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CircaDB specifications

Information


Unique identifier OMICS_04504
Name CircaDB
Alternative name Circadian Expression Profiles Data Base
Restrictions to use None
Maintained Yes

Taxon


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Publication for Circadian Expression Profiles Data Base

CircaDB citations

 (4)
library_books

Computational modeling of the cell autonomous mammalian circadian oscillator

2017
BMC Syst Biol
PMCID: 5333193
DOI: 10.1186/s12918-016-0379-8

[…] knowledge about circadian clock and circadian transcriptomes of different organs and tissues. Data on circadian dynamics of genes transcription in different tissues and cell lines can be found in the CircaDB database [] or a public functional genomics data repository GEO (Gene Expression Omnibus) [].Identification of genes, whose expression follow circadian rhythm, and estimation of rhythm paramet […]

library_books

Microarray Analyses Reveal Marked Differences in Growth Factor and Receptor Expression Between 8 Cell Human Embryos and Pluripotent Stem Cells

2015
PMCID: 4733324
PMID: 26493868
DOI: 10.1089/scd.2015.0284

[…] detection in each cell type and growth factor superfamily, subjected to GenBank descriptions and pathway analyses using DAVID and GeneMANIA, and queried for reported circadian expression according to CircaDB []. Gene elements reported to be expressed in a circadian pattern in mouse tissues are underlined throughout this report. […]

library_books

Circadian systems biology: When time matters

2015
Comput Struct Biotechnol J
PMCID: 4534520
PMID: 26288701
DOI: 10.1016/j.csbj.2015.07.001

[…] ion to approaches acting at the time-domain level, other methods exist that act in the frequency domain, . An algorithm making use of the advantages of both types of approaches was suggested as well .CircaDB is a database that provides many gene expression time courses for circadian genes. The maSigPro package for Bioconductor may be used to identify differentially expressed genes in measured ti […]

library_books

Circadian Regulation of Myocardial Sarcomeric Titin cap (Tcap, Telethonin): Identification of Cardiac Clock Controlled Genes Using Open Access Bioinformatics Data

2014
PLoS One
PMCID: 4133362
PMID: 25121604
DOI: 10.1371/journal.pone.0104907

[…] circadian transcriptional regulation, we designed a workflow based on open access bioinformatics databases (). First, rhythmic expression profiles of murine heart genes were obtained from the online CircaDB database and the JTK_Cycle algorithm –. The reference genes we used as a guide were Per1 , Per2 , Per3 , Nr1d2 (Rev-Erbβ) and Dbp ), (see ). Based on these data, we then searched CircaDB for […]

Citations

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CircaDB institution(s)
The Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA

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