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Secretome Tool

The EDRN is currently working with the investigators to create a tool for searching the secretome data.

Retrieval of secretome proteins

Databases and published papers were identified providing lists of secreted proteins, transmembrane or membrane proteins, signal peptides, G-protein coupled receptors, or proteins existing in the extracellular region.  Each database was then searched for human-specific proteins.

Beta release softwareEarly preview of Secretome tool is now available! Note: EDRN username & password required.

Mapping of identifiers

Maps between Affymetrix hgu133plus2 probeset identifiers and gene symbol, Uniprot Gene Symbol, GENBANK ID, Unigene ID, PDB protein ID, Uniprot Accession, and Uniprot ID were obtained from BioMART - ENSEMBLE GENES 63, Homo sapiens genes GRCh37.p3 (http://www.biomart.org, Sept. 21, 2011), selecting two external IDs per map only - hgu133plus2 probeset and one of the above identifiers.  An additional candidate map for Uniprot ID was obtained from DAVID v6.7 (http://david.abcc.ncifcrf.gov/conversion.jsp, Sept. 21, 2011).  The DAVID map contained conversions for all Affymetrix 3’ arrays, so these were further narrowed down to hgu133plus2 maps only, using the hgu133plus2.db Bioconductor package (v. 2.4.5).  Identifiers from each secretome source database were checked against each map, and the map containing the highest fraction of these identifiers was used.  By this method, all identifiers were mapped to  zero, one, or more Affymetrix hgu133plus2 probeset identifiers in one step.  For each probeset identifier, a record was kept of which databases identified it, and which original identifiers mapped to it, to provide a record of how each probeset was identified.  All computations were performed in the R statistical environment v. 2.12.1 (R development Core Team, 2010).

Contact Information

Michael Birrer

Steven Skates

Levi Waldron

Announcement 09/27/2019
Thank you to everyone who made the 11th EDRN Scientific Workshop a success. The next EDRN Steering Committee Meeting is from Tuesday-Thursday, March 31-April 2, 2020 in Tempe, AZ.
Announcement



 
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