Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.9.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.20214	0.498
27DAP/17DAP	1.09486	0.91
39DAP/27DAP	0.79511	0.41
41DAP/39DAP	1.53906	0.261
42DAP/41DAP	0.8899	1
43DAP/42DAP	1.08534	1
47DAP/43DAP	0.88136	0.603
52DAP/47DAP	1.31917	0.691
57DAP/52DAP	0.99949	0.993

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05221	0.544
17DAP/reference	1.03336	0.33
27DAP/reference	1.01717	0.82
39DAP/reference	1.02867	0.377
41DAP/reference	1.09116	0.158
42DAP/reference	1.01483	0.756
43DAP/reference	1.03537	0.425
47DAP/reference	1.03806	0.433
52DAP/reference	1.06837	0.32
57DAP/reference	1.02763	0.529

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09947	0.708
27DAP/17DAP	1.38968	0.063
39DAP/27DAP	0.83118	0.296
41DAP/39DAP	1.12223	0.719
42DAP/41DAP	0.93976	0.607
43DAP/42DAP	0.98783	0.902
47DAP/43DAP	0.98655	0.928
52DAP/47DAP	1.03717	0.962
57DAP/52DAP	1.44896	0.094
57DAP/7DAP	1.31458	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27858	0.072
17DAP/reference	1.15521	0.525
27DAP/reference	1.10595	0.551
39DAP/reference	1.15696	0.157
41DAP/reference	0.89051	0.223
42DAP/reference	0.91085	0.289
43DAP/reference	1.18979	0.188
47DAP/reference	1.02506	1
52DAP/reference	1.05017	0.781
57DAP/reference	1.03485	0.851

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06011	0.404
17DAP/reference	0.95043	0.129
27DAP/reference	0.9841	0.598
39DAP/reference	1.11754	0.112
41DAP/reference	0.97254	0.451
42DAP/reference	0.94188	0.169
43DAP/reference	1.16271	0.297
47DAP/reference	0.84078	0.008
52DAP/reference	1.05268	0.065
57DAP/reference	1.17445	0.094

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03471	0.809
17DAP/reference	0.9194	0.417
27DAP/reference	1.25429	0.207
39DAP/reference	1.05391	0.773
41DAP/reference	0.99336	0.754
42DAP/reference	0.87558	0.22
43DAP/reference	0.95241	0.416
47DAP/reference	0.99321	0.646
52DAP/reference	1.61297	0.837
57DAP/reference	0.93392	0.339

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06552	0.966
26DAP/20DAP	1.12766	0.793
34DAP/26DAP	0.93224	0.834
51DAP/34DAP	1.16694	0.445
52DAP/51DAP	0.92422	1
53DAP/52DAP	1.18552	0.25
55DAP/53DAP	0.95837	0.82
57DAP/55DAP	0.88018	0.548
62DAP/57DAP	0.9556	0.871
68DAP/62DAP	1.09647	0.7
68DAP/14DAP	0.979	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.15455	0.7

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.9517	0.692
Mature Green Tomato/Ripe Tomato	1.33007	0.752
Immature Eggplant/Mature Eggplant	1.02867	0.528
Ripe Pepper/Ripe Tomato	0.87382	1
Mature Eggplant/Ripe Tomato	0.82775	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.90011	0.944
1-1-2/M82	1.02732	1
12-2/M82	1.0455
12-4/M82	0.85472	0.619
1-3/M82	1.16442
2-1-1/M82	0.82001	0.465
2-1/M82	N/A	N/A
2-6/M82	0.70675	1
3-2/M82	N/A	N/A
4-1-1/M82	0.90599
4-1/M82	0.93129
4-3-2/M82	0.9978	1
4-3/M82	1.0216	1
5-3/M82	0.97784	1
6-2/M82	0.7571	0.481
6-3/M82	1.09729
7-1/M82	1.2441
7-2/M82	1.06543
9-3-2/M82	0.74934

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.02884	1
IL2-6/WTpooled	0.75764	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.16765	1
IL12-4/WTpooled	0.98293	1
IL1-4/WTpooled	1.01443	1
WT/WTpooled	1.00683	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	0.82591	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03757	0.921
DC3000/delta hrp 6h	1.0387	0.95
DC3000/delta hrp 12h	1.10581	1
DC3000/delta hrp 24h	1.21291	0.103

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.16183
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	0.93015	1
Exp 36h	1.43395	0.693
Exp 60h	1.12888	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.049
Var 0h	1.14296	0.98
Var 12h I row2-row1	1.07938	0.692
Var 12h NI row2-row1	1.21466	0.34
Var 36h I row2-row1	0.7193	1
Var 36h NI row2-row1	1.00464	1
Var 60h I row2-row1	0.9582	0.582
Var 60h NI row2-row1	0.93542	1
Time course 0hI-0hNI	1.08075	0.799
Time course 12hI-12hNI	1.05808	0.709
Time course 36hI-36hNI	1.00718	0.89
Time course 60hI-60hNI	1.03626	0.575

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)	1.02501	0.654
transgenic ySAMdc/azygous control (breaker)	0.98262	1
transgenic ySAMdc/azygous control (red)	0.86719	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98761	0.404

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.7026	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.68228	1
Manapal/WT (break)	1.09628	1
Manapal/WT (red)	1.07817	0.413