Predictor of Enriched Protein Domains with Microarray Expression Data (PED-MED) Software

Overview

PEDMED is a lean Perl script for hypothesis generation/validation. It looks for enriched protein domains in a microarray dataset to help posit or reinforce a prediction of structure, mechanism, relatedness etc. in observed probeset markers.

Predictor of Enriched Protein Domains

Input

As an input, PEDMED takes microarray expression data a scientist has already statistically analyzed and designated into groups of foreground (statistically significantly enriched) probesets and background probesets. The input file also has the RefSeq protein identifiers corresponding to the probesets.

Operations

PEDMED searches the NCBI Conserved Domain Database for each predicted protein corresponding to a probeset in the input file. PEDMED then counts each type of protein domain by superfamily and conducts a chi squared analysis using the foreground as the observed frequencies and the background as the expected frequencies. FDR is corrected by implementation of the Benjamini and Hochberg algorithm.

Results

PEDMED’s results show statistically significantly enriched protein domains in the foreground relative to the background and the genes that correspond to the probeset markers containing those enriched domains.

License the PED-MED Software

Academic and non-profit licenses are available – please use the form below. For information about commercial licensing opportunities, please contact Stephen J. Susalka, PhD, at ssusalka@wakehealth.edu. For general questions regarding this software, please contact Eric Jimenez.

Innovators

Eric Jimenez & Lance Miller, Ph.D.

  • Institutional Contact

  • This person is responsible for administering this agreement on behalf of the Institution
  • Technical Contact

  • This person is authorized by Institution to receive the Software and conduct all technical correspondence with WFUHS
  • Please carefully read the following WFUHS Non-Exclusive End- User License Agreement ("Agreement"). By selecting the "Accept the terms in the license agreement" option below this Agreement, you indicate your irrevocable acceptance of its terms and conditions and agree to be bound as set forth therein. Further, your acceptance signifies your understanding and acknowledgment that this Agreement constitutes and contains the total agreement between the Institution and WFUHS with respect to this transaction. In accepting this Agreement, you further acknowledge that any agreements entered into prior or contemporaneously with this Agreement are excluded, whether oral or in writing. By selecting the "Accept the terms in the license agreement" option, you specifically acknowledge, represent, and agree that any other terms and conditions contained in an invoice, acknowledge, purchase order or other document sent by or on behalf of you or the organization you represent in this transaction shall be void and of no effect. Finally, your selection of the "Accept the terms in the license agreement" option is a representation and warranty that you have the requisite authority and legal capacity to bind your organization to this Agreement. By clicking "Accept the terms in the license agreement" without reading the agreement, Institution nevertheless agrees to be bound by all of the terms of the Agreement without limitation.
Back to Top