CIRCA

NEWS (9/12/2018): We added human tissues to the database

About CIRCA

Over the last two decades and together with our collaborators, our lab has created datasets, made databases, and built algorithms in wide use in the circadian community and beyond. This includes the Gene Atlas1 and Gene Wiki2,3, CircaDB4, and several algorithms including JTK5, PSEA6, MetaCycle7, and CYCLOPS8. In the spirit of open science, these resources and algorithms were made available and in use by thousands of researchers all over the world.

We’ve done the definitive work on the mammalian circadian transcriptome. In 2002, we showed that ∼10% of the mouse liver transcriptome was under clock control, including many key components of cellular pathways (e.g. HMG-CoA reductase)9. In 2009 using high resolution time sampling, we found 10x more clock regulated genes and hundreds of 2nd (12hr) and dozens of 3rd (8hr) harmonics of circadian transcription10. Later we showed that these harmonics depend on an intact circadian clock11. In 2014, we completed the profiling of 12 mouse organs and showed that 43% of protein encoding genes and a majority of disease genes and drug targets are clock-regulated genes12. Last year, we published CYCLOPS, an algorithm to extract periodicity from unordered, large scale data, and applied it to thousands of human liver, brain, lung, and cancer samples8. This year we used CYCLOPS to create a database of circadian transcriptional rhythms from 13 human organ systems13. These latter observations have clear implications for chronotherapy, timed dosing of drugs, to improve their therapeutic index in cancer, cardiovascular disease, and many other areas. To make these data available, we built CircaDB.

We have always felt that making data public is the right thing to do but not enough to catalyze real progress. To this end, with our colleagues Andy Su and Angel Pizarro, we created CircaDB. The goal of CircaDB is to allow everyday biologists to answer simple questions like, “what genes cycle in my organ of interest?”, “where does my gene cycle?” CircaDB allows these questions to be answer quickly and effectively, with link outs to Wikipedia, HomoloGene, Refseq, etc.. We put in sensible statistical defaults, but let users select their favorite algorithms14,15, Q-value cutoff, phase range, or download the raw data. For the literati, we link to all the data in the About page, as well as to references for the algorithms used. The database is in use by hundreds of researchers all over the world without restriction. (I am a regular user as it is the most efficient way for me to answer these types of questions too.)

References

Data references

Dataset Paper Source
Human GTEx collections of RNA-seq GTEx consortium, Nat. Genet, 2013 GTEx Portal
Mouse 12 organs 1.0ST 2014 Zhang and Lahens et al., PNAS, 2014 GSE54652
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 download data
Mouse NIH 3T3 Immortalized Cell Line 48 hour Hughes 2009 Hughes et al., PLoS Genetics, 2009 GSE11922
Human U2 OS Hughes 2009 Hughes et al., PLoS Genetics, 2009 GSE13949
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 - 9/12/2018 14 human tissues are added to the database
Update - 8/13/2015 Two new datasets: "Mouse SCN" and "Mouse spleen" are now available
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