Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-3.1.10.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18639	0.725
27DAP/17DAP	1.09026	0.859
39DAP/27DAP	1.1162	0.919
41DAP/39DAP	0.98687	0.83
42DAP/41DAP	1.06019	1
43DAP/42DAP	1.04095	1
47DAP/43DAP	1.11339	0.689
52DAP/47DAP	0.94819	0.832
57DAP/52DAP	1.06155	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79668	0.04
17DAP/reference	0.88848	0.158
27DAP/reference	1.15101	0.509
39DAP/reference	1.21813	0.117
41DAP/reference	0.96049	0.434
42DAP/reference	1.0228	0.628
43DAP/reference	1.45904	0.008
47DAP/reference	1.33361	0.001
52DAP/reference	1.44242	0.012
57DAP/reference	1.28045	0.018

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.35475	0.05
27DAP/17DAP	0.98033	0.887
39DAP/27DAP	1.02414	0.824
41DAP/39DAP	0.98119	0.973
42DAP/41DAP	1.01938	1
43DAP/42DAP	0.86905	0.068
47DAP/43DAP	1.01273	0.969
52DAP/47DAP	1.22815	0.38
57DAP/52DAP	1.13427	0.444
57DAP/7DAP	1.25654	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21517	0.185
17DAP/reference	0.84106	0.024
27DAP/reference	0.8908	0.062
39DAP/reference	1.19051	0.033
41DAP/reference	1.01043	1
42DAP/reference	0.99691	0.751
43DAP/reference	1.0046	0.802
47DAP/reference	1.28975	0.014
52DAP/reference	0.95998	0.398
57DAP/reference	0.96727	0.396

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92796	0.412
17DAP/reference	0.80262	0.011
27DAP/reference	0.82961	0.02
39DAP/reference	0.79962	0.034
41DAP/reference	0.87773	0.115
42DAP/reference	0.84055	0.108
43DAP/reference	0.7201	0.021
47DAP/reference	0.97174	0.359
52DAP/reference	0.66081	0.006
57DAP/reference	0.72294	0.023

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00463	0.75
17DAP/reference	0.76982	0.078
27DAP/reference	0.93367	0.27
39DAP/reference	0.98154	0.504
41DAP/reference	0.91688	0.331
42DAP/reference	1.15083	0.307
43DAP/reference	1.25473	0.116
47DAP/reference	1.22054	0.063
52DAP/reference	1.60149	0.031
57DAP/reference	1.29184	0.141

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.85621	0.131
26DAP/20DAP	1.33049	0.338
34DAP/26DAP	1.33085	0.819
51DAP/34DAP	1.03953	1
52DAP/51DAP	1.30676	0.126
53DAP/52DAP	1.03541	0.901
55DAP/53DAP	1.06815	0.842
57DAP/55DAP	0.58784	0.082
62DAP/57DAP	0.84394	0.28
68DAP/62DAP	1.65493	0.664
68DAP/14DAP	0.7235	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.58664	0.022

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.0377	0.666
Mature Green Tomato/Ripe Tomato	0.62771	0.086
Immature Eggplant/Mature Eggplant	1.34563	0.105
Ripe Pepper/Ripe Tomato	0.81582	0.293
Mature Eggplant/Ripe Tomato	0.68308	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98315	0.944
1-1-2/M82	1.38961	N/A
12-2/M82	N/A	N/A
12-4/M82	0.9767	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.2827	N/A
3-2/M82	1.11502	1
4-1-1/M82	1.09163	N/A
4-1/M82	1.44429	N/A
4-3-2/M82	1.1816	0.508
4-3/M82	1.22376	0.268
5-3/M82	1.09072	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.30907	0.578
7-2/M82	1.06948	N/A
9-3-2/M82	1.47168	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.93768	0.243
IL2-6/WTpooled	0.97095	1
IL7-5/WTpooled	1.04157	1
IL7-3/WTpooled	0.91375	0.418
IL12-4/WTpooled	1.04014	0.673
IL1-4/WTpooled	0.98498	1
WT/WTpooled	0.97094	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	1.09319	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96423	1
DC3000/delta hrp 6h	0.85041	0.95
DC3000/delta hrp 12h	1.0455	1
DC3000/delta hrp 24h	1.1155	0.347

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.35172	0.044
DC3000 delta B/DC3000 delta AB	1.3732	0.135

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.16252	1
Exp 36h	1.19373	1
Exp 60h	1.37366	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98026	1
Var 0h	0.90051	0.933
Var 12h I row2-row1	1.05975	0.654
Var 12h NI row2-row1	1.19882	0.235
Var 36h I row2-row1	1.23317	0.41
Var 36h NI row2-row1	0.89277	0.645
Var 60h I row2-row1	0.79376	0.374
Var 60h NI row2-row1	0.82477	0.69
Time course 0hI-0hNI	1.04223	0.719
Time course 12hI-12hNI	1.1535	0.152
Time course 36hI-36hNI	1.73528	0.005
Time course 60hI-60hNI	3.54999	0.008

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)	0.96	0.567
transgenic ySAMdc/azygous control (breaker)	1.44924	0.178
transgenic ySAMdc/azygous control (red)	1.11799	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.22146	0.204

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.04252	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.00033	1
Manapal/WT (break)	0.92916	1
Manapal/WT (red)	1.26808	0.222