Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.4.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.12746	0.812
27DAP/17DAP	0.97098	0.939
39DAP/27DAP	1.26222	0.667
41DAP/39DAP	0.76518	0.218
42DAP/41DAP	1.24529	0.873
43DAP/42DAP	1.11364	1
47DAP/43DAP	0.64646	0.119
52DAP/47DAP	0.90191	0.626
57DAP/52DAP	1.32167	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00834	1
17DAP/reference	0.94941	0.536
27DAP/reference	1.1549	0.146
39DAP/reference	1.0921	0.691
41DAP/reference	0.96593	0.667
42DAP/reference	1.19443	0.01
43DAP/reference	1.14477	0.05
47DAP/reference	1.32951	0.006
52DAP/reference	1.29486	0.01
57DAP/reference	1.21498	0.019

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.25359	0.445
27DAP/17DAP	1.05093	0.924
39DAP/27DAP	0.89895	0.361
41DAP/39DAP	1.20183	0.656
42DAP/41DAP	0.88628	0.173
43DAP/42DAP	0.90804	0.256
47DAP/43DAP	1.01999	0.939
52DAP/47DAP	1.06103	0.779
57DAP/52DAP	1.05703	0.772
57DAP/7DAP	1.05757	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.99541	0.026
17DAP/reference	1.97803	0.006
27DAP/reference	1.91946	0.006
39DAP/reference	2.26251	0.005
41DAP/reference	2.15408	0.009
42DAP/reference	2.3346	0.006
43DAP/reference	2.5386	0.006
47DAP/reference	2.05087	0.018
52DAP/reference	1.82739	0.007
57DAP/reference	2.11904	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.72325	0.11
17DAP/reference	0.75807	0.307
27DAP/reference	1.01127	1
39DAP/reference	1.18988	0.502
41DAP/reference	1.28708	0.133
42DAP/reference	1.36983	0.043
43DAP/reference	0.71664	0.058
47DAP/reference	1.23016	0.008
52DAP/reference	1.09191	0.471
57DAP/reference	0.94602	0.488

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	6.16949	0.027
17DAP/reference	1.15887	0.531
27DAP/reference	1.50456	0.035
39DAP/reference	1.66536	0.012
41DAP/reference	1.52698	0.017
42DAP/reference	8.03209	0.074
43DAP/reference	5.09935	0.028
47DAP/reference	1.18167	0.147
52DAP/reference	7.58041	0.032
57DAP/reference	2.25781	0.031

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96051	1
26DAP/20DAP	1.11424	0.663
34DAP/26DAP	0.87129	0.619
51DAP/34DAP	1.12402	0.473
52DAP/51DAP	0.93988	1
53DAP/52DAP	2.24128	0.027
55DAP/53DAP	0.98241	0.838
57DAP/55DAP	0.94691	0.744
62DAP/57DAP	0.49584	0.003
68DAP/62DAP	1.46372	0.02
68DAP/14DAP	1.73661	0.048

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.43349	0.055

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.78747	0.279
Mature Green Tomato/Ripe Tomato	1.31589	0.363
Immature Eggplant/Mature Eggplant	0.80648	0.077
Ripe Pepper/Ripe Tomato	1.51259	1
Mature Eggplant/Ripe Tomato	1.00214	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.90136	0.883
1-1-2/M82	1.6122	1
12-2/M82	0.89645	0.955
12-4/M82	0.81642	0.619
1-3/M82	0.80333	1
2-1-1/M82	0.95695	1
2-1/M82	N/A	N/A
2-6/M82	0.64431	0.501
3-2/M82	N/A	N/A
4-1-1/M82	1.56862	1
4-1/M82	0.8712
4-3-2/M82	1.4235	0.508
4-3/M82	1.36376	1
5-3/M82	1.00096	1
6-2/M82	1.32015
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.32512	0.318
9-3-2/M82	1.1403

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.9563	0.321
IL2-6/WTpooled	1.43841	0.659
IL7-5/WTpooled	0.68719	1
IL7-3/WTpooled	0.82855	0.31
IL12-4/WTpooled	1.14336	0.538
IL1-4/WTpooled	0.81557	0.444
WT/WTpooled	1.08281	0.87

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	0.99005	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09924	0.715
DC3000/delta hrp 6h	0.92772	0.95
DC3000/delta hrp 12h	0.99212	1
DC3000/delta hrp 24h	0.88419	0.236

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.09967	0.384
DC3000 delta B/DC3000 delta AB	1.3093	0.105

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.29094	1
Exp 36h	1.17802	1
Exp 60h	1.01255	1

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	1.075	0.305
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.91603	0.377
transgenic ySAMdc/azygous control (breaker)	0.79591	0.173
transgenic ySAMdc/azygous control (red)	0.93751	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05928	0.213

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.67108	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.57326	0.084
Manapal/WT (break)	1.13185	1
Manapal/WT (red)	2.00228	0.222