Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.8.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84493	0.331
27DAP/17DAP	0.92807	0.863
39DAP/27DAP	1.13962	0.903
41DAP/39DAP	0.80114	0.247
42DAP/41DAP	1.40502	0.295
43DAP/42DAP	2.18795	0.025
47DAP/43DAP	0.68994	0.185
52DAP/47DAP	1.21521	0.997
57DAP/52DAP	1.00526	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78313	0.092
17DAP/reference	0.95724	0.567
27DAP/reference	2.34007	0.007
39DAP/reference	1.09367	0.828
41DAP/reference	1.04446	0.855
42DAP/reference	7.0421	0.001
43DAP/reference	1.71846	0.007
47DAP/reference	5.9139	0.001
52DAP/reference	3.43918	0.007
57DAP/reference	1.68208	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.77939	0.336
27DAP/17DAP	1.18446	0.429
39DAP/27DAP	1.15736	0.57
41DAP/39DAP	0.84303	0.398
42DAP/41DAP	1.38755	0.46
43DAP/42DAP	1.21059	0.103
47DAP/43DAP	1.03868	0.977
52DAP/47DAP	0.83055	0.466
57DAP/52DAP	0.92546	0.651
57DAP/7DAP	1.58477	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.37895	0.06
17DAP/reference	0.36635	0.011
27DAP/reference	0.52029	0.01
39DAP/reference	0.609	0.012
41DAP/reference	0.62923	0.027
42DAP/reference	1.67889	0.174
43DAP/reference	1.78062	0.018
47DAP/reference	1.90962	0.014
52DAP/reference	0.49484	0.012
57DAP/reference	0.49162	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.63353	0.006
17DAP/reference	0.846	0.139
27DAP/reference	0.89129	0.304
39DAP/reference	0.71509	0.067
41DAP/reference	0.55222	0.087
42DAP/reference	1.02642	0.655
43DAP/reference	0.86162	0.314
47DAP/reference	0.92954	0.423
52DAP/reference	0.75999	0.031
57DAP/reference	0.94806	0.46

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.38688	0.035
17DAP/reference	0.6522	0.135
27DAP/reference	0.47381	0.035
39DAP/reference	0.43775	0.008
41DAP/reference	0.38643	0.019
42DAP/reference	1.90768	0.099
43DAP/reference	1.49852	0.131
47DAP/reference	2.6652	0.004
52DAP/reference	1.73887	0.06
57DAP/reference	1.57955	0.033

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.22691	0.966
26DAP/20DAP	0.99927	1
34DAP/26DAP	0.78002	0.399
51DAP/34DAP	1.33916
52DAP/51DAP	0.8337	1
53DAP/52DAP	0.86356	0.797
55DAP/53DAP	1.53117	0.566
57DAP/55DAP	0.87726	0.647
62DAP/57DAP	1.46329	0.723
68DAP/62DAP	0.88536	0.834
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.10262	0.033

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.70206	0.188
Mature Green Tomato/Ripe Tomato	0.27406	0.017
Immature Eggplant/Mature Eggplant	0.37838	0.062
Ripe Pepper/Ripe Tomato	0.52537	0.224
Mature Eggplant/Ripe Tomato	0.33302	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	4.0556	0.418
1-1-2/M82	1.52568	1
12-2/M82	0.96011	0.862
12-4/M82	0.91012	1
1-3/M82	0.52793
2-1-1/M82	1.78994	0.764
2-1/M82	0.75755
2-6/M82	2.12117
3-2/M82	0.75041	1
4-1-1/M82	0.36043
4-1/M82	1.78229
4-3-2/M82	1.7023	0.241
4-3/M82	2.91745
5-3/M82	1.40296	1
6-2/M82	N/A	N/A
6-3/M82	1.42791	1
7-1/M82	0.56655	0.443
7-2/M82	3.22696	0.299
9-3-2/M82	1.62056	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.9374	0.321
IL2-6/WTpooled	1.1482	0.584
IL7-5/WTpooled	1.00358	1
IL7-3/WTpooled	1.06285	1
IL12-4/WTpooled	0.75429	0.566
IL1-4/WTpooled	1.064	1
WT/WTpooled	0.90608	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	0.88615	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.12222	0.914
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.99178	1
DC3000/delta hrp 24h	0.96344	0.761

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	1.2207	0.232

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02649	1
Exp 36h	N/A	N/A
Exp 60h	0.84927	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97925	1
Var 0h	1.85456	0.782
Var 12h I row2-row1	0.87074	0.514
Var 12h NI row2-row1	0.83007	0.546
Var 36h I row2-row1	1.17074	0.908
Var 36h NI row2-row1	1.03028	1
Var 60h I row2-row1	0.84523	0.439
Var 60h NI row2-row1	0.83823	0.756
Time course 0hI-0hNI	1.32031	0.537
Time course 12hI-12hNI	0.95545	0.831
Time course 36hI-36hNI	1.08551	0.722
Time course 60hI-60hNI	0.98503	1

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)	0.97137	0.789
transgenic ySAMdc/azygous control (breaker)	2.39555	0.172
transgenic ySAMdc/azygous control (red)	1.19134	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.11269	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.84343	0.096
Manapal/WT (break)	1.36995	0.381
Manapal/WT (red)	1.89696	0.134