CIRCA

NEWS (6/9/2014): We added two new datasets: "Mouse Macrophages" and "Mouse Heart LD"

About CIRCA

Circadian rhythms drive daily oscillations in many different physiologies, including blood pressure, body temperature and behavior. In addition, disruptions of the circadian clock contribute to the pathologies of metabolic disorders as well as cardiovascular disease and cancer. Our lab is interested in the mechanism by which circadian oscillations drive these processes. We are using microarray analysis in combination with curve-fitting and Fourier-transform based statistical algorithms to search the genome for transcripts which oscillate under circadian control. We have identified more than 3000 cycling genes in the liver and smaller subsets of rhythmic genes in the pituitary and fibroblasts. We are currently expanding our initial studies to identify rhythmic transcripts in over 15 different tissue types including the heart, kidneys and brain. These data sets will be mined using bioinformatic techniques to discover novel circadian regulatory elements, characterize components of the circadian clock, and identify regulatory genes responsible for the physiologies and pathologies associated with circadian rhythms.

References

Data references

Dataset Paper GEO number
Mouse Liver 48 hour Hughes 2009 Hughes et al., PLoS Genetics, 2009 GSE11923
Mouse Pituitary 48 hour Hughes 2009 Hughes et al., PLoS Genetics, 2009 GSE11923
Mouse NIH 3T3 Immortalized Cell Line 48 hour Hughes 2009 Hughes et al., PLoS Genetics, 2009 GSE11923
Human U2 OS Hughes 2009 Hughes et al., PLoS Genetics, 2009 GSE11923
Mouse Wild Type Liver Miller et al., WT and Clock livers, 2007 GSE3748
Mouse Wild Type Muscle Andrews et al., WT and Clock skeletal muscle GSE3748
Mouse Liver Panda 2002 Panda et al., Cell, 2002 download data
Mouse SCN MAS4 Panda 2002 Panda et al., Cell, 2002 download data
Mouse SCN gcrma Panda 2002 Panda et al., Cell, 2002 download data
Mouse Aorta MU74v2 Rudic et al., PLoS Biology, 2004 GSE414
Mouse Kidney MU74v2 Rudic et al., PLoS Biology, 2004 GSE414
Mouse Distal Colon 2008 Hoogerwerf et al., Gastroenterology, 2008 GSE10644
Mouse Macrophages DD 2010 Keller et al., Proc Natl Acad Sci U S A, 2009 GSE25585

Links

Requesting Addition of New Data Sets

Researchers can request that a particular data set be added by submitting an issue at our project page hosted at Github.

Source Code

Circadb is open source Ruby on Rails application and available under github.com/circadb. Circadb is licensed under the GNU General Public License (GPL-2.0).

Recent updates

Update - 6/9/2014 We added two new datasets: "Mouse Macrophages" and "Mouse Heart LD"
Update - 9/27/2013 RNA-seq data is now available for all Mouse 1.OST experiments
Update - 9/23/2013 Wildcard search is now enabled
Update - 5/16/2013 Mouse Distal Colon data sets added to CircaDB.
CIRCA