Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.10.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.77208	0.226
27DAP/17DAP	1.10791	0.859
39DAP/27DAP	0.83888	0.414
41DAP/39DAP	1.13198	0.624
42DAP/41DAP	0.86215	1
43DAP/42DAP	1.16409	0.899
47DAP/43DAP	0.99754	0.864
52DAP/47DAP	0.85565	0.639
57DAP/52DAP	0.95139	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03637	0.384
17DAP/reference	0.85737	0.224
27DAP/reference	0.9876	0.725
39DAP/reference	0.95382	0.446
41DAP/reference	0.88093	0.114
42DAP/reference	0.98347	0.384
43DAP/reference	0.95638	0.538
47DAP/reference	0.94463	0.258
52DAP/reference	0.91212	0.183
57DAP/reference	0.97175	0.435

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.77882	0.09
27DAP/17DAP	1.11827	0.761
39DAP/27DAP	1.31268	0.197
41DAP/39DAP	0.97527	0.973
42DAP/41DAP	1.20892	0.2
43DAP/42DAP	1.12832	0.382
47DAP/43DAP	1.03503	0.901
52DAP/47DAP	0.6083	0.048
57DAP/52DAP	1.00141	0.845
57DAP/7DAP	0.94496	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.33698	0.034
17DAP/reference	1.69929	0.007
27DAP/reference	2.59173	0.006
39DAP/reference	3.23145	0.005
41DAP/reference	5.22901	0.011
42DAP/reference	4.10493	0.006
43DAP/reference	3.31262	0.006
47DAP/reference	1.81166	0.285
52DAP/reference	2.90894	0.007
57DAP/reference	3.15372	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00022	0.831
17DAP/reference	1.00215	0.693
27DAP/reference	0.96689	0.467
39DAP/reference	0.82916	0.065
41DAP/reference	0.92458	0.205
42DAP/reference	1.02525	0.951
43DAP/reference	1.11965	0.769
47DAP/reference	1.02447	0.867
52DAP/reference	0.88445	0.072
57DAP/reference	0.90925	0.079

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79478	0.112
17DAP/reference	1.16159	0.215
27DAP/reference	1.72599	0.022
39DAP/reference	2.92596	0.006
41DAP/reference	2.16452	0.007
42DAP/reference	2.41145	0.012
43DAP/reference	1.65803	0.047
47DAP/reference	1.1309	0.405
52DAP/reference	1.15859	0.443
57DAP/reference	1.05573	0.814

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.87178	1
26DAP/20DAP	1.16616	0.647
34DAP/26DAP	0.75567	0.399
51DAP/34DAP	1.05381	0.924
52DAP/51DAP	1.15953	0.689
53DAP/52DAP	1.26909	0.25
55DAP/53DAP	0.95546	0.725
57DAP/55DAP	1.34123	0.525
62DAP/57DAP	1.05509	0.935
68DAP/62DAP	1.56501	0.85
68DAP/14DAP	0.50812

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.73276	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	0.94717
Ripe Pepper/Ripe Tomato	2.25973	1
Mature Eggplant/Ripe Tomato	1.39296	1

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	N/A	N/A
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	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.98151
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	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.37798	0.277
IL2-6/WTpooled	0.99639	1
IL7-5/WTpooled	0.8873
IL7-3/WTpooled	0.89215	0.418
IL12-4/WTpooled	0.89839	0.71
IL1-4/WTpooled	0.99509
WT/WTpooled	1.02086	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	1.04745	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97935	1
DC3000/delta hrp 6h	1.09303	1
DC3000/delta hrp 12h	0.928	1
DC3000/delta hrp 24h	1.10699	0.604

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	0.73023	0.117

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.85325	0.328
Exp 36h	0.7226	0.449
Exp 60h	0.77859	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03003	1
Var 0h	0.91777	1
Var 12h I row2-row1	0.99926	1
Var 12h NI row2-row1	0.92528	0.82
Var 36h I row2-row1	1.10575	0.368
Var 36h NI row2-row1	0.63683	0.432
Var 60h I row2-row1	0.9439	0.292
Var 60h NI row2-row1	1.16694	0.904
Time course 0hI-0hNI	0.88074	0.156
Time course 12hI-12hNI	0.97438	0.814
Time course 36hI-36hNI	1.00104	0.768
Time course 60hI-60hNI	1.25785	0.017

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)	1.01948	0.798
transgenic ySAMdc/azygous control (breaker)	1.14363	0.172
transgenic ySAMdc/azygous control (red)	0.97453	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00362	0.811

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.22707	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.13763	0.105
Manapal/WT (break)	1.36446	0.14
Manapal/WT (red)	2.07245	0.222