Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.13.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.44511	0.018
27DAP/17DAP	2.29238	0.189
39DAP/27DAP	0.79484	0.482
41DAP/39DAP	0.81997	0.37
42DAP/41DAP	1.00526	1
43DAP/42DAP	0.93863	0.895
47DAP/43DAP	1.06304	0.889
52DAP/47DAP	2.07727	0.119
57DAP/52DAP	0.97119	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08561	0.638
17DAP/reference	0.90662	0.069
27DAP/reference	1.27275	0.011
39DAP/reference	1.08183	0.593
41DAP/reference	0.99769	1
42DAP/reference	1.40024	0.001
43DAP/reference	0.90234	0.259
47DAP/reference	0.9975	0.602
52DAP/reference	1.23248	0.072
57DAP/reference	1.15795	0.063

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.34049	0.801
27DAP/17DAP	0.63382	0.1
39DAP/27DAP	1.0002	0.87
41DAP/39DAP	2.55259	0.013
42DAP/41DAP	0.64484	0.022
43DAP/42DAP	1.36044	0.25
47DAP/43DAP	1.0282	0.948
52DAP/47DAP	2.60269	0.045
57DAP/52DAP	1.82165	0.119
57DAP/7DAP	1.49855	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9018	0.27
17DAP/reference	1.08139	0.437
27DAP/reference	0.91642	0.303
39DAP/reference	1.14349	0.198
41DAP/reference	0.95218	0.431
42DAP/reference	1.30835	0.059
43DAP/reference	1.59619	0.007
47DAP/reference	0.72627	0.066
52DAP/reference	1.11773	0.308
57DAP/reference	2.04949	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24033	0.21
17DAP/reference	1.17715	0.311
27DAP/reference	0.9227	0.317
39DAP/reference	0.97699	0.497
41DAP/reference	1.26835	0.063
42DAP/reference	0.97137	0.534
43DAP/reference	1.14887	0.441
47DAP/reference	1.16581	0.092
52DAP/reference	0.89876	0.051
57DAP/reference	1.16713	0.123

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88491	0.29
17DAP/reference	1.04156	0.824
27DAP/reference	1.34124	0.022
39DAP/reference	1.25343	0.03
41DAP/reference	0.84864	0.148
42DAP/reference	0.89505	0.108
43DAP/reference	1.16988	0.254
47DAP/reference	1.27358	0.053
52DAP/reference	1.4701	0.043
57DAP/reference	1.68211	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.29501	0.966
26DAP/20DAP	N/A	N/A
34DAP/26DAP	1.32663	0.819
51DAP/34DAP	1.15159	0.627
52DAP/51DAP	1.57288	1
53DAP/52DAP	1.16264	0.806
55DAP/53DAP	0.88295	0.273
57DAP/55DAP	1.44792	0.906
62DAP/57DAP	1.33858	1
68DAP/62DAP	1.0551	0.872
68DAP/14DAP	1.01778	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.85081	0.131

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.09751	0.03
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.21076	0.224
Mature Eggplant/Ripe Tomato	0.1968	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.12843
1-3/M82	0.96799
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	2.51798
3-2/M82	N/A	N/A
4-1-1/M82	2.10848
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.77307
5-3/M82	0.29855
6-2/M82	3.30134
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.21363
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.97061	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.09347	1
IL12-4/WTpooled	0.86809	0.71
IL1-4/WTpooled	1.16818
WT/WTpooled	0.98294	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	1.26251	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07804	0.921
DC3000/delta hrp 6h	1.09912	1
DC3000/delta hrp 12h	1.02209	1
DC3000/delta hrp 24h	0.99636	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.14526	0.196
Exp 36h	2.10559	0.326
Exp 60h	1.47758	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00008	1
Var 0h	0.9331	1
Var 12h I row2-row1	0.98535	1
Var 12h NI row2-row1	0.98233	1
Var 36h I row2-row1	0.9542	1
Var 36h NI row2-row1	0.94215	0.791
Var 60h I row2-row1	0.99013	0.952
Var 60h NI row2-row1	0.82691	0.63
Time course 0hI-0hNI	1.17705	0.189
Time course 12hI-12hNI	1.91431	0.005
Time course 36hI-36hNI	5.14521	0.004
Time course 60hI-60hNI	3.32709	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)	1.32404	0.305
transgenic ySAMdc/azygous control (breaker)	0.25733	0.118
transgenic ySAMdc/azygous control (red)	1.20638	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94392	0.05

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.21752	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.04847	1
Manapal/WT (break)	0.99113	1
Manapal/WT (red)	0.55043	0.181