Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.17.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04836	0.901
27DAP/17DAP	0.95193	0.932
39DAP/27DAP	1.04638	0.857
41DAP/39DAP	0.90823	0.645
42DAP/41DAP	1.29435	0.556
43DAP/42DAP	1.33541	0.619
47DAP/43DAP	1.00685	0.879
52DAP/47DAP	1.41046	0.61
57DAP/52DAP	0.93683	0.923

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78247	0.052
17DAP/reference	0.97449	0.63
27DAP/reference	0.96303	0.497
39DAP/reference	1.00691	0.991
41DAP/reference	0.96664	0.542
42DAP/reference	1.07749	0.182
43DAP/reference	1.12728	0.189
47DAP/reference	1.40866	0.002
52DAP/reference	1.25001	0.158
57DAP/reference	1.30329	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.32289	0.34
27DAP/17DAP	0.78952	0.295
39DAP/27DAP	0.92663	0.514
41DAP/39DAP	1.07702	0.887
42DAP/41DAP	0.74891	0.047
43DAP/42DAP	1.28714	0.413
47DAP/43DAP	0.98061	0.93
52DAP/47DAP	0.85046	0.42
57DAP/52DAP	1.28698	0.32
57DAP/7DAP	0.76313

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.35959	0.166
17DAP/reference	1.34706	0.009
27DAP/reference	1.09558	1
39DAP/reference	0.9166	0.23
41DAP/reference	0.90808	0.259
42DAP/reference	1.20224	0.405
43DAP/reference	0.9535	0.368
47DAP/reference	1.1454	0.48
52DAP/reference	0.8861	0.163
57DAP/reference	1.25594	0.612

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93459	0.362
17DAP/reference	0.9669	0.499
27DAP/reference	1.00013	0.663
39DAP/reference	1.03749	0.783
41DAP/reference	0.87967	0.05
42DAP/reference	0.97409	0.482
43DAP/reference	0.96444	0.468
47DAP/reference	1.00287	0.79
52DAP/reference	1.02021	1
57DAP/reference	0.92092	0.259

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00765	0.699
17DAP/reference	0.83536	0.159
27DAP/reference	1.05371	0.934
39DAP/reference	1.05328	0.813
41DAP/reference	1.01806	1
42DAP/reference	0.94557	0.552
43DAP/reference	0.88038	0.305
47DAP/reference	1.40767	0.008
52DAP/reference	1.24508	0.483
57DAP/reference	1.51745	0.013

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09531	0.966
26DAP/20DAP	1.11982	0.689
34DAP/26DAP	1.02858	1
51DAP/34DAP	0.97834	0.747
52DAP/51DAP	0.76363	1
53DAP/52DAP	1.12442	0.819
55DAP/53DAP	1.3956	0.256
57DAP/55DAP	0.92647	0.658
62DAP/57DAP	0.83592	0.162
68DAP/62DAP	1.08025	0.945
68DAP/14DAP	1.60433	0.346

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.92735	0.422

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.13502	0.058
Mature Green Tomato/Ripe Tomato	0.39201
Immature Eggplant/Mature Eggplant	1.09573	0.174
Ripe Pepper/Ripe Tomato	0.3632	0.224
Mature Eggplant/Ripe Tomato	1.38891	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.85731	0.605
1-1-2/M82	1.02107	1
12-2/M82	N/A	N/A
12-4/M82	0.85929
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.05857	0.594
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	0.85953
4-3-2/M82	N/A	N/A
4-3/M82	0.85166
5-3/M82	1.52924	0.455
6-2/M82	N/A	N/A
6-3/M82	1.00581	1
7-1/M82	N/A	N/A
7-2/M82	1.30322	0.324
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.87208	1
IL2-6/WTpooled	1.07251	0.46
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.84399	0.294
IL12-4/WTpooled	0.8429	0.478
IL1-4/WTpooled	1.03821	1
WT/WTpooled	0.99532	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	1.18184	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.90151	0.941
DC3000/delta hrp 6h	1.22117	0.631
DC3000/delta hrp 12h	1.10683
DC3000/delta hrp 24h	0.88957	0.363

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.30193	0.313
DC3000 delta B/DC3000 delta AB	1.21505	0.479

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.99403	1
Exp 36h	0.8842	0.82
Exp 60h	1.02771	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9378	1
Var 0h	1.18199	1
Var 12h I row2-row1	1.40207	0.406
Var 12h NI row2-row1	0.84963	0.546
Var 36h I row2-row1	1.08372	0.41
Var 36h NI row2-row1	0.80125	0.706
Var 60h I row2-row1	0.84908	0.582
Var 60h NI row2-row1	0.9996	1
Time course 0hI-0hNI	0.92571	0.617
Time course 12hI-12hNI	0.93227	0.535
Time course 36hI-36hNI	0.86975	0.097
Time course 60hI-60hNI	0.79398	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)	1.04724	0.541
transgenic ySAMdc/azygous control (breaker)	1.07172	1
transgenic ySAMdc/azygous control (red)	0.92916	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.98035	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.61971	0.172
Manapal/WT (break)	0.86879	1
Manapal/WT (red)	0.8358	0.183