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a catalog of biological databases

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Database information

Bioclock (The Aedes aegypti Circadian Database)

General information

Description: Bioclock is a searchable repository of diel and circadian microarray expression data
Year founded: 2014
Last update: 2014-12-17
Version: v1.0
Accessibility:
Manual:
Accessible
Real time : Checking...
Country/Region: United States
Data type:
DNA
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: University of Notre Dame
Address: Galvin Life Sciences Bldg, Notre Dame, IN 46556, USA
City: Notre Dame
Province/State: IN
Country/Region: United States
Contact name (PI/Team): Joseph E O’Tousa
Contact email (PI/Helpdesk): jotousa@nd.edu

Related Database

Record metadata

Created on: 2015-06-30
Curated by:
Mengwei Li [2016-03-31]
Mengwei Li [2016-03-29]
Lin Liu [2015-12-29]
Mengwei Li [2015-11-29]

Ranking

All databases:
1783/4549 (60.827%)
Expression:
342/800 (57.375%)
1783
Total Rank
18
Citations
3
z-index

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Publications

25516260
A database of circadian and diel rhythmic gene expression in the yellow fever mosquito Aedes aegypti. [PMID: 25516260]
Leming MT, Rund SS, Behura SK, Duffield GE, O'Tousa JE.

The mosquito species Aedes aegypti is the primary vector of many arboviral diseases, including dengue and yellow fevers, that are responsible for a large worldwide health burden. The biological rhythms of mosquitoes regulate many of the physiological processes and behaviors that influence the transmission of these diseases. For insight into the molecular basis of biological rhythms, diel and circadian gene expression profiling has been carried out for many species. To bring these resources to Aedes aegypti researchers, we used microarray technology to carry out a genome wide assessment of gene expression during the 24 hour light/dark (LD) cycle and during constant darkness (DD). The purpose of this report is to describe the methods, the validation of the results, and the organization of this database resource. The Aedes aegypti Circadian Database is a publicly accessible database that can be searched via a text-based query to visualize 44 hour temporal expression patterns of a given gene in Ae. aegypti heads under diel (observed under a 12 hour/12 hour LD cycle) and circadian (observed under DD) conditions. Profiles of gene expression under these conditions were assayed by Nimblegen 12-plex microarrays and rhythmicity was objectively assessed by the JTK_CYCLE algorithm. The output of the search is a graphical representation of the expression data along with computed period length, the time-of-day of gene expression peaks, and statistical determination for rhythmicity. Our results show that at least 7.9% of the gene set present in the Aedes aegypti head are rhythmic under LD conditions and 6.7% can be considered circadian, oscillating under constant dark conditions. We present these results in the Aedes aegypti Circadian Database through Bioclock, a public website hosted by the University of Notre Dame at http://www.nd.edu/~bioclock/. This website allows searchable browsing of this quantitative gene expression information. The visualization allows for gene-by-gene comparison of transcript expression under both diel and circadian conditions, and the results are presented graphically in a plot profile of gene expression. The Ae. aegypti Circadian Database provides a community resource for observing diel and circadian fluctuations in gene expression across the Ae. aegypti genome.

BMC Genomics. 2014:15() | 18 Citations (from Europe PMC, 2020-02-15)