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