Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.14.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00894	0.997
27DAP/17DAP	1.05814	0.873
39DAP/27DAP	1.12105	0.888
41DAP/39DAP	1.01273	0.914
42DAP/41DAP	1.01658	0.994
43DAP/42DAP	1.01527	1
47DAP/43DAP	1.03352	0.889
52DAP/47DAP	1.0471	0.906
57DAP/52DAP	1.04329	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98332	0.578
17DAP/reference	0.93599	0.298
27DAP/reference	0.9569	0.187
39DAP/reference	0.93892	0.128
41DAP/reference	1.04186	0.365
42DAP/reference	1.11445	0.003
43DAP/reference	1.04199	0.382
47DAP/reference	1.06925	0.048
52DAP/reference	1.12753	0.056
57DAP/reference	1.19068	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01886	0.934
27DAP/17DAP	1.01999	0.942
39DAP/27DAP	0.9804	0.852
41DAP/39DAP	0.97652	0.934
42DAP/41DAP	0.98344	0.816
43DAP/42DAP	1.01967	0.351
47DAP/43DAP	0.99909	1
52DAP/47DAP	0.9812	0.886
57DAP/52DAP	1.03284	0.783
57DAP/7DAP	0.95566	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11523	0.257
17DAP/reference	1.3062	0.012
27DAP/reference	1.58007	0.03
39DAP/reference	1.22939	0.411
41DAP/reference	1.21071	0.06
42DAP/reference	1.23425
43DAP/reference	1.24717	0.02
47DAP/reference	1.02569	0.632
52DAP/reference	1.8478
57DAP/reference	1.75023	0.158

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05931	0.373
17DAP/reference	1.01936	0.824
27DAP/reference	0.94598	0.304
39DAP/reference	0.94949	0.214
41DAP/reference	0.99046	0.531
42DAP/reference	1.0137	1
43DAP/reference	1.04933	0.611
47DAP/reference	1.0924	0.023
52DAP/reference	1.0256	0.471
57DAP/reference	1.12411	0.045

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12416	0.251
17DAP/reference	1.12892	0.436
27DAP/reference	1.4742	0.26
39DAP/reference	1.47439	0.034
41DAP/reference	1.44209	0.205
42DAP/reference	1.56771	0.327
43DAP/reference	1.41193	0.164
47DAP/reference	1.04643	0.655
52DAP/reference	1.18103	0.583
57DAP/reference	0.9641	0.359

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00122	1
26DAP/20DAP	1.00308	1
34DAP/26DAP	1.02704	1
51DAP/34DAP	0.97107	0.77
52DAP/51DAP	0.9974	1
53DAP/52DAP	0.9539	0.917
55DAP/53DAP	0.98958	0.886
57DAP/55DAP	0.95628	0.828
62DAP/57DAP	1.10249	0.767
68DAP/62DAP	1.11798	0.539
68DAP/14DAP	1.20044	0.039

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.02265	0.627

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.93077	0.551
Mature Green Tomato/Ripe Tomato	0.86131	0.256
Immature Eggplant/Mature Eggplant	1.26196	0.101
Ripe Pepper/Ripe Tomato	1.3867	1
Mature Eggplant/Ripe Tomato	1.50512	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95585	0.944
1-1-2/M82	1.06862	1
12-2/M82	0.97814	1
12-4/M82	1.02835	1
1-3/M82	0.98386	1
2-1-1/M82	0.92087	0.465
2-1/M82	0.86955	0.74
2-6/M82	0.93895	1
3-2/M82	0.95938	1
4-1-1/M82	0.95665	1
4-1/M82	1.00642	1
4-3-2/M82	0.90784	1
4-3/M82	0.96751	1
5-3/M82	1.01542	1
6-2/M82	1.0326	1
6-3/M82	1.04908	1
7-1/M82	1.01308	1
7-2/M82	0.93243	0.881
9-3-2/M82	0.92115	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.83128	0.348
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.07787	1
IL12-4/WTpooled	1.06701	0.839
IL1-4/WTpooled	0.81456
WT/WTpooled	0.97376	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	0.9407

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05636	0.921
DC3000/delta hrp 6h	1.49097	1
DC3000/delta hrp 12h	1.01175	1
DC3000/delta hrp 24h	1.06492	0.567

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.10503	0.27
DC3000 delta B/DC3000 delta AB	1.07895	0.406

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00622	1
Var 0h	0.87335	0.933
Var 12h I row2-row1	1.13786	0.215
Var 12h NI row2-row1	1.00017	1
Var 36h I row2-row1	1.01079	1
Var 36h NI row2-row1	0.89677	0.522
Var 60h I row2-row1	1.09425	1
Var 60h NI row2-row1	1.02892	1
Time course 0hI-0hNI	1.04311	0.867
Time course 12hI-12hNI	1.04678	0.682
Time course 36hI-36hNI	1.11198	0.063
Time course 60hI-60hNI	1.16462	0.216

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)	0.95983	0.722
transgenic ySAMdc/azygous control (breaker)	1.43709	1
transgenic ySAMdc/azygous control (red)	1.50354	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98396	0.248

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.28226	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.1163	1
Manapal/WT (break)	0.88959	1
Manapal/WT (red)	0.81056	0.242