Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.11.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0897	0.681
27DAP/17DAP	1.11228	0.849
39DAP/27DAP	1.03585	1
41DAP/39DAP	1.18108	0.224
42DAP/41DAP	0.9154	1
43DAP/42DAP	0.97961	0.925
47DAP/43DAP	0.97051	0.876
52DAP/47DAP	0.96425	0.884
57DAP/52DAP	1.11821	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	N/A	N/A
17DAP/reference	N/A	N/A
27DAP/reference	N/A	N/A
39DAP/reference	0.92244	0.691
41DAP/reference	1.76572	0.022
42DAP/reference	1.09016	0.931
43DAP/reference	N/A	N/A
47DAP/reference	1.14706	0.306
52DAP/reference	1.93541
57DAP/reference	0.59649	0.147

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00611	1
27DAP/17DAP	1.04895	0.842
39DAP/27DAP	0.91553	0.477
41DAP/39DAP	1.02999	0.801
42DAP/41DAP	0.96591	0.721
43DAP/42DAP	0.99889	1
47DAP/43DAP	0.97314	0.774
52DAP/47DAP	1.00416	1
57DAP/52DAP	0.98121	0.75
57DAP/7DAP	0.98308	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23695	0.054
17DAP/reference	1.5702	0.006
27DAP/reference	1.56085	0.01
39DAP/reference	1.6435	0.006
41DAP/reference	1.55809	0.015
42DAP/reference	1.96645	0.006
43DAP/reference	1.99052	0.006
47DAP/reference	1.29124	0.504
52DAP/reference	1.88536	0.007
57DAP/reference	1.75979	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95993	0.564
17DAP/reference	0.95916	0.26
27DAP/reference	1.21576	1
39DAP/reference	0.93525	0.214
41DAP/reference	0.86437	0.156
42DAP/reference	0.85946
43DAP/reference	0.93917	0.45
47DAP/reference	1.01646
52DAP/reference	0.97618	0.38
57DAP/reference	0.99573	0.68

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07151	0.56
17DAP/reference	1.06405	0.675
27DAP/reference	1.43457	0.017
39DAP/reference	1.37329	0.018
41DAP/reference	1.28788	0.038
42DAP/reference	1.47688	0.01
43DAP/reference	1.40653	0.055
47DAP/reference	1.01112	0.966
52DAP/reference	1.31633	0.161
57DAP/reference	1.71987	0.385

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00541	0.966
26DAP/20DAP	0.9957	1
34DAP/26DAP	1.01774	1
51DAP/34DAP	1.02467	0.909
52DAP/51DAP	0.97299	1
53DAP/52DAP	N/A	N/A
55DAP/53DAP	0.91672	0.024
57DAP/55DAP	0.88597	0.443
62DAP/57DAP	0.99187	1
68DAP/62DAP	0.93251	0.7
68DAP/14DAP	1.38067	0.146

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.98873	0.635

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.07469	0.666
Mature Green Tomato/Ripe Tomato	0.87705	0.446
Immature Eggplant/Mature Eggplant	0.80048	0.292
Ripe Pepper/Ripe Tomato	5.37155	1
Mature Eggplant/Ripe Tomato	2.54811	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02926	1
1-1-2/M82	0.99094	1
12-2/M82	0.91654	0.955
12-4/M82	0.97138	1
1-3/M82	1.03118	1
2-1-1/M82	0.92549	0.683
2-1/M82	0.97829
2-6/M82	0.96224	1
3-2/M82	0.97854	0.752
4-1-1/M82	1.07052	1
4-1/M82	0.91787	0.665
4-3-2/M82	0.92836	1
4-3/M82	0.94464	0.72
5-3/M82	1.03573	0.572
6-2/M82	1.17559	1
6-3/M82	1.02935	1
7-1/M82	1.00909	1
7-2/M82	0.90049	0.796
9-3-2/M82	0.86986	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.22319	0.277
IL2-6/WTpooled	0.83216	0.358
IL7-5/WTpooled	1.00041	1
IL7-3/WTpooled	0.85943	0.31
IL12-4/WTpooled	1.07139	1
IL1-4/WTpooled	0.74399	0.415
WT/WTpooled	1.05031	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	0.88245	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99328	1
DC3000/delta hrp 6h	0.95496	0.95
DC3000/delta hrp 12h	0.93948	1
DC3000/delta hrp 24h	1.04118	0.76

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.07047	0.476
DC3000 delta B/DC3000 delta AB	1.0215	0.625

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.78491	1
Exp 36h	0.8328	0.539
Exp 60h	0.96117	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03749	1
Var 0h	0.39505	0.457
Var 12h I row2-row1	1.11364	0.242
Var 12h NI row2-row1	0.92729	0.488
Var 36h I row2-row1	0.78357	0.805
Var 36h NI row2-row1	0.97036	0.645
Var 60h I row2-row1	1.17446	1
Var 60h NI row2-row1	1.17997	0.904
Time course 0hI-0hNI	1.00586	1
Time course 12hI-12hNI	1.05657	0.714
Time course 36hI-36hNI	0.96475	0.396
Time course 60hI-60hNI	0.95511	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)	1.03343	0.863
transgenic ySAMdc/azygous control (breaker)	1.37393	1
transgenic ySAMdc/azygous control (red)	1.44526	0.92

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	0.98966	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.20918	0.14
Manapal/WT (break)	1.45221	1
Manapal/WT (red)	1.22429	0.222