This paper proposes an approach to evaluate the relatedness between two genes and within a set of genes belonging to coherent organizations. Specifically, we consider families and pathways. Our method is grounded in the ontological annotation of a specialized corpus of texts consisting of gene summaries that condense the description of functions and processes in which genes are involved. First, we derive a set of descriptor terms by annotating each summary with different ontologies. Then, the relatedness between two genes is measured by the overlapping of their descriptor terms. To explore the relatedness of genes within a coherent organization, we evaluate the relatedness for all the possible pair-wise combination of genes belonging to that organization. This results in a discrete variable distribution whose statistical parameters give information about how genes relate coherently within organizations.

Evaluating relatedness of gene sets

DESSI, NICOLETTA;PES, BARBARA;PASCARIELLO, SERGIO EMANUELE
2014-01-01

Abstract

This paper proposes an approach to evaluate the relatedness between two genes and within a set of genes belonging to coherent organizations. Specifically, we consider families and pathways. Our method is grounded in the ontological annotation of a specialized corpus of texts consisting of gene summaries that condense the description of functions and processes in which genes are involved. First, we derive a set of descriptor terms by annotating each summary with different ontologies. Then, the relatedness between two genes is measured by the overlapping of their descriptor terms. To explore the relatedness of genes within a coherent organization, we evaluate the relatedness for all the possible pair-wise combination of genes belonging to that organization. This results in a discrete variable distribution whose statistical parameters give information about how genes relate coherently within organizations.
2014
9788890643743
Gene Relatedness, Semantic Similarity, Ontology annotation
File in questo prodotto:
File Dimensione Formato  
CIBB2014.pdf

Solo gestori archivio

Descrizione: Articolo principale
Tipologia: versione post-print
Dimensione 202.62 kB
Formato Adobe PDF
202.62 kB Adobe PDF   Visualizza/Apri   Richiedi una copia

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11584/186630
Citazioni
  • ???jsp.display-item.citation.pmc??? ND
  • Scopus ND
  • ???jsp.display-item.citation.isi??? ND
social impact