SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata

PLoS ONE

Volumn 12, Issue 4, 2017, Pages

  Hitz, Benjamin C ^a   Rowe, Laurence D ^a   Podduturi, Nikhil R ^a   Glick, David I ^a   Baymuradov, Ulugbek K ^a   Malladi, Venkat S ^a   Chan, Esther T ^a   Davidson, Jean M ^a   Gabdank, Idan ^a   Narayana, Aditi K ^a   Onate, Kathrina C ^a   Hilton, Jason ^a   Ho, Marcus C ^a   Lee, Brian T ^b   Miyasato, Stuart R ^a   Dreszer, Timothy R ^a   Sloan, Cricket A ^a   Strattan, J Seth ^a   Tanaka, Forrest Y ^a   Hong, Eurie L ^a   Cherry, J Michael ^a   more..

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b University of California Santa Cruz   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL LINE; CHROMATIN STRUCTURE; COORDINATION; DATA BASE; DNA TRANSCRIPTION; EXPERIMENTAL MODEL; HUMAN; HUMAN CELL; HUMAN GENOME PROJECT; HUMAN TISSUE; LANDSCAPE; METADATA; MUSCLE; PUBLICATION; SOFTWARE; STORAGE; TRANSCRIPTION REGULATION; VALIDATION PROCESS; ANIMAL; GENETIC DATABASE; GENETICS; GENOME; GENOMICS; MOUSE; PROCEDURES;

DNA;

ANIMALS; DATABASES, GENETIC; DNA; GENOME; GENOMICS; HUMANS; METADATA; MICE; SOFTWARE;

EID: 85017544746     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0175310     Document Type: Article

References (34)

1. International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature. 2004; 431: 931-945. https://doi.org/10.1038/nature03001 PMID: 15496913
2. Rosenbloom KR, Sloan CA, Malladi VS, Dreszer TR, Learned K, Kirkup VM, et al. ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res. 2013; 41: D56-63. https://doi.org/10.1093/nar/gks1172 PMID: 23193274
3. Ho JWK, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, et al. Comparative analysis of metazoan chromatin organization. Nature. 2014; 512: 449-452. https://doi.org/10.1038/nature13415 PMID: 25164756
4. Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, et al. Comparative analysis of regulatory information and circuits across distant species. Nature. 2014; 512: 453-456. https://doi.org/10.1038/nature13668 PMID: 25164757
5. Gerstein MB, Rozowsky J, Yan K-K, Wang D, Cheng C, Brown JB, et al. Comparative analysis of the transcriptome across distant species. Nature. 2014; 512: 445-448. https://doi.org/10.1038/nature13424 PMID: 25164755
6. Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 2014; 515: 355-364. https://doi.org/10.1038/nature13992 PMID: 25409824
7. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al. Initial sequencing and analysis of the human genome. Nature. 2001; 409: 860-921. https://doi.org/10.1038/35057062 PMID: 11237011
8. Malladi VS, Erickson DT, Podduturi NR, Rowe LD, Chan ET, Davidson JM, et al. Ontology application and use at the ENCODE DCC. Database. 2015; 2015.
9. Sloan CA, Chan ET, Davidson JM, Malladi VS, Strattan JS, Hitz BC, et al. ENCODE data at the ENCODE portal. Nucleic Acids Res. 2016; 44: D726-32. https://doi.org/10.1093/nar/gkv1160 PMID: 26527727
10. Hong EL, Sloan CA, Chan ET, Davidson JM, Malladi VS, Strattan JS, et al. Principles of metadata organization at the ENCODE data coordination center. Database. 2016; 2016.
11. ENCODE Project Consortium. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011; 9: e1001046. https://doi.org/10.1371/journal.pbio.1001046 PMID: 21526222
12. Pazin MJ. Using the ENCODE Resource for Functional Annotation of Genetic Variants. Cold Spring Harb Protoc. 2015; 2015: 522-536. https://doi.org/10.1101/pdb.top084988 PMID: 25762420
13. Diehl AG, Boyle AP. Deciphering ENCODE. Trends Genet. 2016
14. Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012; 22: 1760-1774. https://doi.org/10.1101/gr.135350.111 PMID: 22955987
15. Haase K, Mösch A, Frishman D. Differential expression analysis of human endogenous retroviruses based on ENCODE RNA-seq data. BMC Med Genomics. 2015; 8: 71. https://doi.org/10.1186/s12920-015-0146-5 PMID: 26530187
16. Vierstra J, Stamatoyannopoulos JA. Genomic footprinting. Nat Methods. 2016; 13: 213-221. https://doi.org/10.1038/nmeth.3768 PMID: 26914205
17. Siggens L, Ekwall K. Epigenetics, chromatin and genome organization: recent advances from the ENCODE project. J Intern Med. 2014; 276: 201-214. https://doi.org/10.1111/joim.12231 PMID: 24605849
18. Ma Y, Smith CE, Lai C-Q, Irvin MR, Parnell LD, Lee Y-C, et al. The effects of omega-3 polyunsaturated fatty acids and genetic variants on methylation levels of the interleukin-6 gene promoter. Mol Nutr Food Res. 2016; 60: 410-419. https://doi.org/10.1002/mnfr.201500436 PMID: 26518637
19. Fan Y, Zhang Y, Xu S, Kong N, Zhou Y, Ren Z, et al. Insights from ENCODE on Missing Proteins: Why β-Defensin Expression Is Scarcely Detected. J Proteome Res. 2015; 14: 3635-3644. https://doi.org/10. 1021/acs.jproteome.5b00565 PMID: 26258396
20. Li G, Fullwood MJ, Xu H, Mulawadi FH, Velkov S, Vega V, et al. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol. 2010; 11: R22. https://doi.org/10.1186/gb-2010-11-2-r22 PMID: 20181287
21. Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009; 326: 289-293. https://doi.org/10.1126/science.1181369 PMID: 19815776
22. Zhao J, Ohsumi TK, Kung JT, Ogawa Y, Grau DJ, Sarma K, et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol Cell. 2010; 40: 939-953. https://doi.org/10.1016/j.molcel. 2010.12.011 PMID: 21172659
23. Hoffman MM, Ernst J, Wilder SP, Kundaje A, Harris RS, Libbrecht M, et al. Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Res. 2013; 41: 827-841. https://doi.org/10. 1093/nar/gks1284 PMID: 23221638
24. Yip KY, Cheng C, Bhardwaj N, Brown JB, Leng J, Kundaje A, et al. Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol. 2012; 13: R48. https://doi.org/10.1186/gb-2012-13-9-r48 PMID: 22950945
25. Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan K-K, Cheng C, et al. Architecture of the human regulatory network derived from ENCODE data. Nature. 2012; 489: 91-100. https://doi.org/10.1038/nature11245 PMID: 22955619
26. Cheng Y, Ma Z, Kim B-H, Wu W, Cayting P, Boyle AP, et al. Principles of regulatory information conservation between mouse and human. Nature. 2014; 515: 371-375. https://doi.org/10.1038/nature13985 PMID: 25409826
27. Boley N, Nathan B, Wan KH, Bickel PJ, Celniker SE. Navigating and mining modENCODE data. Methods. 2014; 68: 38-47. https://doi.org/10.1016/j.ymeth.2014.03.007 PMID: 24636835
28. Brown JB, Celniker SE. Lessons from modENCODE. Annu Rev Genomics Hum Genet. 2015; 16: 31-53. https://doi.org/10.1146/annurev-genom-090413-025448 PMID: 26133010
29. ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012; 489: 57-74. https://doi.org/10.1038/nature11247 PMID: 22955616
30. Mouse ENCODE Consortium, Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, et al. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol. 2012; 13: 418. https://doi.org/10.1186/gb-2012-13-8-418 PMID: 22889292
31. Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, et al. Integrative analysis of 111 reference human epigenomes. Nature. 2015; 518: 317-330. https://doi.org/10. 1038/nature14248 PMID: 25693563
32. Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, et al. Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics. 2014; 30: 1003-1005. https://doi.org/10.1093/bioinformatics/btt637 PMID: 24227676
33. Jupp S, Malone J, Bolleman J, Brandizi M, Davies M, Garcia L, et al. The EBI RDF platform: linked open data for the life sciences. Bioinformatics. 2014; 30: 1338-1339. https://doi.org/10.1093/bioinformatics/btt765 PMID: 24413672
34. Speir ML, Zweig AS, Rosenbloom KR, Raney BJ, Paten B, Nejad P, et al. The UCSC Genome Browser database: 2016 update. Nucleic Acids Res. 2016; 44: D717-25. https://doi.org/10.1093/nar/gkv1275 PMID: 26590259