Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps

Genome Research

Volumn 23, Issue 12, 2013, Pages 2136-2148

  Mortazavi, Ali ^a   Pepke, Shirley ^b   Jansen, Camden ^a   Marinov, Georgi K ^b   Ernst, Jason ^c   Kellis, Manolis ^d,e   Hardison, Ross C ^f   Myers, Richard M ^g   Wold, Barbara J ^b,h  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^e BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^f PENNSYLVANIA STATE UNIVERSITY   (United States)

^g HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY   (United States)

^h CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE; HISTONE; TRANSCRIPTION FACTOR;

ARTICLE; CELL TYPE; CHROMATIN STRUCTURE; CONTROLLED STUDY; GENETIC PARAMETERS; GENOMICS; HISTONE MODIFICATION; HUMAN; HUMAN CELL; PRIORITY JOURNAL; PROMOTER REGION; SELF ORGANIZING MAP; SEQUENCE ANALYSIS;

ALGORITHMS; CELL LINE; CHROMATIN; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; DATA MINING; GENE ONTOLOGY; HISTONES; HUMAN UMBILICAL VEIN ENDOTHELIAL CELLS; HUMANS; K562 CELLS; PROMOTER REGIONS, GENETIC; TRANSCRIPTION FACTORS; USER-COMPUTER INTERFACE;

EID: 84890502397     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.158261.113     Document Type: Article

References (27)

1. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE,Wang Z,Wei G, Chepelev I, Zhao K. 2007.High-resolution profiling of histone methylations in the human genome. Cell 129: 823-837.
2. Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker JR, et al. 2010. The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol 28: 1045-1048.
3. Eisen MB, Spellman PT, Brown PO, Botstein D. 1998. Cluster analysis of genome-wide expression patterns. Proc Natl Acad Sci 95: 14863-14868.
4. The ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74.
5. Ernst J, Kellis M. 2010. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol 28: 817-825.
6. Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, et al. 2011. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473: 43-49.
7. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, et al. 1999. Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science 286: 531-537.
8. Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, et al. 2012. GENCODE: The reference human genome annotation for the ENCODE Project. Genome Res 22: 1760-1774.
9. Hesselberth JR, Chen X, Zhang Z, Sabo PJ, Sandstrom R, Reynolds AP, Thurman RE, Neph S, Kuehn MS, Noble WS, et al. 2009. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods 6: 283-289.
10. Hoffman MM, Buske OJ, Wang J, Weng Z, Bilmes JA, Noble WS. 2012. Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat Methods 9: 473-476.
11. Hon GC, Hawkins RD, Ren B. 2009. Predictive chromatin signatures in the mammalian genome. Hum Mol Genet 18: R195-R201.
12. Johnson DS, Mortazavi A, Myers RM,Wold B. 2007. Genome-wide mapping of in vivo protein-DNA interactions. Science 316: 1497-1502.
13. Kohonen T. 2001. Self-organizing maps, 3rd ed. Springer, New York.
14. Lee JS, Smith E, Shilatifard A. 2010. The language of histone crosstalk. Cell 142: 682-685.
15. McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB,Wenger AM, Bejerano G. 2010. GREAT improves functional interpretation of cisregulatory regions. Nat Biotechnol 28: 495-501.
16. Milone DH, Stegmayer GS, Kamenetzky L, Lopez M, Lee JM, Giovannoni JJ, Carrari F. 2010. *omeSOM: A software for clustering and visualization of transcriptional and metabolite data mined from interspecific crosses of crop plants. BMC Bioinformatics 11: 438.
17. Moorman C, Sun LV, Wang J, de Wit E, Talhout W, Ward LD, Greil F, Lu X, White KP, Bussemaker HJ, et al. 2006. Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proc Natl Acad Sci 103: 12027-12032.
18. Mortazavi A, Leeper Thompson EC, Garcia ST, Myers RM, Wold B. 2006. Comparative genomics modeling of the NRSF/REST repressor network: From single conserved sites to genome-wide repertoire. Genome Res 16: 1208-1221.
19. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifyingmammalian transcriptomes by RNA-seq. NatMethods 5: 621-628.
20. Newman AM, Cooper JB. 2010. AutoSOME: A clustering method for identifying gene expression modules without prior knowledge of cluster number. BMC Bioinformatics 11: 117.
21. Pepke S, Wold B, Mortazavi A. 2009. Computation for ChIP-seq and RNAseq studies. Nat Methods 6: S22-S32.
22. Saldanha AJ. 2004. Java Treeview-extensible visualization of microarray data. Bioinformatics 20: 3246-3248.
23. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. 2005. Evolutionary conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15: 1034-1050.
24. Spencer WC, Zeller G, Watson JD, Henz SR, Watkins KL, McWhirter RD, Petersen S, Sreedharan VT, Widmer C, Jo J, et al. 2011. A spatial and temporal map of C. elegans gene expression. Genome Res 21: 325-341.
25. Suzuki M, Oda M, Ramos MP, Pascual M, Lau K, Stasiek E, Agyiri F, Thompson RF, Glass JL, Jing Q, et al. 2011. Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome. Genome Res 21: 1833-1840.
26. Ultsch A. 1999. Data mining and knowledge discovery with emergent selforganizing feature maps for multivariate time series. In Kohonen maps (ed. Oja E), pp. 33-46. Elsevier Science, New York.
27. Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY, Peng W, Zhang MQ, et al. 2008. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet 40: 897-903.