Locally adaptive statistical procedures for the integrative analysis on genomic and transcriptional data

Mattia Zampieri, Ingrid Cifola, Dario Basso, Roberta Spinelli, Luca Beltrame, Clelia Peano, Cristina Battaglia, Silvio Bicciato

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

The systematic integration of expression profiles and other types of gene information, such as copy number, chromosomal localization, and sequence characteristics, still represents a challenge in the genomic arena. In particular, the integrative analysis of genomic and transcriptional data in context of the physical location of genes in a genome appears promising in detecting chromosomal regions with structural and transcriptional imbalances often characterizing cancer. A computational framework based on locally adaptive statistical procedures (Global Smoothing Copy Number, GLSCN, and Locally Adaptive Statistical Procedure, LAP), which incorporate genomic and transcriptional data with structural information for the identification of imbalanced chromosomal regions, is described. Both GLSCN and LAP accounts for variations in the distance between genes and in gene density by smoothing standard statistics on gene position before testing the significance of copy number and gene expression signals. The application of GLSCN and LAP to the integrative analysis of a human metastatic clear cell renal carcinoma cell line (Caki-1) allowed identifying chromosomal regions that are directly involved in known chromosomal aberrations characteristic of tumors.

Original languageEnglish
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pages682-689
Number of pages8
Volume4578 LNAI
Publication statusPublished - 2007
Event7th International Workshop on Fuzzy Logic and Applications, WILF 2007 - Camogli, Italy
Duration: Jul 7 2007Jul 10 2007

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4578 LNAI
ISSN (Print)03029743
ISSN (Electronic)16113349

Other

Other7th International Workshop on Fuzzy Logic and Applications, WILF 2007
CountryItaly
CityCamogli
Period7/7/077/10/07

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Keywords

  • Gene expression
  • Genotyping
  • Integrative genomics
  • Microarray

ASJC Scopus subject areas

  • Computer Science(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Theoretical Computer Science

Cite this

Zampieri, M., Cifola, I., Basso, D., Spinelli, R., Beltrame, L., Peano, C., Battaglia, C., & Bicciato, S. (2007). Locally adaptive statistical procedures for the integrative analysis on genomic and transcriptional data. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 4578 LNAI, pp. 682-689). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4578 LNAI).