Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.19.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.64225	0.512
27DAP/17DAP	2.99123	0.065
39DAP/27DAP	3.78531	0.369
41DAP/39DAP	3.31654	0.363
42DAP/41DAP	0.87813	1
43DAP/42DAP	1.28407	1
47DAP/43DAP	0.1717	0.032
52DAP/47DAP	1.19177	0.98
57DAP/52DAP	0.95011	0.94

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.69637	0.024
17DAP/reference	0.70716	0.013
27DAP/reference	0.90062	0.232
39DAP/reference	0.70725	0.053
41DAP/reference	0.77349	0.154
42DAP/reference	1.89486	0.001
43DAP/reference	0.67284	0.017
47DAP/reference	0.8215	0.006
52DAP/reference	0.70005	0.067
57DAP/reference	0.84778	0.091

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.61791	0.153
27DAP/17DAP	2.03784	0.333
39DAP/27DAP	4.88132	0.042
41DAP/39DAP	5.38383	0.005
42DAP/41DAP	0.53644	0.007
43DAP/42DAP	0.30418	0.02
47DAP/43DAP	1.10031	0.713
52DAP/47DAP	1.53058	0.619
57DAP/52DAP	0.74824	0.399
57DAP/7DAP	0.40119	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.54167	0.054
17DAP/reference	1.49247	0.574
27DAP/reference	2.74846	0.246
39DAP/reference	2.58916	0.05
41DAP/reference	0.70777	0.076
42DAP/reference	1.75038	0.686
43DAP/reference	1.3722	0.974
47DAP/reference	1.78948	0.158
52DAP/reference	2.46695	0.016
57DAP/reference	3.10997	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.56066	0.007
17DAP/reference	0.81601	0.05
27DAP/reference	0.94925	0.407
39DAP/reference	2.55754	0.017
41DAP/reference	1.88601	0.009
42DAP/reference	1.80199	0.031
43DAP/reference	4.21189	0.029
47DAP/reference	3.80206	0.011
52DAP/reference	1.36761	0.023
57DAP/reference	4.11101	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.67723	0.092
17DAP/reference	1.21491	0.854
27DAP/reference	0.75169	0.029
39DAP/reference	1.51624	0.175
41DAP/reference	1.84779	0.077
42DAP/reference	0.73032	0.108
43DAP/reference	0.85965	0.206
47DAP/reference	0.69247	0.006
52DAP/reference	0.68175	0.072
57DAP/reference	1.19487	0.385

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.70131	0.159
26DAP/20DAP	1.04729	1
34DAP/26DAP	1.90653	0.819
51DAP/34DAP	0.9732
52DAP/51DAP	1.26995	0.068
53DAP/52DAP	1.11808	0.882
55DAP/53DAP	1.24861	0.79
57DAP/55DAP	0.84249	0.527
62DAP/57DAP	1.12015	0.902
68DAP/62DAP	1.04718	1
68DAP/14DAP	1.28227	0.419

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	7.36879	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	12.3085	0.015
Immature Eggplant/Mature Eggplant	14.3507	0.123
Ripe Pepper/Ripe Tomato	0.0859
Mature Eggplant/Ripe Tomato	0.01302	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.60608
1-1-2/M82	1.29259	1
12-2/M82	1.12286	1
12-4/M82	1.48593	1
1-3/M82	2.22998	0.248
2-1-1/M82	N/A	N/A
2-1/M82	3.93989
2-6/M82	1.558	0.452
3-2/M82	4.2858
4-1-1/M82	4.35478
4-1/M82	N/A	N/A
4-3-2/M82	5.92
4-3/M82	0.8467	1
5-3/M82	1.70896	0.496
6-2/M82	12.8729	0.253
6-3/M82	1.08048	1
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	3.14793	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.16893
IL2-6/WTpooled	1.04951	0.788
IL7-5/WTpooled	1.38142
IL7-3/WTpooled	1.02963	1
IL12-4/WTpooled	1.2115	0.595
IL1-4/WTpooled	0.90368
WT/WTpooled	1.08637	0.911

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	1.57606	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00664	1
DC3000/delta hrp 6h	1.44237	0.177
DC3000/delta hrp 12h	1.12127	1
DC3000/delta hrp 24h	3.0749	0.026

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.04893	0.042
DC3000 delta B/DC3000 delta AB	5.01803	0.023

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.81098	1
Exp 36h	1.59236	0.693
Exp 60h	2.95384	0.226

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98735	1
Var 0h	0.88895	0.933
Var 12h I row2-row1	1.07849	0.692
Var 12h NI row2-row1	2.86942	0.235
Var 36h I row2-row1	1.38948	1
Var 36h NI row2-row1	0.51971	0.478
Var 60h I row2-row1	0.89902	0.287
Var 60h NI row2-row1	0.52084	0.329
Time course 0hI-0hNI	2.10562	0.603
Time course 12hI-12hNI	2.05742	0.507
Time course 36hI-36hNI	10.8597	0.004
Time course 60hI-60hNI	134.607	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)	0.34399	0.246
transgenic ySAMdc/azygous control (breaker)	0.49976	0.137
transgenic ySAMdc/azygous control (red)	0.93762	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.88637	0.055

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.19067	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.20221	1
Manapal/WT (break)	0.34026	0.333
Manapal/WT (red)	0.28007	0.242