Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.19.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18637	0.798
27DAP/17DAP	1.01281	0.967
39DAP/27DAP	0.98631	0.769
41DAP/39DAP	0.99149	0.919
42DAP/41DAP	1.36036	0.722
43DAP/42DAP	0.97419	0.912
47DAP/43DAP	1.19787	0.889
52DAP/47DAP	1.04122	0.95
57DAP/52DAP	0.9577	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.37257	0.023
17DAP/reference	1.32045	0.077
27DAP/reference	1.24785	0.111
39DAP/reference	1.21829	0.359
41DAP/reference	1.34212	0.021
42DAP/reference	1.39169	0.001
43DAP/reference	1.34668	0.325
47DAP/reference	1.30734	0.002
52DAP/reference	1.40625	0.036
57DAP/reference	1.13242	0.379

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08219	0.445
27DAP/17DAP	0.94861	0.724
39DAP/27DAP	0.95932	0.536
41DAP/39DAP	0.97578	0.98
42DAP/41DAP	0.94664	0.524
43DAP/42DAP	0.91371	0.132
47DAP/43DAP	1.01446	0.93
52DAP/47DAP	1.01979	0.933
57DAP/52DAP	1.01184	0.984
57DAP/7DAP	0.88308	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85582	0.168
17DAP/reference	0.81262	0.02
27DAP/reference	0.91518	0.264
39DAP/reference	0.97743	0.552
41DAP/reference	1.01382	0.811
42DAP/reference	1.18993	0.233
43DAP/reference	1.04268	1
47DAP/reference	1.0341	1
52DAP/reference	1.12336	0.352
57DAP/reference	1.01403	0.67

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03088	0.823
17DAP/reference	1.31265	0.052
27DAP/reference	1.13245	0.583
39DAP/reference	1.16861	0.164
41DAP/reference	1.15011	0.183
42DAP/reference	1.24755	0.324
43DAP/reference	1.04747	1
47DAP/reference	1.33554	0.021
52DAP/reference	1.47968	0.026
57DAP/reference	1.4321	0.063

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02337	0.963
17DAP/reference	0.9865	0.739
27DAP/reference	0.99684	0.763
39DAP/reference	1.11948	0.318
41DAP/reference	1.18512	0.205
42DAP/reference	1.118	0.49
43DAP/reference	1.3491	0.154
47DAP/reference	1.10002	0.82
52DAP/reference	1.26342	0.405
57DAP/reference	1.03597	0.801

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.45022	0.966
26DAP/20DAP	1.01721	1
34DAP/26DAP	0.90601	0.381
51DAP/34DAP	1.02595	0.909
52DAP/51DAP	1.09168	0.171
53DAP/52DAP	0.79666	0.254
55DAP/53DAP	1.0335	0.976
57DAP/55DAP	1.04347	0.955
62DAP/57DAP	0.90322	0.681
68DAP/62DAP	1.09832	0.912
68DAP/14DAP	1.20838	0.139

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.09611	0.184

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.26039
Mature Green Tomato/Ripe Tomato	1.22562	0.752
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	2.32632
Mature Eggplant/Ripe Tomato	2.78828	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.94419	0.907
1-1-2/M82	0.99318	1
12-2/M82	1.12008	1
12-4/M82	1.20125
1-3/M82	0.65772
2-1-1/M82	1.12866
2-1/M82	N/A	N/A
2-6/M82	1.08581	0.364
3-2/M82	1.05226
4-1-1/M82	1.00349	1
4-1/M82	0.76064
4-3-2/M82	1.19955
4-3/M82	0.90176	1
5-3/M82	1.02968	1
6-2/M82	0.98869
6-3/M82	1.11871
7-1/M82	N/A	N/A
7-2/M82	1.14828
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.94978	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.28612	1
IL12-4/WTpooled	1.04343	0.891
IL1-4/WTpooled	1.0004	1
WT/WTpooled	1.00583	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	1.09365	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91343	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	0.88025	0.178

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.16674	0.134
DC3000 delta B/DC3000 delta AB	1.02328	0.694

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.82428	1
Exp 36h	N/A	N/A
Exp 60h	0.95077	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98057	1
Var 0h	1.07172	0.98
Var 12h I row2-row1	1.13881	0.406
Var 12h NI row2-row1	1.09186	1
Var 36h I row2-row1	0.97682	1
Var 36h NI row2-row1	0.90936	0.469
Var 60h I row2-row1	1.05939	0.562
Var 60h NI row2-row1	1.1288	0.904
Time course 0hI-0hNI	0.87432	0.169
Time course 12hI-12hNI	1.02477	0.833
Time course 36hI-36hNI	0.99758	0.783
Time course 60hI-60hNI	0.92166	0.081

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)	1.05489	0.722
transgenic ySAMdc/azygous control (breaker)	0.80405	0.49
transgenic ySAMdc/azygous control (red)	0.73724	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.8958	0.112

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.89164	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.12277	1
Manapal/WT (break)	0.91629	1
Manapal/WT (red)	1.16348	1