Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.13.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95759	0.722
27DAP/17DAP	1.22864	0.804
39DAP/27DAP	0.72982	0.327
41DAP/39DAP	1.30144	0.306
42DAP/41DAP	1.09643	0.913
43DAP/42DAP	0.98257	0.93
47DAP/43DAP	0.97886	0.804
52DAP/47DAP	1.37823	0.468
57DAP/52DAP	0.99582	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01472	1
17DAP/reference	0.97984	0.664
27DAP/reference	1.07118	0.264
39DAP/reference	1.02084	0.514
41DAP/reference	1.02037	0.587
42DAP/reference	1.06939	0.033
43DAP/reference	1.00145	1
47DAP/reference	0.99809	0.674
52DAP/reference	1.02688	0.453
57DAP/reference	1.01231	0.744

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98623	0.763
27DAP/17DAP	1.00816	0.969
39DAP/27DAP	0.99601	1
41DAP/39DAP	1.03773	0.79
42DAP/41DAP	0.97538	0.737
43DAP/42DAP	0.97753	0.482
47DAP/43DAP	1.00603	0.948
52DAP/47DAP	0.99261	0.935
57DAP/52DAP	1.04924	0.659
57DAP/7DAP	1.03881	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90852	0.168
17DAP/reference	0.95339	0.049
27DAP/reference	0.88691	0.016
39DAP/reference	0.98007	0.552
41DAP/reference	0.97916	0.375
42DAP/reference	1.01716	0.889
43DAP/reference	1.12438	0.178
47DAP/reference	0.90774	0.079
52DAP/reference	1.09095	0.139
57DAP/reference	1.20882	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98104	0.639
17DAP/reference	1.08214	0.191
27DAP/reference	0.99727	0.735
39DAP/reference	0.97028	0.306
41DAP/reference	1.0803	0.204
42DAP/reference	1.03553	0.664
43DAP/reference	1.05791	0.327
47DAP/reference	1.00303	1
52DAP/reference	0.97518	0.28
57DAP/reference	0.99973	0.874

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96033	0.249
17DAP/reference	1.02917	0.72
27DAP/reference	1.05961	0.207
39DAP/reference	1.07039	0.182
41DAP/reference	0.94267	0.185
42DAP/reference	0.98467	0.671
43DAP/reference	0.99636	0.796
47DAP/reference	1.02923	0.309
52DAP/reference	1.07613	0.534
57DAP/reference	0.96151	0.38

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05893	0.966
26DAP/20DAP	0.97924	1
34DAP/26DAP	0.98186	0.972
51DAP/34DAP	0.99714	0.957
52DAP/51DAP	1.0236	0.758
53DAP/52DAP	0.9705	0.807
55DAP/53DAP	0.93875	0.648
57DAP/55DAP	0.93648	0.724
62DAP/57DAP	1.06099	0.902
68DAP/62DAP	0.81175	0.227
68DAP/14DAP	1.09756	0.211

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.99494	0.774

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.50635	0.115
Mature Green Tomato/Ripe Tomato	0.83785	0.029
Immature Eggplant/Mature Eggplant	1.02947	0.606
Ripe Pepper/Ripe Tomato	0.33475	0.224
Mature Eggplant/Ripe Tomato	0.25285	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98315	0.961
1-1-2/M82	1.07137	1
12-2/M82	1.07124	1
12-4/M82	0.91889	1
1-3/M82	1.00652	1
2-1-1/M82	0.92784	0.683
2-1/M82	1.04286
2-6/M82	0.94403	1
3-2/M82	0.92736	1
4-1-1/M82	1.03074	1
4-1/M82	0.88716	0.737
4-3-2/M82	1.01413	1
4-3/M82	0.98285	1
5-3/M82	1.07877	1
6-2/M82	0.98578	1
6-3/M82	1.02803	1
7-1/M82	0.91295	0.803
7-2/M82	0.97813	1
9-3-2/M82	0.865

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.115	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.79445	0.418
IL12-4/WTpooled	0.95277	0.71
IL1-4/WTpooled	1.15488
WT/WTpooled	1.02315	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	2.42821	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03454	0.921
DC3000/delta hrp 6h	1.63101	0.777
DC3000/delta hrp 12h	0.83318
DC3000/delta hrp 24h	1.01181	0.779

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.0374	0.29
DC3000 delta B/DC3000 delta AB	1.10693	0.363

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01491	1
Var 0h	0.86332	0.261
Var 12h I row2-row1	1.05584	0.263
Var 12h NI row2-row1	1.04133	1
Var 36h I row2-row1	0.85342	1
Var 36h NI row2-row1	1.09297	1
Var 60h I row2-row1	1.13535	0.562
Var 60h NI row2-row1	1.09392	0.904
Time course 0hI-0hNI	1.09966	0.852
Time course 12hI-12hNI	1.06286	0.621
Time course 36hI-36hNI	0.98456	0.589
Time course 60hI-60hNI	1.24187	0.009

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)	1.64555	0.397
transgenic ySAMdc/azygous control (breaker)	0.54576	0.118
transgenic ySAMdc/azygous control (red)	1.13856	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99684	0.712

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.17563	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.57019	0.172
Manapal/WT (break)	0.52852	0.333
Manapal/WT (red)	0.52939	0.181