Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-6.4.2.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.33017	0.498
27DAP/17DAP	0.80694	0.724
39DAP/27DAP	1.25758	0.833
41DAP/39DAP	1.65825	0.432
42DAP/41DAP	1.12586	0.929
43DAP/42DAP	1.18547	1
47DAP/43DAP	0.83939	0.487
52DAP/47DAP	1.39505	0.601
57DAP/52DAP	1.20238	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83302	0.025
17DAP/reference	0.6631	0.007
27DAP/reference	1.01311	0.885
39DAP/reference	0.7825	0.011
41DAP/reference	0.63942	0.009
42DAP/reference	0.96397	0.295
43DAP/reference	0.8471	0.039
47DAP/reference	1.06236	1
52DAP/reference	1.68536	0.02
57DAP/reference	1.71215	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.38559	0.05
27DAP/17DAP	0.77528	0.537
39DAP/27DAP	1.07996	0.478
41DAP/39DAP	0.96888	0.893
42DAP/41DAP	1.18165	0.106
43DAP/42DAP	1.00881	0.83
47DAP/43DAP	1.03111	0.951
52DAP/47DAP	1.18733	0.449
57DAP/52DAP	1.40625	0.091
57DAP/7DAP	1.31252	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.72122	0.122
17DAP/reference	N/A	N/A
27DAP/reference	0.84347	N/A
39DAP/reference	0.7758	0.034
41DAP/reference	0.81553	0.259
42DAP/reference	0.78549	0.029
43DAP/reference	1.03134	0.727
47DAP/reference	1.17763	0.36
52DAP/reference	0.7688	0.031
57DAP/reference	1.61101	0.014

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88308	0.182
17DAP/reference	0.86825	0.089
27DAP/reference	1.14671	0.639
39DAP/reference	1.23049	0.449
41DAP/reference	1.54876	0.01
42DAP/reference	1.2438	0.031
43DAP/reference	1.00405	0.581
47DAP/reference	0.90021	0.113
52DAP/reference	1.21613	0.074
57DAP/reference	0.82835	0.107

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75262	N/A
17DAP/reference	1.19795	0.728
27DAP/reference	1.08742	N/A
39DAP/reference	1.12798	0.528
41DAP/reference	1.04977	1
42DAP/reference	0.82097	N/A
43DAP/reference	1.95106	0.03
47DAP/reference	1.12247	0.63
52DAP/reference	0.8288	0.193
57DAP/reference	2.19444	0.015

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.66971	0.42
26DAP/20DAP	1.21926	0.642
34DAP/26DAP	1.23073	1
51DAP/34DAP	1.05323	1
52DAP/51DAP	1.7298	0.053
53DAP/52DAP	0.76077	0.101
55DAP/53DAP	1.32523	0.048
57DAP/55DAP	0.53642	0.013
62DAP/57DAP	1.19898	0.723
68DAP/62DAP	3.12697	0.022
68DAP/14DAP	3.85625	0.022

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.6341	0.059

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.27708	0.176
Mature Green Tomato/Ripe Tomato	0.7037	0.148
Immature Eggplant/Mature Eggplant	1.29654	0.092
Ripe Pepper/Ripe Tomato	1.41748	1
Mature Eggplant/Ripe Tomato	1.0616	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92846	0.56
1-1-2/M82	1.07089	1
12-2/M82	0.99389	0.955
12-4/M82	0.99321	1
1-3/M82	0.77745	0.378
2-1-1/M82	0.86948	0.683
2-1/M82	0.99125	1
2-6/M82	1.16291	0.695
3-2/M82	1.21882	0.967
4-1-1/M82	0.78038	1
4-1/M82	0.99502	N/A
4-3-2/M82	0.97109	N/A
4-3/M82	1.05119	1
5-3/M82	1.05728	1
6-2/M82	1.17271	N/A
6-3/M82	1.10991	1
7-1/M82	0.77039	0.476
7-2/M82	1.00585	1
9-3-2/M82	0.84443	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.85522	1
IL2-6/WTpooled	0.93402	N/A
IL7-5/WTpooled	1.57293	N/A
IL7-3/WTpooled	0.67035	1
IL12-4/WTpooled	1.04942	1
IL1-4/WTpooled	1.03786	1
WT/WTpooled	1.01	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	1.10593	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02898	0.921
DC3000/delta hrp 6h	1.00196	0.95
DC3000/delta hrp 12h	1.31876	1
DC3000/delta hrp 24h	1.09496	0.212

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.10825	0.11
DC3000 delta B/DC3000 delta AB	1.14153	0.381

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96669	1
Exp 36h	0.93537	0.879
Exp 60h	1.03091	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04514	1
Var 0h	0.51808	0.98
Var 12h I row2-row1	0.9272	0.627
Var 12h NI row2-row1	1.17925	0.649
Var 36h I row2-row1	1.21506	0.298
Var 36h NI row2-row1	0.95847	0.706
Var 60h I row2-row1	0.92153	0.832
Var 60h NI row2-row1	0.90546	0.866
Time course 0hI-0hNI	0.95213	0.649
Time course 12hI-12hNI	0.99864	1
Time course 36hI-36hNI	1.08845	0.166
Time course 60hI-60hNI	1.36411	0.06

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)	0.9496	0.377
transgenic ySAMdc/azygous control (breaker)	0.75376	0.173
transgenic ySAMdc/azygous control (red)	0.8873	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01023	0.766

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.02024	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.07621	1
Manapal/WT (break)	0.86368	1
Manapal/WT (red)	0.99913	0.863