EASE makes use of several public resources and technologies including:

 

The algorithm that is used in EASE for the fast and accurate estimation of Gaussian hypergeometric probability

was developed by Catherine Loader of Bell Labs:

      http://cm.bell-labs.com/cm/ms/departments/sia/catherine/dbinom/

     

 

FILES INCLUDED BUT NOT AUTOMATICALLY UPDATEABLE:

Assignment of Affymetrix Probesets to LocusLink numbers was initiated with data available at Affymetrix's NetAffx website:

      https://www.affymetrix.com/index2.jsp

     

Further assignment of Affymetrix Probesets to LocusLink numbers was done with data from Jean Marie Rouillard at:

      http://dot.ped.med.umich.edu:2000/ourimage/pub/shared/JMR_pub_affyannot.html

     

... with a few remaining LocusLink numbers mapped via the 'loc2acc' file on the LocusLink FTPsite.

 

Categorical files for BBID pathway assignment were created from data tables kindly provided by Kevin Becker:

      Becker KG, White SL, Muller J, Engel J. (2000)

      "BBID: the biological biochemical image database."

      Bioinformatics 16(8):745-6.

 

FILES USED IN THE AUTOMATED UPDATE PROCESS:

The National Center for Biotechnology Information's LocusLink FTP files:

      Pruitt KD, Katz KS, Sicotte H, Maglott DR (2000)

      "Introducing RefSeq and LocusLink: curated human genome resources at the NCBI"

      Trends Genet. 16(1):44-47.

 

LocusLink in turn provides access to the 'At-A-Glance' gene-classification system from Proteome Inc.:

      http://www.proteome.com/databases/HumanPD/Mammaliansearch-long.html

 

The "Homologenes" and "Homologe COGs" files used to optionally enhance categorical data and annotation are generated from data from Homologene:

      Zhang Z, Schwartz S, Wagner L, Miller W. (2000)

      "A greedy algorithm for aligning DNA sequences."

      J Comp Biol. 7:203-214.

 

Gene ontology mappings are derived from both LocusLink and the Gene Ontology Consortium, and

all superordinate Gene Ontology terms are obtained from the Gene Ontology Consortium:

      The Gene Ontology Consortium (2000)

      "Gene Ontology: tool for the unification of biology"

      Nature Genet. 25:25-29.

     

Pathway membership and other data are derived from KEGG:

      Kanehisa M, Goto S, Kawashima S, Nakaya A (2002)

      "The KEGG databases at GenomeNet"

      Nucleic Acids Res. 30:42-46.

 

SwissProt Keywords are derived from SwissProt:

      Boeckmann B, et al. (2003)

      "The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003"

      Nucleic Acids Res. 31:365-370.

 

Note that the use of SwissProt Keywords may require a separate license from the Swiss Institute of Bioinformatics, as indicated by the SwissProt copyright notice:

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SWISS-PROT is copyright.  It is produced through a collaboration between the

Swiss Institute  of  Bioinformatics   and the EMBL Outstation - the European

Bioinformatics Institute. There are no restrictions on its use by non-profit

institutions as long as its  content is in no way modified. Usage by and for

commercial entities requires a license agreement.  For information about the

licensing  scheme  see: http://www.isb-sib.ch/announce/ or send  an email to

license@isb-sib.ch.

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The development of EASE has been funded with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, under Contract No. NO1-C0-56000.  The contents of this tool does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products or organizations imply endorsement by the United States government.