Bioinformatics resource manager v2.3: An integrated software environment for systems biology with microRNA and cross-species analysis tools

BMC Bioinformatics

Volumn 13, Issue 1, 2012, Pages

  Tilton, Susan C ^a   Tal, Tamara L ^b,c   Scroggins, Sheena M ^a   Franzosa, Jill A ^b   Peterson, Elena S ^a   Tanguay, Robert L ^b   Waters, Katrina M ^a  

^a PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^b OREGON STATE UNIVERSITY   (United States)

^c U S ENVIRONMENTAL PROTECTION AGENCY   (United States)

Author keywords

Bioinformatics; Genomics; MicroRNA; Systems biology; Zebrafish

Indexed keywords

ANALYSIS TOOLS; ANALYTIC TOOLS; BIOINFORMATICS RESOURCES; BIOLOGICAL DATA; BIOLOGICAL PROCESS; COMPLEX DATA; COMPUTATIONAL TOOLS; CROSS-SPECIES; CROSS-SPECIES COMPARISONS; DEVELOPMENTAL STAGE; FREE DISTRIBUTION; FUNCTIONAL ANNOTATION; GENOMICS; HIGH-THROUGHPUT; HYPOTHESIS GENERATION; INTEGRATED SOFTWARE ENVIRONMENTS; MICROARRAY DATA SETS; MICRORNAS; MIRNA TARGETS; MODEL SPECIES; NERVOUS SYSTEM DEVELOPMENT; NEUROGENESIS; NON-CODING RNAS; NUMBER OF SPECIES; OPEN-SOURCE TECHNOLOGY; ORTHOLOGS; POST-FERTILIZATION; POST-TRANSCRIPTIONAL REGULATIONS; PROTEIN-CODING GENES; PUBLIC DATA SOURCE; SOFTWARE ENVIRONMENTS; SYSTEMS BIOLOGY; SYSTEMS LEVELS; WORK-FLOWS; ZEBRAFISH;

BIOINFORMATICS; BIOLOGY; DATA INTEGRATION; DATA REDUCTION; DIGITAL STORAGE; GENES; GENETIC ENGINEERING; INFORMATION MANAGEMENT; MANAGERS; NICOTINE; PYRIDINE;

RNA;

DANIO RERIO;

MESSENGER RNA; MICRORNA;

ANIMAL; ARTICLE; BIOLOGY; CHEMISTRY; COMPUTER PROGRAM; DNA MICROARRAY; GENE EXPRESSION REGULATION; GENETICS; HUMAN; METABOLISM; METHODOLOGY; SEQUENCE ANALYSIS; STATISTICS; SYSTEMS BIOLOGY; ZEBRA FISH;

ANIMALS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION; HUMANS; MICRORNAS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA; SOFTWARE; SYSTEMS BIOLOGY; ZEBRAFISH;

MLCS; MLOWN;

EID: 84869861839     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-311     Document Type: Article

References (28)

1. Chen K, Rajewsky N. The evolution of gene regulation by transcription factors and microRNAs. Nat Rev Genet 2007, 8(2):93-103.
2. Friedman RC, Farh KK, Burge CB, Bartel DP. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 2009, 19(1):92-105. 2612969, 18955434.
3. Sun W, Julie Li YS, Huang HD, Shyy JY, Chien S. microRNA: a master regulator of cellular processes for bioengineering systems. Annu Rev Biomed Eng 2010, 12:1-27. 10.1146/annurev-bioeng-070909-105314, 20415587.
4. Chuang JC, Jones PA. Epigenetics and microRNAs. Pediatr Res 2007, 61(5 Pt 2):24R-29R.
5. Sinkkonen L, Hugenschmidt T, Berninger P, Gaidatzis D, Mohn F, Artus-Revel CG, Zavolan M, Svoboda P, Filipowicz W. MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells. Nat Struct Mol Biol 2008, 15(3):259-267. 10.1038/nsmb.1391, 18311153.
6. Szulwach KE, Li X, Smrt RD, Li Y, Luo Y, Lin L, Santistevan NJ, Li W, Zhao X, Jin P. Cross talk between microRNA and epigenetic regulation in adult neurogenesis. J Cell Biol 2010, 189(1):127-141. 10.1083/jcb.200908151, 2854370, 20368621.
7. Betel D, Wilson M, Gabow A, Marks DS, Sander C. The microRNA.org resource: targets and expression. Nucleic Acids Res 2008, 36(Database issue):D149-D153. 2238905, 18158296.
8. Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, et al. Combinatorial microRNA target predictions. Nat Genet 2005, 37(5):495-500. 10.1038/ng1536, 15806104.
9. Megraw M, Sethupathy P, Corda B, Hatzigeorgiou AG. miRGen: a database for the study of animal microRNA genomic organization and function. Nucleic Acids Res 2007, 35(Database issue):D149-D155. 1669779, 17108354.
10. Sethupathy P, Corda B, Hatzigeorgiou AG. Tarbase: A comprehensive database of experimentally supported animal microRNA targets. RNA 2006, 12(2):192-197. 1370898, 16373484.
11. Cho S, Jun Y, Lee S, Choi HS, Jung S, Jang Y, Park C, Kim S, Kim W. miRGator v2.0: an integrated system for functional investigation of microRNAs. Nucleic Acids Res 2011, 39(Database issue):D158-D162. 3013691, 21062822.
12. Nam S, Li M, Choi K, Balch C, Kim S, Nephew KP. MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression. Nucleic Acids Res 2009, 37(Web Server issue):W356-W362. 2703907, 19420067.
13. Sales G, Coppe A, Bisognin A, Biasiolo M, Bortoluzzi S, Romualdi C. MAGIA, a web-based tool for miRNA and genes integrated analysis. Nucleic Acids Res 2010, 38(Web Server issue):W352-W359. 2896126, 20484379.
14. Shah AR, Singhal M, Klicker KR, Stephan EG, Wiley HS, Waters KM. Enabling high-throughput data management for systems biology: the Bioinformatics Resource Manager. Bioinformatics 2007, 23(7):906-909. 10.1093/bioinformatics/btm031, 17324940.
15. Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Federhen S, et al. Database resources of the national center for biotechnology information. Nucleic Acids Res 2012, 40(Database issue):D13-D25. 3245031, 22140104.
16. UniProt Consortium Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 2012, 40(Database issue):D71-D75. 3245120, 22102590, UniProt Consortium.
17. Davidsen T, Beck E, Ganapathy A, Montgomery R, Zafar N, Yang Q, Madupu R, Goetz P, Galinsky K, White O, et al. The comprehensive microbial resource. Nucleic Acids Res 2010, 38(Database issue):D340-D345. 2808947, 19892825.
18. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet 2000, 25(1):25-29. 10.1038/75556, 3037419, 10802651.
19. Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 2012, 40(Database issue):D109-D114. 3245020, 22080510.
20. Waters KM, Pounds JG, Thrall BD. Data merging for integrated microarray and proteomic analysis. Brief Funct Genomic Proteomic 2006, 5(4):261-272. 10.1093/bfgp/ell019, 16772273.
21. Shannon PT, Reiss DJ, Bonneau R, Baliga NS. The gaggle: an open-source software system for integrating bioinformatics software and data sources. BMC Bioinformatics 2006, 7:176. 10.1186/1471-2105-7-176, 1464137, 16569235.
22. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13(11):2498-2504. 10.1101/gr.1239303, 403769, 14597658.
23. Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, Howe EA, Li J, Thiagarajan M, White JA, Quackenbush J. TM4 microarray software suite. Methods Enzymol 2006, 411:134-193.
24. da Huang W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009, 4(1):44-57.
25. Shah AR, Singhal M, Gibson TD, Sivaramakrishnan C, Waters KM, Gorton I. An extensible, scalable architecture for managing bioinformatics data and analysis. IEEE 4th International Conference on e-Science: December 7-12 2008 2008 2008, 190-197. Indianapolis Indiana: IEEE Computer Society.
26. Griffiths-Jones S, Saini HK, Van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res 2008, 36(Database issue):D154-D158. 2238936, 17991681.
27. Maziere P, Enright AJ. Prediction of microRNA targets. Drug Discov Today 2007, 12(11-12):452-458.
28. Tal TL, Franzosa JA, Tilton SC, Philbrick KA, Iwaniec UT, Turner RT, Waters KM, Tanguay RL. MicroRNAs control neurobehavioral development and function in zebrafish. FASEB J 2012, 26(4):1452-1461. 10.1096/fj.11-194464, 22253472.