Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.20.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.61244	0.116
27DAP/17DAP	1.071	0.92
39DAP/27DAP	1.16993	0.876
41DAP/39DAP	1.83328	0.478
42DAP/41DAP	1.07522	1
43DAP/42DAP	1.22104	1
47DAP/43DAP	1.43169	0.542
52DAP/47DAP	0.95583	0.771
57DAP/52DAP	1.15423	0.988

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97466	0.513
17DAP/reference	0.97571	0.63
27DAP/reference	0.83352	0.018
39DAP/reference	0.77467	0.011
41DAP/reference	0.72243	0.009
42DAP/reference	0.99269	0.517
43DAP/reference	0.92683	0.234
47DAP/reference	0.99714	0.535
52DAP/reference	0.83934	0.044
57DAP/reference	0.83354	0.056

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.75458	0.036
27DAP/17DAP	0.65539	0.218
39DAP/27DAP	1.02543	1
41DAP/39DAP	1.38288	0.036
42DAP/41DAP	0.99939	0.777
43DAP/42DAP	0.92284	0.293
47DAP/43DAP	1.10424	0.788
52DAP/47DAP	1.43954	0.29
57DAP/52DAP	1.41986	0.547
57DAP/7DAP	1.06733	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12083	0.223
17DAP/reference	1.19714	0.015
27DAP/reference	1.4323	0.008
39DAP/reference	1.38148	0.008
41DAP/reference	1.30261	0.031
42DAP/reference	1.56041	0.007
43DAP/reference	1.41394	0.006
47DAP/reference	1.15505	0.421
52DAP/reference	1.58427	0.013
57DAP/reference	1.33115	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91443	0.238
17DAP/reference	0.85838	0.039
27DAP/reference	0.9202	0.212
39DAP/reference	0.91235	0.152
41DAP/reference	0.92356	0.199
42DAP/reference	0.91024	0.055
43DAP/reference	1.0149	0.692
47DAP/reference	0.96152	0.302
52DAP/reference	0.78869	0.004
57DAP/reference	0.85116	0.063

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.28486	0.049
17DAP/reference	0.88686	0.203
27DAP/reference	1.27306	0.036
39DAP/reference	1.17815	0.029
41DAP/reference	1.33822	0.019
42DAP/reference	1.20892	0.099
43DAP/reference	0.90048	0.11
47DAP/reference	1.22971	0.05
52DAP/reference	1.3195	0.106
57DAP/reference	1.35639	0.094

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07958	0.966
26DAP/20DAP	1.54135	0.099
34DAP/26DAP	1.2184	0.819
51DAP/34DAP	2.23107	0.032
52DAP/51DAP	1.2708	0.186
53DAP/52DAP	0.99092	0.902
55DAP/53DAP	1.06353	0.782
57DAP/55DAP	0.8512	0.309
62DAP/57DAP	1.06146	0.935
68DAP/62DAP	1.88008	0.013
68DAP/14DAP	2.49072	0.023

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.6965	0.045

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.3906
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	1.07305	0.912
Ripe Pepper/Ripe Tomato	0.84031
Mature Eggplant/Ripe Tomato	2.73926	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.59506
1-1-2/M82	0.96362	1
12-2/M82	N/A	N/A
12-4/M82	0.77226	0.25
1-3/M82	0.7213
2-1-1/M82	0.93082
2-1/M82	N/A	N/A
2-6/M82	1.07019	1
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	1.09648	1
5-3/M82	1.12653	0.572
6-2/M82	N/A	N/A
6-3/M82	1.33313
7-1/M82	N/A	N/A
7-2/M82	0.91962
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.373	0.243
IL2-6/WTpooled	0.96866	1
IL7-5/WTpooled	0.60412	0.559
IL7-3/WTpooled	0.99271	1
IL12-4/WTpooled	1.06666	0.839
IL1-4/WTpooled	0.9502	1
WT/WTpooled	1.05854	0.999

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	0.9147	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.84497	1
DC3000/delta hrp 6h	0.77033	0.95
DC3000/delta hrp 12h	1.05837	1
DC3000/delta hrp 24h	1.5046	0.516

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.14895	0.313
DC3000 delta B/DC3000 delta AB	0.94023	0.483

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96132	1
Exp 36h	1.16494	1
Exp 60h	1.43151	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01386
Var 0h	N/A	N/A
Var 12h I row2-row1	0.88795	0.77
Var 12h NI row2-row1	1.13727	0.161
Var 36h I row2-row1	0.91238	1
Var 36h NI row2-row1	1.39665	0.253
Var 60h I row2-row1	0.8183	0.439
Var 60h NI row2-row1	0.94461	1
Time course 0hI-0hNI	0.86851	0.201
Time course 12hI-12hNI	1.03159	0.818
Time course 36hI-36hNI	0.81846	0.162
Time course 60hI-60hNI	0.9621	0.646

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)	1.0038	0.921
transgenic ySAMdc/azygous control (breaker)	0.96612	1
transgenic ySAMdc/azygous control (red)	0.88917	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.11955	0.04

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.9508	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.94671	1
Manapal/WT (break)	0.88416	1
Manapal/WT (red)	1.01208	1