Document Detail


Inferring Epigenetic and Transcriptional Regulation during Blood Cell Development with a Mixture of Sparse Linear Models.
MedLine Citation:
PMID:  22730432     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
MOTIVATION: Blood cell development is thought to be controlled by a circuit of transcription factors and chromatin modifications that determine the cell fate via activating cell type specific expression programs. To shed light on the interplay between histone marks and transcription factors during blood cell development, we model gene expression from regulatory signals by means of combinations of sparse linear regression models. RESULTS: The mixture of sparse linear regression models was able to improve the gene expression prediction in relation to the use of a single linear model. Moreover, it performed an efficient selection of regulatory signals even when analyzing all transcription factors with known motifs (> 600). The method identified interesting roles for histone modifications and a selection of transcription factors related to blood development and chromatin remodelling. AVAILABILITY: The method and data sets are available from http://www.cin.ufpe.br/~igcf/SparseMix. CONTACT: igcf@cin.ufpe.br.
Authors:
Thais G do Rego; Helge G Roider; Francisco A T de Carvalho; Ivan G Costa
Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2012-6-23
Journal Detail:
Title:  Bioinformatics (Oxford, England)     Volume:  -     ISSN:  1367-4811     ISO Abbreviation:  -     Publication Date:  2012 Jun 
Date Detail:
Created Date:  2012-6-25     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  9808944     Medline TA:  Bioinformatics     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Affiliation:
Center of Informatics, Federal University of Pernambuco, Recife, Brazil.
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