Title :
Protein-based analysis of alternative splicing in the human genome
Author :
Loraine, Ann E. ; Helt, Gregg A. ; Cline, Melissa S. ; Siani-Rose, Michael A.
Author_Institution :
Affymetrix Inc., Emeryville, CA, USA
Abstract :
Understanding the functional significance of alternative splicing and other mechanisms that generate RNA transcript diversity is an important challenge facing modern-day molecular biology. Using homology-based, protein sequence analysis methods, it should be possible to investigate how transcript diversity impacts protein structure and function. To test this, a data mining technique ("DiffHit") was developed to identify and catalog genes producing protein isoforms which exhibit distinct profiles of conserved protein motifs. We found that out of a test set of over 1,300 alternatively spliced genes with solved genomic structure, over 30% exhibited a differential profile of conserved InterPro and/or Blocks protein motifs across distinct isoforms. These results suggest that motif databases such as Blocks and InterPro are potentially useful tools for investigating how alternative transcript structure affects gene function.
Keywords :
biology computing; data mining; genetics; proteins; DiffHit; RNA transcript diversity; alternative splicing; conserved Blocks protein motifs; conserved InterPro protein motifs; conserved protein motifs; data mining; differential profile; gene cataloguing; gene identification; homology-based protein sequence analysis; human genome; molecular biology; motif databases; protein function; protein isoforms; protein structure; protein-based analysis; transcript structure; Bioinformatics; Data mining; Databases; Genomics; Humans; Protein engineering; Protein sequence; RNA; Splicing; Testing;
Conference_Titel :
Bioinformatics Conference, 2002. Proceedings. IEEE Computer Society
Print_ISBN :
0-7695-1653-X
DOI :
10.1109/CSB.2002.1039335