Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.2.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.62267	0.028
27DAP/17DAP	0.6817	0.08
39DAP/27DAP	0.88638	0.564
41DAP/39DAP	0.80507	0.322
42DAP/41DAP	1.18488	0.691
43DAP/42DAP	0.99174	0.937
47DAP/43DAP	0.98629	0.699
52DAP/47DAP	0.92396	0.752
57DAP/52DAP	1.06729	0.962

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.30683	0.006
17DAP/reference	1.63181	0.012
27DAP/reference	2.08617	0.008
39DAP/reference	0.82467	0.121
41DAP/reference	0.64794	0.01
42DAP/reference	0.8831	0.05
43DAP/reference	0.6173	0.013
47DAP/reference	0.6663	0.003
52DAP/reference	0.72572	0.047
57DAP/reference	0.8087	0.035

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85613	0.062
27DAP/17DAP	0.87184	0.279
39DAP/27DAP	0.888	0.152
41DAP/39DAP	0.65366	0.016
42DAP/41DAP	1.0341	0.976
43DAP/42DAP	1.15733	0.212
47DAP/43DAP	0.97412	0.833
52DAP/47DAP	0.86361	0.42
57DAP/52DAP	0.97741	0.756
57DAP/7DAP	1.20078	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.50176	0.046
17DAP/reference	1.32526	0.084
27DAP/reference	1.19764	0.073
39DAP/reference	0.9204	0.23
41DAP/reference	0.84231	0.026
42DAP/reference	0.80837	0.042
43DAP/reference	1.12979	0.873
47DAP/reference	0.88624	0.383
52DAP/reference	1.79215	0.025
57DAP/reference	1.34042	0.087

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.65443	0.116
17DAP/reference	2.09141	0.012
27DAP/reference	1.76002	0.063
39DAP/reference	0.72378	0.034
41DAP/reference	1.03648	0.981
42DAP/reference	1.34682	0.044
43DAP/reference	0.65275	0.023
47DAP/reference	0.66266	0.009
52DAP/reference	0.59598	0.004
57DAP/reference	0.47213	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.62403	0.016
17DAP/reference	1.56333	0.099
27DAP/reference	1.31947	0.038
39DAP/reference	1.1899	0.062
41DAP/reference	1.19977	0.067
42DAP/reference	1.26304	0.184
43DAP/reference	1.12896	0.617
47DAP/reference	0.53327	0.006
52DAP/reference	1.12033	0.908
57DAP/reference	1.12112	0.371

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05209	1
26DAP/20DAP	0.94393	1
34DAP/26DAP	0.98162	0.98
51DAP/34DAP	0.89154	0.225
52DAP/51DAP	1.01949	0.821
53DAP/52DAP	0.88902	0.311
55DAP/53DAP	1.05487	0.82
57DAP/55DAP	0.92455	0.664
62DAP/57DAP	1.65978	0.445
68DAP/62DAP	1.5061	0.034
68DAP/14DAP	0.88789	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.67958	0.027

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.04593	0.058
Mature Green Tomato/Ripe Tomato	2.21264	0.032
Immature Eggplant/Mature Eggplant	0.48249	0.062
Ripe Pepper/Ripe Tomato	5.24451	0.256
Mature Eggplant/Ripe Tomato	5.56423	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9644	0.961
1-1-2/M82	1.08544	1
12-2/M82	0.91212	0.955
12-4/M82	0.83199	0.619
1-3/M82	1.63035
2-1-1/M82	0.75672
2-1/M82	N/A	N/A
2-6/M82	1.05266	1
3-2/M82	0.81636
4-1-1/M82	N/A	N/A
4-1/M82	0.73946
4-3-2/M82	0.87476
4-3/M82	0.99652	1
5-3/M82	1.09603	1
6-2/M82	1.11331
6-3/M82	0.72856
7-1/M82	0.72267
7-2/M82	1.02369
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.82777	0.321
IL2-6/WTpooled	0.73902
IL7-5/WTpooled	0.94715
IL7-3/WTpooled	1.2218	0.362
IL12-4/WTpooled	1.06343	0.737
IL1-4/WTpooled	0.89328	0.699
WT/WTpooled	1.0578	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	0.85362	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06455	0.758
DC3000/delta hrp 6h	1.01726	1
DC3000/delta hrp 12h	1.01665	1
DC3000/delta hrp 24h	0.17944	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.47091	0.023
DC3000 delta B/DC3000 delta AB	0.6206	0.023

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95324	1
Exp 36h	0.97314	0.879
Exp 60h	1.06041	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01222	1
Var 0h	1.52323	0.936
Var 12h I row2-row1	0.86734	0.338
Var 12h NI row2-row1	0.95211	0.82
Var 36h I row2-row1	1.12024	0.41
Var 36h NI row2-row1	1.41874	1
Var 60h I row2-row1	0.96524	0.374
Var 60h NI row2-row1	1.13528	0.904
Time course 0hI-0hNI	1.00817	1
Time course 12hI-12hNI	0.9632	0.701
Time course 36hI-36hNI	0.84583	0.05
Time course 60hI-60hNI	0.46864	0.006

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)	0.82919	0.289
transgenic ySAMdc/azygous control (breaker)	1.08685	1
transgenic ySAMdc/azygous control (red)	0.97347	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.80999	0.16

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.15102	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.03365	0.307
Manapal/WT (break)	1.21334	0.381
Manapal/WT (red)	1.28087	0.222