Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-2.2.2.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	44.3002	0.008
27DAP/17DAP	1.29165	0.742
39DAP/27DAP	1.11465	0.972
41DAP/39DAP	0.43524	0.041
42DAP/41DAP	0.54427	0.397
43DAP/42DAP	0.65298	0.467
47DAP/43DAP	1.00199	0.89
52DAP/47DAP	0.92947	0.803
57DAP/52DAP	1.90311	0.454

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.47738	0.033
17DAP/reference	8.32273	0.013
27DAP/reference	13.0926	0.007
39DAP/reference	5.23597	0.012
41DAP/reference	4.95421	0.009
42DAP/reference	2.26767	0.001
43DAP/reference	0.73979	0.013
47DAP/reference	1.20782	0.463
52DAP/reference	2.41469	0.045
57DAP/reference	2.42602	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	6.50507	0.041
27DAP/17DAP	1.39633	0.045
39DAP/27DAP	0.54283	0.028
41DAP/39DAP	0.97907	0.923
42DAP/41DAP	1.0535	0.924
43DAP/42DAP	0.33799	0.008
47DAP/43DAP	0.68404	0.009
52DAP/47DAP	1.68348	0.099
57DAP/52DAP	1.07491	0.992
57DAP/7DAP	0.96805	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23431	1
17DAP/reference	7.17838	0.006
27DAP/reference	4.64221	0.006
39DAP/reference	4.58232	0.006
41DAP/reference	2.62886	0.008
42DAP/reference	2.03379	0.03
43DAP/reference	0.46256	0.011
47DAP/reference	1.09032	0.595
52DAP/reference	0.60423	0.012
57DAP/reference	0.68721	0.021

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.14186	0.005
17DAP/reference	6.36235	0.007
27DAP/reference	8.85357	0.012
39DAP/reference	7.92149	0.011
41DAP/reference	3.08396	0.005
42DAP/reference	5.51175	0.007
43DAP/reference	2.08758	0.018
47DAP/reference	3.2823	0.016
52DAP/reference	5.91517	0.006
57DAP/reference	1.41351	0.593

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.34917	0.045
17DAP/reference	2.00673	0.097
27DAP/reference	4.7361	0.008
39DAP/reference	2.20998	0.004
41DAP/reference	1.65987	0.011
42DAP/reference	1.07339	0.907
43DAP/reference	0.86218	0.226
47DAP/reference	0.32708	0.005
52DAP/reference	0.5394	0.103
57DAP/reference	3.72786	0.009

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.42306	0.966
26DAP/20DAP	0.98422	1
34DAP/26DAP	1.23929	0.819
51DAP/34DAP	2.09064	0.034
52DAP/51DAP	0.60761	0.064
53DAP/52DAP	5.46329	0.019
55DAP/53DAP	1.161	0.348
57DAP/55DAP	1.22411	0.694
62DAP/57DAP	0.5369	0.003
68DAP/62DAP	0.74097	0.464
68DAP/14DAP	3.63863	0.021

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	11.0179	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.97522	0.765
Mature Green Tomato/Ripe Tomato	3.44028	0.015
Immature Eggplant/Mature Eggplant	19.7448	0.05
Ripe Pepper/Ripe Tomato	0.17608	0.224
Mature Eggplant/Ripe Tomato	0.40591	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.60877	0.841
1-1-2/M82	0.85278	1
12-2/M82	1.42238	1
12-4/M82	0.86266	0.619
1-3/M82	3.43751	0.479
2-1-1/M82	0.98937	1
2-1/M82	0.9906	1
2-6/M82	0.71587	1
3-2/M82	1.33821	0.463
4-1-1/M82	0.86146	0.962
4-1/M82	1.18733	N/A
4-3-2/M82	0.43228	N/A
4-3/M82	0.70606	0.475
5-3/M82	1.17841	0.496
6-2/M82	0.87365	1
6-3/M82	1.08075	1
7-1/M82	1.36015	N/A
7-2/M82	1.00793	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.73925	0.321
IL2-6/WTpooled	0.68275	0.358
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.04221	1
IL12-4/WTpooled	0.74175	0.71
IL1-4/WTpooled	0.92772	0.834
WT/WTpooled	0.95652	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	0.83966	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98865	1
DC3000/delta hrp 6h	0.9764	0.95
DC3000/delta hrp 12h	1.51521	1
DC3000/delta hrp 24h	0.5027	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.70856	0.413
DC3000 delta B/DC3000 delta AB	0.73768	0.042

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.05224	1
Exp 36h	0.45606	0.41
Exp 60h	0.30439	0.258

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9861	1
Var 0h	0.80893	0.594
Var 12h I row2-row1	0.7654	0.565
Var 12h NI row2-row1	0.86823	0.82
Var 36h I row2-row1	1.02687	1
Var 36h NI row2-row1	1.74636	0.253
Var 60h I row2-row1	1.48144	0.562
Var 60h NI row2-row1	1.04887	1
Time course 0hI-0hNI	1.09782	0.662
Time course 12hI-12hNI	0.84489	0.252
Time course 36hI-36hNI	0.57917	0.023
Time course 60hI-60hNI	0.05097	0.005

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)	1.02901	0.863
transgenic ySAMdc/azygous control (breaker)	1.08968	1
transgenic ySAMdc/azygous control (red)	0.8615	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.99407	0.036

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.01996	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.69329	1
Manapal/WT (break)	0.2364	0.285
Manapal/WT (red)	0.78846	0.315