GeneSets


Gene sets are lists of genes associated with 1's or 0's, depending on whether or not they have a particular attribute. The attributes can be ontologies (GO), pathways (KEGG), etc. Below is a list of gene set tables currently available, and automatically updated from their respective sources every Monday. All files are matrices (genes vs. attributes) in tab-delimited format (.tab.gz), and can be loaded directly into Genomica.

The following gene sets can be used for both commercial and non-commercial studies. Please refer to the bottom of this page for terms of use on all gene sets. If you would like a full list of gene sets, including sets that can only be used non-commercially (KEGG, GRID, MIPS, etc.), please e-mail Josiah Altschuler.

Click here for acknowledgment of all data sources

Click here to see a list of applications which use gene sets

Click here to go to ArraySets

 
Organism Anatomy Clusters Function Genetic Diseases Localization MicroRNA Targets Pathways Phenotypes Protein- Protein Transcriptional Regulatory Elements
Arabidopsis thaliana   AtGenExpress

GO
GO-IDA-IC-TAS
GO-IEA-ISS-RCA
GO-IEP-IGI-IMP-IPI

      AraCyc      
Caenorhabditis elegans    

GO
GO-IDA-IC-TAS
GO-IEA-ISS-RCA
GO-IPI-IEP-IGI-IMP-IPI

           
Candida albicans     GO
GO-IC-IDA-TAS
GO-IEA-ISS-RCA
GO-IEP-IGI-IMP-IPI
             
Caulobacter crescentus                    
Drosophila melanogaster FlyBase anatomy ontology (No longer updated)  

GO
GO-IC-IDA-TAS
GO-IEA-ISS-RCA
GO-IEP-IGI-IMP-IPI

             
Escherichia coli    

GO

     
EcoCyc
     
Homo sapiens    

GO
GO-IC-IDA-TAS
GO-IEA-ISS-RCA
GO-IEP-IGI-IMP-IPI

    Marks


HumanCyc
BioCarta
SuperArray

  Reactome

 

Mus musculus    

GO-MGD
GO-IC-IDA-TAS
GO-IEA-ISS-RCA
GO-IEP-IGI-IMP-IPI

GO-FANTOM

Genetic Association    
BioCarta
SuperArray
     
Rattus norvegicus    

GO
GO-IC-IDA-TAS
GO-IEA-ISS-RCA
GO-IEP-IGI-IMP-IPI

             
Saccharomyces cerevisiae    

GO
GO-IC-IDA-TAS
GO-IEA-ISS-RCA
GO-IEP-IGI-IMP-IPI

  O'Shea    

Genetic footprinting

Rosetta mutants

TATA dependency
Transcription factors
Schizosaccharomyces pombe     GO
GO-IC-IDA-TAS
GO-IEA-ISS-RCA
GO-IEP-IGI-IMP-IPI
             

Any questions/comments, feel free to e-mail Josiah Altschuler
This work was supported by the NIGMS
 

Terms of Use

Please read these terms carefully. By clicking on a gene set below or otherwise using this Website (the “Gene Sets”) you are agreeing to be bound by these terms.

1. Disclaimers . You acknowledge that the Gene Sets are being supplied "AS IS" without any accompanying services or improvements from the President and Fellows of Harvard College (the “College”) or the Bauer Center for Genomic Research (the “Bauer Center,” collectively with the College, “Harvard”). HARVARD MAKES NO REPRESENTATIONS OR WARRANTIES WITH RESPECT TO THE GENE SETS AND EXPRESSLY DISCLAIMS ALL WARRANTIES OF ANY KIND (EXPRESS, IMPLIED OR OTHERWISE), INCLUDING BUT NOT LIMITED TO ANY IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND NON-INFRINGEMENT.

2. No Liability . The Gene Sets are being provided to You free of charge. ACCORDINGLY, YOU ACKNOWLEDGE AND AGREE THAT HARVARD, MEMBERS OF ITS GOVERNING BOARDS, ITS OFFICERS, EMPLOYEES AND AFFILIATES WILL HAVE NO LIABILITY IN CONNECTION WITH OR ARISING FROM YOUR USE OF THE GENE SETS. IN NO EVENT SHALL HARVARD, OR ANY MEMBER OF ITS GOVERNING BOARD, OFFICER, EMPLOYEE OR AFFILIATE OF HARVARD, BE LIABLE TO YOU FOR ANY CONSEQUENTIAL, INCIDENTAL, INDIRECT, OR SPECIAL DAMAGES WHATSOEVER (INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF PROFITS, BUSINESS INTERRUPTION, LOSS OF INFORMATION, AND THE LIKE), WHETHER FORESEEABLE OR UNFORESEEABLE, ARISING OUT OF THE USE OF OR INABILITY TO USE THE GENE SETS OR ACCOMPANYING WRITTEN MATERIALS, REGARDLESS OF THE BASIS OF THE CLAIM, EVEN IF HARVARD IS NEGLIGENT OR OTHERWISE AT FAULT, AND REGARDLESS OF WHETHER HARVARD HAS BEEN ADVISED OR SHOULD KNOW OF THE POSSIBILITY OF SUCH DAMAGE. Neither the name of the College, the Bauer Center nor the names of their contributors may be used to endorse or promote products derived from the Gene Sets without specific prior written permission.

3. Remedy . YOUR ONLY RIGHT OR REMEDY WITH RESPECT TO ANY PROBLEMS OR DISSATISFACTION WITH THE GENE SETS IS CEASE USE OF SUCH GENE SET.