Glbase: A framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing data

Cell Regeneration

Volumn 3, Issue 1, 2014, Pages 3:1-

  Hutchins, Andrew P ^a   Jauch, Ralf ^a,b   Dyla, Mateusz ^b,c   Miranda Saavedra, Diego ^d  

^a GUANGZHOU INSTITUTES OF BIOMEDICINE AND HEALTH   (China)

^b GENOME INSTITUTE OF SINGAPORE   (Singapore)

^c AARHUS UNIVERSITY   (Denmark)

^d NEWCASTLE UNIVERSITY   (United Kingdom)

Author keywords

Bioinformatics; ChIP seq; Genomics; Microarray; Motifs; RNA seq; Transcription factor

Indexed keywords

ARTICLE; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; DATA ANALYSIS; GENE EXPRESSION SYSTEM; GENE LIBRARY; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC DATABASE; HIGH THROUGHPUT SEQUENCING; INTERNET; MICROARRAY ANALYSIS; NEXT GENERATION SEQUENCING; ONLINE SYSTEM; PHYLOGENY; PRIORITY JOURNAL; RNA SEQUENCE; VALIDATION PROCESS;

EID: 84988231210     PISSN: None     EISSN: 20459769     Source Type: Journal    
DOI: 10.1186/2045-9769-3-1     Document Type: Article

References (21)

1. Goecks J, Nekrutenko A, Taylor J. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 2010, 11(8):R86. 10.1186/gb-2010-11-8-r86, 2945788, 20738864.
2. Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010, 26(6):841-842. 10.1093/bioinformatics/btq033, 2832824, 20110278.
3. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The sequence alignment/map format and SAMtools. Bioinformatics 2009, 25(16):2078-2079. 10.1093/bioinformatics/btp352, 2723002, 19505943.
4. Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, de Hoon MJ. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 2009, 25(11):1422-1423. 10.1093/bioinformatics/btp163, 2682512, 19304878.
5. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehvaslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E. The Bioperl toolkit: Perl modules for the life sciences. Genome Res 2002, 12(10):1611-1618. 10.1101/gr.361602, 187536, 12368254.
6. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5(10):R80. 10.1186/gb-2004-5-10-r80, 545600, 15461798.
7. Sandve GK, Gundersen S, Johansen M, Glad IK, Gunathasan K, Holden L, Holden M, Liestol K, Nygard S, Nygaard V, Paulsen J, Rydbeck H, Trengereid K, Clancy T, Drablos F, Ferkingstad E, Kalas M, Lien T, Rye MB, Frigessi A, Hovig E. The genomic hyperbrowser: an analysis web server for genome-scale data. Nucleic Acids Res 2013, 41(Web Server issue):W133-W141. 3692097, 23632163.
8. Killion PJ, Iyer VR. ArrayPlex: distributed, interactive and programmatic access to genome sequence, annotation, ontology, and analytical toolsets. Genome Biol 2008, 9(11):R159. 10.1186/gb-2008-9-11-r159, 2614491, 19014503.
9. Pedersen BS, Yang IV, De S. CruzDB: software for annotation of genomic intervals with UCSC genome-browser database. Bioinformatics 2013, 29(23):3003-3006. 10.1093/bioinformatics/btt534, 24037212.
10. Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 2010, 38(4):576-589. 10.1016/j.molcel.2010.05.004, 2898526, 20513432.
11. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 2009, 37(Web Server issue):W202-W208. 2703892, 19458158.
12. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, Haussler D. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 2005, 15(8):1034-1050. 10.1101/gr.3715005, 1182216, 16024819.
13. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol 2008, 9(9):R137. 10.1186/gb-2008-9-9-r137, 2592715, 18798982.
14. Hutchins AP, Poulain S, Miranda-Saavedra D. Genome-wide analysis of STAT3 binding in vivo predicts effectors of the anti-inflammatory response in macrophages. Blood 2012, 119(13):e110-e119. 10.1182/blood-2011-09-381483, 22323479.
15. Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J, Loh YH, Yeo HC, Yeo ZX, Narang V, Govindarajan KR, Leong B, Shahab A, Ruan Y, Bourque G, Sung WK, Clarke ND, Wei CL, Ng HH. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008, 133(6):1106-1117. 10.1016/j.cell.2008.04.043, 18555785.
16. Consortium EP. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 2011, 9(4):e1001046. 10.1371/journal.pbio.1001046, 3079585, 21526222.
17. Wilson D, Charoensawan V, Kummerfeld SK, Teichmann SA. DBD-taxonomically broad transcription factor predictions: new content and functionality. Nucleic Acids Res 2008, 36(Database issue):D88-D92. 2238844, 18073188.
18. Hutchins AP, Diez D, Takahashi Y, Ahmad S, Jauch R, Tremblay ML, Miranda-Saavedra D. Distinct transcriptional regulatory modules underlie STAT3's cell type-independent and cell type-specific functions. Nucleic Acids Res 2013, 41(4):2155-2170. 10.1093/nar/gks1300, 3575808, 23295670.
19. Hutchins AP, Poulain S, Fujii H, Miranda-Saavedra D. Discovery and characterization of new transcripts from RNA-seq data in mouse CD4(+) T cells. Genomics 2012, 100(5):303-313. 10.1016/j.ygeno.2012.07.014, 22884873.
20. Aksoy I, Jauch R, Chen J, Dyla M, Divakar U, Bogu GK, Teo R, Leng Ng CK, Herath W, Lili S, Hutchins AP, Robson P, Kolatkar PR, Stanton LW. Oct4 switches partnering from Sox2 to Sox17 to reinterpret the enhancer code and specify endoderm. EMBO J 2013, 32(7):938-953. 10.1038/emboj.2013.31, 23474895.
21. Jauch R, Aksoy I, Hutchins AP, Ng CK, Tian XF, Chen J, Palasingam P, Robson P, Stanton LW, Kolatkar PR. Conversion of Sox17 into a pluripotency reprogramming factor by reengineering its association with Oct4 on DNA. Stem Cells 2011, 29(6):940-951. 10.1002/stem.639, 21472822.