Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.1.10.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16637	0.463
27DAP/17DAP	1.01236	1
39DAP/27DAP	1.20823	0.516
41DAP/39DAP	1.06307	0.859
42DAP/41DAP	1.34104	0.582
43DAP/42DAP	0.93489	0.801
47DAP/43DAP	0.99505	0.904
52DAP/47DAP	1.64399	0.308
57DAP/52DAP	0.78588	0.55

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94302	0.308
17DAP/reference	0.8209	0.018
27DAP/reference	0.85444	0.012
39DAP/reference	0.98505	0.762
41DAP/reference	0.92127	0.201
42DAP/reference	0.99841	0.645
43DAP/reference	1.01524	0.928
47DAP/reference	0.90374	0.023
52DAP/reference	0.84661	0.037
57DAP/reference	0.89541	0.031

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.7857	0.064
27DAP/17DAP	1.14664	0.333
39DAP/27DAP	0.90151	0.269
41DAP/39DAP	0.86653	0.186
42DAP/41DAP	1.06677	0.763
43DAP/42DAP	1.03	0.585
47DAP/43DAP	1.05083	0.798
52DAP/47DAP	0.968	0.9
57DAP/52DAP	0.96304	0.678
57DAP/7DAP	0.84712	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.25109	0.032
17DAP/reference	4.1166	0.006
27DAP/reference	4.76003	0.006
39DAP/reference	4.06666	0.035
41DAP/reference	3.1597	0.09
42DAP/reference	2.9242	0.233
43DAP/reference	5.85937	0.006
47DAP/reference	2.72441	0.254
52DAP/reference	5.89972	0.007
57DAP/reference	5.26425	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98262	0.77
17DAP/reference	0.99894	0.728
27DAP/reference	0.98364	0.554
39DAP/reference	0.91792	0.132
41DAP/reference	0.9737	0.315
42DAP/reference	0.91546	0.237
43DAP/reference	1.03872	0.91
47DAP/reference	1.0103	0.841
52DAP/reference	0.94002	0.239
57DAP/reference	1.28096	0.14

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.67907	0.019
17DAP/reference	2.50457	0.241
27DAP/reference	5.08776	0.02
39DAP/reference	6.82887	0.005
41DAP/reference	5.37709	0.007
42DAP/reference	5.51752	0.009
43DAP/reference	4.49021	0.026
47DAP/reference	1.00219	0.754
52DAP/reference	4.33069	0.052
57DAP/reference	0.90168	0.299

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95374	1
26DAP/20DAP	1.02871	1
34DAP/26DAP	0.8444	0.152
51DAP/34DAP	0.81272	0.077
52DAP/51DAP	1.0626	0.42
53DAP/52DAP	1.03157	0.944
55DAP/53DAP	0.80121	0.489
57DAP/55DAP	1.03163	1
62DAP/57DAP	1.18272	0.569
68DAP/62DAP	0.97466	0.834
68DAP/14DAP	1.04314	0.889

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.85106	0.211

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	5.44503	0.058
Mature Green Tomato/Ripe Tomato	1.22046	0.399
Immature Eggplant/Mature Eggplant	10.6939	0.05
Ripe Pepper/Ripe Tomato	0.2365	1
Mature Eggplant/Ripe Tomato	5.19946	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0916	1
1-1-2/M82	0.86737	1
12-2/M82	1.18269	1
12-4/M82	1.07288	1
1-3/M82	0.92824	0.501
2-1-1/M82	0.98899	1
2-1/M82	1.35186	1
2-6/M82	0.95289	1
3-2/M82	0.95558	0.455
4-1-1/M82	0.95556	0.985
4-1/M82	0.89073	0.737
4-3-2/M82	0.96466	1
4-3/M82	0.8661	1
5-3/M82	1.03334	1
6-2/M82	1.01487	1
6-3/M82	0.97973	1
7-1/M82	0.92107	1
7-2/M82	1.04646	1
9-3-2/M82	0.89201	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.95334	1
IL2-6/WTpooled	1.02157	1
IL7-5/WTpooled	0.70341	1
IL7-3/WTpooled	1.1056	1
IL12-4/WTpooled	1.00328	1
IL1-4/WTpooled	0.97555	0.435
WT/WTpooled	0.93893	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	0.90811	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01049	0.921
DC3000/delta hrp 6h	1.11021	1
DC3000/delta hrp 12h	1.06108	1
DC3000/delta hrp 24h	1.11755	0.553

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.48763	0.023
DC3000 delta B/DC3000 delta AB	0.53283	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.7432	1
Exp 36h	2.6124	0.693
Exp 60h	1.11989	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98425	1
Var 0h	1.05703	1
Var 12h I row2-row1	0.94078	0.627
Var 12h NI row2-row1	0.98388	0.906
Var 36h I row2-row1	0.91471	0.438
Var 36h NI row2-row1	1.11702	1
Var 60h I row2-row1	0.91023	0.374
Var 60h NI row2-row1	0.9496	0.932
Time course 0hI-0hNI	1.04738	0.662
Time course 12hI-12hNI	0.97195	0.79
Time course 36hI-36hNI	0.8704	0.029
Time course 60hI-60hNI	0.90409	0.161

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)	1.34038	0.339
transgenic ySAMdc/azygous control (breaker)	0.80683	0.173
transgenic ySAMdc/azygous control (red)	0.91409	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00137	0.958

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.40839	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.58662	1
Manapal/WT (break)	1.00183	1
Manapal/WT (red)	0.29482	0.229