Ranking and 1-dimensional projection of cell development transcription profiles

Lan Zagar, Francesca Mulas, Riccardo Bellazzi, Blaz Zupan

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

Abstract

Genome-scale transcription profile is known to be a good reporter of the state of the cell. Much of the early predictive modelling and cell-type clustering relied on this relation and has experimentally confirmed it. We have examined if this also holds for prediction of cell's staging, and focused on the inference of stage prediction models for stem cell development. We show that the problem relates to rank learning and, from the user's point of view, to projection of transcription profile data to a single dimension. Our comparison of several state-of-the-art algorithms on 10 data sets from Gene Expression Omnibus shows that rank-learning can be successfully applied to developmental cell staging, and that relatively simple techniques can perform surprisingly well.

Original languageEnglish
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pages85-89
Number of pages5
Volume6747 LNAI
DOIs
Publication statusPublished - 2011
Event13th Conference on Artificial Intelligence in Medicine, AIME 2011 - Bled, Slovenia
Duration: Jul 2 2011Jul 6 2011

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume6747 LNAI
ISSN (Print)03029743
ISSN (Electronic)16113349

Other

Other13th Conference on Artificial Intelligence in Medicine, AIME 2011
CountrySlovenia
CityBled
Period7/2/117/6/11

Keywords

  • cell development
  • projection
  • ranking
  • regression
  • staging
  • temporal ordering

ASJC Scopus subject areas

  • Computer Science(all)
  • Theoretical Computer Science

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  • Cite this

    Zagar, L., Mulas, F., Bellazzi, R., & Zupan, B. (2011). Ranking and 1-dimensional projection of cell development transcription profiles. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 6747 LNAI, pp. 85-89). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6747 LNAI). https://doi.org/10.1007/978-3-642-22218-4_11