Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.8.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.25494	0.512
27DAP/17DAP	1.17792	0.849
39DAP/27DAP	1.51126	0.38
41DAP/39DAP	0.99727	0.902
42DAP/41DAP	1.28519	0.608
43DAP/42DAP	1.05354	1
47DAP/43DAP	0.76979	0.298
52DAP/47DAP	1.27569	0.496
57DAP/52DAP	0.86882	0.759

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.4378	0.038
17DAP/reference	1.69128	0.014
27DAP/reference	1.24987	0.285
39DAP/reference	1.29802	0.301
41DAP/reference	1.73805	0.014
42DAP/reference	1.09325	0.609
43DAP/reference	1.19218	0.403
47DAP/reference	1.00628	0.674
52DAP/reference	0.88561	0.167
57DAP/reference	0.85352	0.156

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16209	0.06
27DAP/17DAP	1.08483	0.788
39DAP/27DAP	0.97339	0.852
41DAP/39DAP	1.1197	0.565
42DAP/41DAP	1.02717	0.927
43DAP/42DAP	0.88571	0.045
47DAP/43DAP	1.03708	0.833
52DAP/47DAP	1.58443	0.11
57DAP/52DAP	1.49656	0.066
57DAP/7DAP	1.64989	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9429	0.445
17DAP/reference	0.82415	0.192
27DAP/reference	0.7592	0.025
39DAP/reference	1.01247	0.745
41DAP/reference	0.93495	0.341
42DAP/reference	0.80412	0.033
43DAP/reference	0.8677	0.072
47DAP/reference	0.85714	0.293
52DAP/reference	1.18782	0.197
57DAP/reference	0.95517	0.367

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93191	0.503
17DAP/reference	1.28072	0.176
27DAP/reference	0.96984	0.537
39DAP/reference	1.29252	0.136
41DAP/reference	1.11556	0.688
42DAP/reference	1.18411	0.133
43DAP/reference	0.99564	0.787
47DAP/reference	1.25414	0.013
52DAP/reference	1.21535	0.259
57DAP/reference	1.222	0.119

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30057	0.022
17DAP/reference	1.05465	0.865
27DAP/reference	0.85716
39DAP/reference	1.24917	0.318
41DAP/reference	1.38868	0.054
42DAP/reference	1.20113	0.199
43DAP/reference	1.31803	0.205
47DAP/reference	1.14428	0.115
52DAP/reference	1.30054	0.377
57DAP/reference	0.99017	0.593

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.80653	0.966
26DAP/20DAP	1.25093	0.798
34DAP/26DAP	2.36825	0.819
51DAP/34DAP	1.31452	0.387
52DAP/51DAP	1.99568	0.043
53DAP/52DAP	0.78329	0.062
55DAP/53DAP	1.41794	0.066
57DAP/55DAP	0.84395	0.386
62DAP/57DAP	1.25127	0.8
68DAP/62DAP	1.84888	0.845
68DAP/14DAP	1.1255	0.676

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.6012	0.022

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.14204	0.523
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.18211
Mature Eggplant/Ripe Tomato	0.46753

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.37285
12-2/M82	N/A	N/A
12-4/M82	1.27722
1-3/M82	N/A	N/A
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	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	2.00982	0.466
4-3-2/M82	1.20397	0.508
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.26943	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.27111	0.493
IL2-6/WTpooled	0.8504	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.07668	1
IL12-4/WTpooled	1.41736	0.538
IL1-4/WTpooled	1.04964	1
WT/WTpooled	0.76967	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	1.18447	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9342	1
DC3000/delta hrp 6h	0.9925	0.95
DC3000/delta hrp 12h	1.13965	1
DC3000/delta hrp 24h	0.49536	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.27243	0.042
DC3000 delta B/DC3000 delta AB	1.44658	0.117

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0208	1
Exp 36h	0.72318	0.449
Exp 60h	0.91739	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01936	1
Var 0h	0.87403	0.933
Var 12h I row2-row1	1.00502	1
Var 12h NI row2-row1	1.08648	0.34
Var 36h I row2-row1	1.26034	0.742
Var 36h NI row2-row1	3.00704	1
Var 60h I row2-row1	0.78048	0.374
Var 60h NI row2-row1	0.79472	0.572
Time course 0hI-0hNI	0.98371	0.955
Time course 12hI-12hNI	1.23728	0.12
Time course 36hI-36hNI	1.62692	0.005
Time course 60hI-60hNI	2.72898	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)	1.23039	0.798
transgenic ySAMdc/azygous control (breaker)	1.36284	1
transgenic ySAMdc/azygous control (red)	0.97947	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.11482	0.234

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.58796	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.61469	0.096
Manapal/WT (break)	1.90717	0.14
Manapal/WT (red)	0.96359	0.863