
27DAP/17DAP	1.09593	0.849
39DAP/27DAP	1.22656	0.546
41DAP/39DAP	0.8988	0.574
42DAP/41DAP	0.93484	1
43DAP/42DAP	0.97621	0.895
47DAP/43DAP	0.95667	0.835
52DAP/47DAP	1.39612	0.462
57DAP/52DAP	0.99026	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27446	0.016
17DAP/reference	0.93213	0.368
27DAP/reference	1.03098	0.782
39DAP/reference	1.17392	0.343
41DAP/reference	1.068	0.855
42DAP/reference	1.22249	0.002
43DAP/reference	1.15992	0.019
47DAP/reference	1.74837	0.001
52DAP/reference	1.07246	0.548
57DAP/reference	1.28968	0.014

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97857	0.732
27DAP/17DAP	1.12873	0.488
39DAP/27DAP	0.9284	0.456
41DAP/39DAP	1.03894	0.849
42DAP/41DAP	0.98231	0.795
43DAP/42DAP	0.9855	0.875
47DAP/43DAP	0.99305	0.983
52DAP/47DAP	0.97582	0.9
57DAP/52DAP	0.93336	0.428
57DAP/7DAP	0.77829	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80005	0.108
17DAP/reference	0.80553	0.021
27DAP/reference	1.1028	0.16
39DAP/reference	0.71712	0.011
41DAP/reference	0.84732	0.082
42DAP/reference	0.94689	0.304
43DAP/reference	0.98136	0.502
47DAP/reference	0.88532	0.222
52DAP/reference	0.95346	0.254
57DAP/reference	0.8845	0.061

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02342	0.979
17DAP/reference	1.07814	0.448
27DAP/reference	1.06035	1
39DAP/reference	0.95528	0.359
41DAP/reference	1.0255	1
42DAP/reference	1.06226	0.398
43DAP/reference	1.29254	0.497
47DAP/reference	1.72489	0.011
52DAP/reference	0.93588	0.203
57DAP/reference	1.22889	0.523

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96129	0.526
17DAP/reference	0.99459	0.751
27DAP/reference	0.92939	0.195
39DAP/reference	1.00961	0.889
41DAP/reference	0.95859	0.417
42DAP/reference	1.09767	0.108
43DAP/reference	0.98231	0.614
47DAP/reference	1.48981	0.006
52DAP/reference	1.20397	0.428
57DAP/reference	1.24612	0.111

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94624	1
26DAP/20DAP	1.31619	0.204
34DAP/26DAP	0.98701	0.998
51DAP/34DAP	0.86258	0.281
52DAP/51DAP	1.06243	0.651
53DAP/52DAP	0.95762	0.854
55DAP/53DAP	0.77932	0.024
57DAP/55DAP	0.98113	0.875
62DAP/57DAP	1.4694	0.115
68DAP/62DAP	0.98566	0.834
68DAP/14DAP	0.88272	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.27219	0.017

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.37719	0.077
Mature Green Tomato/Ripe Tomato	1.44637	0.149
Immature Eggplant/Mature Eggplant	1.51644	0.05
Ripe Pepper/Ripe Tomato	1.39792	1
Mature Eggplant/Ripe Tomato	1.14736	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00702	1
1-1-2/M82	0.9572
12-2/M82	1.36012
12-4/M82	0.9968	1
1-3/M82	1.07523
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	1.21158
4-1-1/M82	0.71086
4-1/M82	1.49685
4-3-2/M82	N/A	N/A
4-3/M82	1.30014
5-3/M82	0.8783	1
6-2/M82	1.41578	1
6-3/M82	1.4604
7-1/M82	N/A	N/A
7-2/M82	1.62993
9-3-2/M82	1.00025	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.1742
IL2-6/WTpooled	1.06634	1
IL7-5/WTpooled	1.4362
IL7-3/WTpooled	0.89909	1
IL12-4/WTpooled	0.94396	1
IL1-4/WTpooled	0.93138
WT/WTpooled	1.137	0.785

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	0.98893	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01465	1
DC3000/delta hrp 6h	0.92186	0.95
DC3000/delta hrp 12h	1.12207	1
DC3000/delta hrp 24h	0.96164	0.761

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.99396	1
DC3000 delta B/DC3000 delta AB	0.99546	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02805	1
Exp 36h	1.11251	0.693
Exp 60h	0.92826	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97283	1
Var 0h	0.92544	1
Var 12h I row2-row1	1.02138	1
Var 12h NI row2-row1	1.10878	1
Var 36h I row2-row1	1.13127	0.41
Var 36h NI row2-row1	1.05692	1
Var 60h I row2-row1	0.88898	0.439
Var 60h NI row2-row1	0.91835	0.63
Time course 0hI-0hNI	0.95301	0.692
Time course 12hI-12hNI	1.02606	0.773
Time course 36hI-36hNI	1.26112	0.007
Time course 60hI-60hNI	1.16253	0.115

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)	0.94333	0.428
transgenic ySAMdc/azygous control (breaker)	0.9453	1
transgenic ySAMdc/azygous control (red)	1.00704	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04897	0.854

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.28076	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.16626	0.14
Manapal/WT (break)	1.72079	0.14
Manapal/WT (red)	1.387	0.15