Large-scale profiling of microRNAs for the Cancer Genome Atlas

Nucleic Acids Research

Volumn 44, Issue 1, 2016, Pages e3-

  Chu, Andy ^a   Robertson, Gordon ^a   Brooks, Denise ^a   Mungall, Andrew J ^a   Birol, Inanc ^a,b   Coope, Robin ^a   Ma, Yussanne ^a   Jones, Steven ^a,b,c   Marra, Marco A ^a,b  

^a BRITISH COLUMBIA CANCER AGENCY   (Canada)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^c SIMON FRASER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; DATA ANALYSIS; GENE IDENTIFICATION; GENETIC DATABASE; HUMAN; INFORMATION PROCESSING; INTERMETHOD COMPARISON; LARGE SCALE PRODUCTION; MIRDEEP2; MOLECULAR DYNAMICS; PRIORITY JOURNAL; QUALITY CONTROL; SEQUENCE ANALYSIS; SHORTSTACK; THE CANCER GENOME ATLAS; BIOLOGY; GENE EXPRESSION PROFILING; GENETICS; GENOMICS; NEOPLASM; PROCEDURES;

COMPUTATIONAL BIOLOGY; DATASETS AS TOPIC; GENE EXPRESSION PROFILING; GENOMICS; HUMANS; MICRORNAS; NEOPLASMS;

EID: 84959526423     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv808     Document Type: Article

References (25)

1. Gurtan,A.M. and Sharp,P.A. (2013) The role of miRNAs in regulating gene expression networks. J. Mol. Biol., 425, 3582-3600.
2. Hausser,J. and Zavolan,M. (2014) Identification and consequences of miRNA-target interactions-beyond repression of gene expression. Nat. Rev. Genet., 15, 599-612.
3. Friedlander,M.R., Chen,W., Adamidi,C., Maaskola,J., Einspanier,R., Knespel,S. and Rajewsky,N. (2008) Discovering microRNAs from deep sequencing data using miRDeep. Nat. Biotechnol., 26, 407-415.
4. Axtell,M.J. (2013) ShortStack: comprehensive annotation and quantification of small RNA genes. RNA, 19, 740-751.
5. Kozomara,A. and Griffiths-Jones,S. (2014) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res., 42, D68-D73.
6. Rosenbloom,K.R., Armstrong,J., Barber,G.P., Casper,J., Clawson,H., Diekhans,M., Dreszer,T.R., Fujita,P.A., Guruvadoo,L., Haeussler,M. et al. (2015) The UCSC Genome Browser database: 2015 update. Nucleic Acids Res., 43, D670-D681.
7. Cunningham,F., Amode,M.R., Barrell,D., Beal,K., Billis,K., Brent,S., Carvalho-Silva,D., Clapham,P., Coates,G., Fitzgerald,S. et al. (2015) Ensembl 2015. Nucleic Acids Res., 43, D662-D669.
8. Li,H., Handsaker,B., Wysoker,A., Fennell,T., Ruan,J., Homer,N., Marth,G., Abecasis,G., Durbin,R. and Genome Project Data Processing, S. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078-2079.
9. Li,H. and Durbin,R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
10. de Hoon,M.J., Taft,R.J., Hashimoto,T., Kanamori-Katayama,M., Kawaji,H., Kawano,M., Kishima,M., Lassmann,T., Faulkner,G.J., Mattick,J.S. et al. (2010) Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. Genome Res., 20, 257-264.
11. Gaujoux,R. and Seoighe,C. (2010) A flexible R package for nonnegative matrix factorization. BMC Bioinformatics, 11, 367.
12. Lovmar,L., Ahlford,A., Jonsson,M. and Syvanen,A.C. (2005) Silhouette scores for assessment of SNP genotype clusters. BMC Genomics, 6, 35.
13. Li,J. and Tibshirani,R. (2013) Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data. Stat. Methods Med. Res., 22, 519-536.
14. Mullokandov,G., Baccarini,A., Ruzo,A., Jayaprakash,A.D., Tung,N., Israelow,B., Evans,M.J., Sachidanandam,R. and Brown,B.D. (2012) High-throughput assessment of microRNA activity and function using microRNA sensor and decoy libraries. Nat. Methods, 9, 840-846.
15. Cancer Genome Atlas Research Network. (2014) Comprehensive molecular characterization of urothelial bladder carcinoma. Nature, 507, 315-322.
16. Cancer Genome Atlas Network. (2012) Comprehensive molecular portraits of human breast tumours. Nature, 490, 61-70.
17. Cancer Genome Atlas Network. (2012) Comprehensive molecular characterization of human colon and rectal cancer. Nature, 487, 330-337.
18. Cancer Genome Atlas Network. (2015) Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature, 517, 576-582.
19. Cancer Genome Atlas Research Network. (2012) Comprehensive genomic characterization of squamous cell lung cancers. Nature, 489, 519-525.
20. Cancer Genome Atlas Research Network. (2013) Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N. Engl. J. Med., 368, 2059-2074.
21. Cancer Genome Atlas Research Network. (2013) Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature, 499, 43-49.
22. Cancer Genome Atlas Research Network. (2014) Comprehensive molecular profiling of lung adenocarcinoma. Nature, 511, 543-550.
23. Cancer Genome Atlas Research Network. (2014) Integrated genomic characterization of papillary thyroid carcinoma. Cell, 159, 676-690.
24. Cancer Genome Atlas Research Network. (2014) Comprehensive molecular characterization of gastric adenocarcinoma. Nature, 513, 202-209.
25. Cancer Genome Atlas Research Network, Kandoth,C., Schultz,N., Cherniack,A.D., Akbani,R., Liu,Y., Shen,H., Robertson,A.G., Pashtan,I., Shen,R. et al. (2013) Integrated genomic characterization of endometrial carcinoma. Nature, 497, 67-73.