LinkNMF: Identification of histone modification modules in the human genome using nonnegative matrix factorization

Gene

Volumn 518, Issue 1, 2013, Pages 215-221

  Jung, Inkyung ^a   Kim, Dongsup ^a  

^a Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

Author keywords

ChIP seq; Gene expression; Histone modification; NMF

Indexed keywords

ALGORITHM; ARTICLE; CD4+ T LYMPHOCYTE; GENE ACTIVATION; GENE EXPRESSION; GENE REPRESSION; GENOME; HISTONE MODIFICATION; HUMAN; HUMAN CELL; LINKNMF; PRIORITY JOURNAL; PROTEIN ANALYSIS;

ALGORITHMS; CD4-POSITIVE T-LYMPHOCYTES; CHROMATIN; CLUSTER ANALYSIS; GENE EXPRESSION; GENOME, HUMAN; HISTONES; HUMANS; PROMOTER REGIONS, GENETIC; TRANSCRIPTIONAL ACTIVATION;

EID: 84875378077     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2012.11.027     Document Type: Article

References (26)

1. Asp P., et al. PNAS Plus: Genome-wide remodeling of the epigenetic landscape during myogenic differentiation. Proc. Natl. Acad. Sci. U. S. A. 2011, 108:E149-E158.
2. Barski A., et al. High-resolution profiling of histone methylations in the human genome. Cell 2007, 129:823-837.
3. C-J L. Projected Gradient Methods for Non-negative Matrix Factorization 2005, 352. Department of Computer Science National Taiwan University.
4. Ernst J., Kellis M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat. Biotechnol. 2010, 28:817-825.
5. Fuks F. DNA methylation and histone modifications: teaming up to silence genes. Curr. Opin. Genet. Dev. 2005, 15:490-495.
6. Hon G., Ren B., Wang W. ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome. PLoS Comput. Biol. 2008, 4:e1000201.
7. Jung I., Kim D. Regulatory Patterns of Histone Modifications to Control the DNA Methylation Status at CpG Islands. IBC 2009, 1:1-7.
8. Jung I., Kim D. Histone modification profiles characterize function-specific gene regulation. J. Theor. Biol. 2012, 310:132-142.
9. Jung I., et al. H2B monoubiquitylation is a 5'-enriched active transcription mark and correlates with exon-intron structure in human cells. Genome Res. 2012, 22:1026-1035.
10. Karlic R., Chung H.R., Lasserre J., Vlahovicek K., Vingron M. Histone modification levels are predictive for gene expression. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:2926-2931.
11. Karolchik D., Hinrichs A.S., Kent W.J. The UCSC Genome Browser. Curr. Protoc. Bioinformatics 2009, 28:1.4.1-1.4.26.
12. Kouzarides T. Chromatin modifications and their function. Cell 2007, 128:693-705.
13. Lai W.K., Buck M.J. ArchAlign: coordinate-free chromatin alignment reveals novel architectures. Genome Biol. 2010, 11:R126.
14. Lee D.D., Seung H.S. Learning the parts of objects by non-negative matrix factorization. Nature 1999, 401:788-791.
15. Liu Y., Taverna S.D., Muratore T.L., Shabanowitz J., Hunt D.F., Allis C.D. RNAi-dependent H3K27 methylation is required for heterochromatin formation and DNA elimination in Tetrahymena. Genes Dev. 2007, 21:1530-1545.
16. Ram O., et al. Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell 2011, 147:1628-1639.
17. Ren B., et al. Genome-wide location and function of DNA binding proteins. Science 2000, 290:2306-2309.
18. Rosenfeld J.A., Wang Z., Schones D.E., Zhao K., DeSalle R., Zhang M.Q. Determination of enriched histone modifications in non-genic portions of the human genome. BMC Genomics 2009, 10:143.
19. Roy S., et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 2011, 330:1787-1797.
20. Schwartz Y.B., Pirrotta V. Polycomb silencing mechanisms and the management of genomic programmes. Nat. Rev. Genet. 2007, 8:9-22.
21. Su A.I., et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl. Acad. Sci. U. S. A. 2004, 101:6062-6067.
22. Subramanian A., et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. U. S. A. 2005, 102:15545-15550.
23. Ucar D., Hu Q., Tan K. Combinatorial chromatin modification patterns in the human genome revealed by subspace clustering. Nucleic Acids Res. 2011, 39:4063-4075.
24. Wang Z., et al. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat. Genet. 2008, 40:897-903.
25. Wang Z., et al. Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive Genes. Cell 2009, 138:1019-1031.
26. Whitington T., Perkins A.C., Bailey T.L. High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites. Nucleic Acids Res. 2009, 37:14-25.