Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-1.2.11.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.77212	0.097
27DAP/17DAP	1.08287	0.89
39DAP/27DAP	1.03921	0.857
41DAP/39DAP	0.74413	0.256
42DAP/41DAP	1.40023	0.552
43DAP/42DAP	1.08578	1
47DAP/43DAP	1.0304	0.95
52DAP/47DAP	1.03355	0.837
57DAP/52DAP	0.97967	0.966

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27862	0.5
17DAP/reference	1.45806	0.138
27DAP/reference	1.50236	0.069
39DAP/reference	1.30836	0.083
41DAP/reference	1.39891	0.241
42DAP/reference	1.26921	0.182
43DAP/reference	1.57594	0.013
47DAP/reference	1.26026	0.223
52DAP/reference	0.81609	0.084
57DAP/reference	0.80274	0.118

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06749	1
27DAP/17DAP	1.12843	0.751
39DAP/27DAP	1.06973	0.793
41DAP/39DAP	1.00626	1
42DAP/41DAP	1.21133	0.102
43DAP/42DAP	1.2108	0.032
47DAP/43DAP	1.05386	0.889
52DAP/47DAP	0.87506	0.413
57DAP/52DAP	1.0973	0.768
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89072	0.122
17DAP/reference	1.02209	0.693
27DAP/reference	0.89816	0.048
39DAP/reference	0.76482	0.049
41DAP/reference	0.75744	0.043
42DAP/reference	0.71365	0.01
43DAP/reference	1.00219	0.694
47DAP/reference	0.76419	0.038
52DAP/reference	0.87883	0.077
57DAP/reference	0.92974	0.27

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06031	0.863
17DAP/reference	1.29593	0.508
27DAP/reference	1.19692	0.552
39DAP/reference	0.54715	N/A
41DAP/reference	1.18612	0.335
42DAP/reference	0.56782	0.024
43DAP/reference	1.08354	0.748
47DAP/reference	1.36657	0.034
52DAP/reference	0.64463	0.171
57DAP/reference	1.08958	0.916

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11838	0.273
17DAP/reference	1.02928	1
27DAP/reference	1.01801	0.749
39DAP/reference	0.94057	0.43
41DAP/reference	0.9688	0.56
42DAP/reference	0.99559	0.816
43DAP/reference	0.8767	0.267
47DAP/reference	1.07389	0.251
52DAP/reference	1.01685	0.888
57DAP/reference	0.61096	0.154

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.56749	0.65
26DAP/20DAP	1.00733	1
34DAP/26DAP	1.1907	1
51DAP/34DAP	1.70802	0.032
52DAP/51DAP	0.84881	1
53DAP/52DAP	1.10891	0.768
55DAP/53DAP	0.87012	0.263
57DAP/55DAP	1.58643	0.07
62DAP/57DAP	0.95445	0.871
68DAP/62DAP	1.05292	N/A
68DAP/14DAP	0.40309	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.86944	0.285

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.28167	0.363
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	9.22096	N/A
Mature Eggplant/Ripe Tomato	0.54397	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.9586	0.742
1-1-2/M82	1.31284	0.977
12-2/M82	0.90518	N/A
12-4/M82	0.78849	0.619
1-3/M82	N/A	N/A
2-1-1/M82	0.86256	N/A
2-1/M82	0.63419	N/A
2-6/M82	1.49961	N/A
3-2/M82	1.22851	N/A
4-1-1/M82	N/A	N/A
4-1/M82	0.56738	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.45462	N/A
5-3/M82	1.02887	1
6-2/M82	N/A	N/A
6-3/M82	0.93681	1
7-1/M82	1.34338	N/A
7-2/M82	0.69919	N/A
9-3-2/M82	1.0463	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.42365	0.277
IL2-6/WTpooled	0.58951	0.473
IL7-5/WTpooled	0.95135	1
IL7-3/WTpooled	1.74346	1
IL12-4/WTpooled	1.01928	1
IL1-4/WTpooled	1.28205	0.426
WT/WTpooled	1.04248	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	0.98719	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.86532	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.11719	1
DC3000/delta hrp 24h	1.29291	0.113

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.90652	0.46
DC3000 delta B/DC3000 delta AB	0.93927	0.619

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.4786	1
Exp 36h	N/A	N/A
Exp 60h	1.66343	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.92294	1
Var 0h	1.2522	0.98
Var 12h I row2-row1	0.91705	0.565
Var 12h NI row2-row1	1.11258	1
Var 36h I row2-row1	1.27571	0.305
Var 36h NI row2-row1	0.83731	0.645
Var 60h I row2-row1	0.96514	0.832
Var 60h NI row2-row1	0.90614	0.977
Time course 0hI-0hNI	0.9954	1
Time course 12hI-12hNI	0.98482	0.914
Time course 36hI-36hNI	0.9882	0.632
Time course 60hI-60hNI	0.93773	0.319

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)	1.72412	0.571
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	1.34617	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.42464	0.273

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.78127	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.73777	1
Manapal/WT (break)	1.11542	1
Manapal/WT (red)	1.41644	0.164