CWords - systematic microRNA regulatory motif discovery from mRNA expression data

Silence

Volumn 4, Issue 1, 2013, Pages

  Rasmussen, Simon H ^a   Jacobsen, Anders ^b   Krogh, Anders ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

Author keywords

MicroRNA; Motif discovery; Post transcriptional regulation; RNA binding proteins; SiRNA

Indexed keywords

ARGONAUTE PROTEIN; MESSENGER RNA; MICRORNA; SMALL INTERFERING RNA;

ALGORITHM; ARTICLE; BINDING SITE; CASE CONTROL STUDY; CELL STRAIN HEK293; COMPUTER PROGRAM; CONTROLLED STUDY; DATA ANALYSIS; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENETIC REGULATION; HUMAN; HUMAN CELL; INTERNET; MICRORNA BINDING MOTIF; MICRORNA REGULATORY MOTIF; NUCLEOTIDE MOTIF; POSTTRANSCRIPTIONAL CONTROL; PRIORITY JOURNAL; PROTEIN STRUCTURE; STATISTICAL ANALYSIS;

EID: 84877849011     PISSN: None     EISSN: 1758907X     Source Type: Journal    
DOI: 10.1186/1758-907X-4-2     Document Type: Article

References (32)

1. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS, Johnson JM. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 2005, 7027:769-773.
2. Grimson A, Farh KK-H, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 2007, 27:91-105. 10.1016/j.molcel.2007.06.017, 17612493.
3. Bartel DP. MicroRNAs: Target Recognition and Regulatory Functions. Cell 2009, 136:215-233. 10.1016/j.cell.2009.01.002, 19167326.
4. Betel D, Koppal A, Agius P, Sander C, Leslie C. Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol 2010, 11:R90. 10.1186/gb-2010-11-8-r90, 2945792, 20799968.
5. Frankel LB, Christoffersen NR, Jacobsen A, Lindow M, Krogh A, Lund AH. Programmed cell death 4 (PDCD4) is an important functional target of the microRNA miR-21 in breast cancer cells. J Biol Chem 2008, 283:1026-1033. 10.1074/jbc.M707224200, 17991735.
6. Krützfeldt J, Rajewsky N, Braich R, Rajeev KG, Tuschl T, Manoharan M, Stoffel M. Silencing of microRNAs in vivo with " antagomirs" Nature 2005, 438:685-689. 10.1038/nature04303, 16258535.
7. Jacobsen A, Wen J, Marks DS, Krogh A. Signatures of RNA binding proteins globally coupled to effective microRNA target sites. Genome Res 2010, 20:1010-1019. 10.1101/gr.103259.109, 2909566, 20508147.
8. Sood P, Krek A, Zavolan M, Macino G, Rajewsky N. Cell-type-specific signatures of microRNAs on target mRNA expression. PNAS 2006, 103:2746-2751. 10.1073/pnas.0511045103, 1413820, 16477010.
9. Dongen SV, Abreu-Goodger C, Enright AJ. Detecting microRNA binding and siRNA off-target effects from expression data. Nat Methods 2008, 5:1023-1025. 10.1038/nmeth.1267, 2635553, 18978784.
10. Gregersen LH, Jacobsen AB, Frankel LB, Wen J, Krogh A, Lund AH. MicroRNA-145 targets YES and STAT1 in colon cancer cells. PLoS One 2010, 5:e8836. 10.1371/journal.pone.0008836, 2809101, 20098684.
11. Bailey TL. Discovering sequence motifs. Methods Mol Biol 2008, 452:231-251. 10.1007/978-1-60327-159-2_12, 18566768.
12. Tompa M, Li N, Bailey TL, Church GM, Moor BD, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, Régnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z. Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol 2005, 23:137-144. 10.1038/nbt1053, 15637633.
13. Lawrance CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF, Wootton JC. Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment. Science 1993, 262:208-214. 10.1126/science.8211139, 8211139.
14. Bailey TL, Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 1994, 2:28-36.
15. Pavesi G, Mauri G, Pesole G. An algorithm for finding signals of unknown length in DNA sequences. Bioinformatics 2001, 17:207-214.
16. Redhead E, Bailey TL. Discriminative motif discovery in DNA and protein sequences using the DEME algorithm. BMC Bioinformatics 2007, 8:385. 10.1186/1471-2105-8-385, 2194741, 17937785.
17. Valen E, Sandelin A, Winther O, Krogh A. Discovery of regulatory elements is improved by a discriminatory approach. PLoS Comput Biol 2009, 5:e1000562. 10.1371/journal.pcbi.1000562, 2770120, 19911049.
18. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov J. Gene set enrichment: A knowledge-based approach for interpreting genome-wide expression profiles. PNAS 2005, 102:15545-15550. 10.1073/pnas.0506580102, 1239896, 16199517.
19. Schnall-Levin M, Rissland OS, Johnston WK, Perrimon N, Bartel DP, Berger B. Unusually effective microRNA targeting within repeat-rich coding regions of mammalian mRNAs. Genome Res 2011, 21:1395-1403. 10.1101/gr.121210.111, 3166825, 21685129.
20. Zeng Y, Yi R, Cullen BR. MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms. Proc Natl Acad Sci USA 2003, 100:9779-9784. 10.1073/pnas.1630797100, 187842, 12902540.
21. Saxena S, Jónsson ZO, Dutta A. Small RNAs with Imperfect Match to Endogenous mRNA Repress Translation. J Biol Chem 2003, 1278:44312-44319.
22. Doench JG, Petersen CP, Sharp PA. siRNAs can function as miRNAs. Genes Dev 2003, 17:438-442. 10.1101/gad.1064703, 195999, 12600936.
23. Jackson AL, Burchard J, Schelter J, Chau BN, Cleary M, Lim L, Linsley PS. Widespread siRNA " off-target" transcript silencing mediated by seed region sequence complementarity. RNA 2006, 12:1179-1187. 10.1261/rna.25706, 1484447, 16682560.
24. Jackson AL, Bartz SR, Schelter J, Kobayashi SV, Burchard J, Mao M, Li B, Cavet G, Linsley PS. Expression profiling reveals off-target gene regulation by RNAi. RNA 2003, 21:635-637.
25. Jackson AL, Burchard J, Leake D, Reynolds A, Schelter J, Guo J, Johnson JM, Lim L, Karpilow J, Nichols K, Marshall W, Khvorova A, Linsley PS. Position-specific chemical modification of siRNAs reduces " off-target" transcript silencing. RNA 2006, 12:1197-1205. 10.1261/rna.30706, 1484422, 16682562.
26. Landthaler M, Gaidatzis D, Rothballer A, Chen PY, Soll SJ, Dinic L, Ojo T, Hafner M, Zavolan M, Tuschl T. Molecular characterization of human Argonaute-containing ribonucleoprotein complexes and their bound target mRNAs. RNA 2008, 14:2580-2596. 10.1261/rna.1351608, 2590962, 18978028.
27. Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V, Chiaretti S, Foà R, Schliwka J, Fuchs U, Novosel A, Müller RU, Schermer B, Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G, Frezzetti D, Trompeter HI. A Mammalian microRNA Expression Atlas Based on Small RNA Library Sequencing. Cell 2007, 129:1401-1414. 10.1016/j.cell.2007.04.040, 2681231, 17604727.
28. Schbath S. On Overview of the Distribution of Word Counts in Markov Chains. J Comput Biol 2000, 7:193-201. 10.1089/10665270050081469, 10890396.
29. Feller W. The asymptotic distribution of the range of sums of independent random variables. Ann Mathematical Stat 1951, 22:427-432.
30. Mises RV. Mathematical theory of probability and statistics 1964, New York: Academic.
31. Marsaglia G, Tsang WW, Wang J. Evaluating Kolmogorov's Distribution. J Stat Software 2003, 08(18):1-4.
32. Durbin R, Eddy S, Krogh A. Biological Sequence Analysis 2007, Cambridge, UK: Cambridge University Press.