Lee RC, Feinbaum RL, Ambros V: The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell. 1993, 75 (5): 843-854. 10.1016/0092-8674(93)90529-Y.
Article
CAS
PubMed
Google Scholar
Wightman B, Ha I, Ruvkun G: Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell. 1993, 75 (5): 855-862. 10.1016/0092-8674(93)90530-4.
Article
CAS
PubMed
Google Scholar
Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR, Ruvkun G: The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature. 2000, 403 (6772): 901-906. 10.1038/35002607.
Article
CAS
PubMed
Google Scholar
Bartel DP: MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004, 116 (2): 281-297. 10.1016/S0092-8674(04)00045-5.
Article
CAS
PubMed
Google Scholar
Huntzinger E, Izaurralde E: Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nature reviews Genetics. 2011, 12 (2): 99-110. 10.1038/nrg2936.
Article
CAS
PubMed
Google Scholar
Miska EA: How microRNAs control cell division, differentiation and death. Current opinion in genetics & development. 2005, 15 (5): 563-568. 10.1016/j.gde.2005.08.005.
Article
CAS
Google Scholar
Sood P, Krek A, Zavolan M, Macino G, Rajewsky N: Cell-type-specific signatures of microRNAs on target mRNA expression. Proceedings of the National Academy of Sciences of the United States of America. 2006, 103 (8): 2746-2751. 10.1073/pnas.0511045103.
Article
PubMed Central
CAS
PubMed
Google Scholar
Chen JF, Mandel EM, Thomson JM, Wu Q, Callis TE, Hammond SM, Conlon FL, Wang DZ: The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation. Nature genetics. 2006, 38 (2): 228-233. 10.1038/ng1725.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zhao Y, Samal E, Srivastava D: Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature. 2005, 436 (7048): 214-220. 10.1038/nature03817.
Article
CAS
PubMed
Google Scholar
Cui Q, Yu Z, Purisima EO, Wang E: Principles of microRNA regulation of a human cellular signaling network. Molecular systems biology. 2006, 2: 46-
Article
PubMed Central
PubMed
Google Scholar
Poy MN, Eliasson L, Krutzfeldt J, Kuwajima S, Ma X, Macdonald PE, Pfeffer S, Tuschl T, Rajewsky N, Rorsman P, et al: A pancreatic islet-specific microRNA regulates insulin secretion. Nature. 2004, 432 (7014): 226-230. 10.1038/nature03076.
Article
CAS
PubMed
Google Scholar
Xu C, Lu Y, Pan Z, Chu W, Luo X, Lin H, Xiao J, Shan H, Wang Z, Yang B: The muscle-specific microRNAs miR-1 and miR-133 produce opposing effects on apoptosis by targeting HSP60, HSP70 and caspase-9 in cardiomyocytes. Journal of cell science. 2007, 120 (Pt 17): 3045-3052.
Article
CAS
PubMed
Google Scholar
Esteller M: Non-coding RNAs in human disease. Nature reviews Genetics. 2011, 12 (12): 861-874. 10.1038/nrg3074.
Article
CAS
PubMed
Google Scholar
Wang J, Lu M, Qiu C, Cui Q: TransmiR: a transcription factor-microRNA regulation database. Nucleic acids research. 2010, D119-122. 38 Database
Friard O, Re A, Taverna D, De Bortoli M, Cora D: CircuitsDB: a database of mixed microRNA/transcription factor feed-forward regulatory circuits in human and mouse. BMC bioinformatics. 2010, 11: 435-10.1186/1471-2105-11-435.
Article
PubMed Central
PubMed
Google Scholar
Yang JH, Li JH, Jiang S, Zhou H, Qu LH: ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. Nucleic acids research. 2013, D177-187. 41 Database
Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS: MicroRNA targets in Drosophila. Genome biology. 2003, 5 (1): R1-10.1186/gb-2003-5-1-r1.
Article
PubMed Central
PubMed
Google Scholar
Garcia DM, Baek D, Shin C, Bell GW, Grimson A, Bartel DP: Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nature structural & molecular biology. 2011, 18 (10): 1139-1146. 10.1038/nsmb.2115.
Article
CAS
Google Scholar
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. Nature genetics. 2005, 37 (5): 495-500. 10.1038/ng1536.
Article
CAS
PubMed
Google Scholar
Chi SW, Zang JB, Mele A, Darnell RB: Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature. 2009, 460 (7254): 479-486.
PubMed Central
CAS
PubMed
Google Scholar
Helwak A, Kudla G, Dudnakova T, Tollervey D: Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell. 2013, 153 (3): 654-665. 10.1016/j.cell.2013.03.043.
Article
PubMed Central
CAS
PubMed
Google Scholar
Yan Z, Shah PK, Amin SB, Samur MK, Huang N, Wang X, Misra V, Ji H, Gabuzda D, Li C: Integrative analysis of gene and miRNA expression profiles with transcription factor-miRNA feed-forward loops identifies regulators in human cancers. Nucleic acids research. 2012, 40 (17): e135-10.1093/nar/gks395.
Article
PubMed Central
CAS
PubMed
Google Scholar
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 research. 2010, W352-359. 38 Web Server
Bisognin A, Sales G, Coppe A, Bortoluzzi S, Romualdi C: MAGIA(2): from miRNA and genes expression data integrative analysis to microRNA-transcription factor mixed regulatory circuits (2012 update). Nucleic acids research. 2012, W13-21. 40 Web Server
Huang GT, Athanassiou C, Benos PV: mirConnX: condition-specific mRNA-microRNA network integrator. Nucleic acids research. 2011, W416-423. 39 Web Server
Ye S, Yang L, Zhao X, Song W, Wang W, Zheng S: Bioinformatics Method to Predict Two Regulation Mechanism: TF-miRNA-mRNA and lncRNA-miRNA-mRNA in Pancreatic Cancer. Cell biochemistry and biophysics. 2014
Google Scholar
Esau C, Davis S, Murray SF, Yu XX, Pandey SK, Pear M, Watts L, Booten SL, Graham M, McKay R, et al: miR-122 regulation of lipid metabolism revealed by in vivo antisense targeting. Cell metabolism. 2006, 3 (2): 87-98. 10.1016/j.cmet.2006.01.005.
Article
CAS
PubMed
Google Scholar
Krutzfeldt J, Rajewsky N, Braich R, Rajeev KG, Tuschl T, Manoharan M, Stoffel M: Silencing of microRNAs in vivo with 'antagomirs'. Nature. 2005, 438 (7068): 685-689. 10.1038/nature04303.
Article
PubMed
Google Scholar
Kutay H, Bai S, Datta J, Motiwala T, Pogribny I, Frankel W, Jacob ST, Ghoshal K: Downregulation of miR-122 in the rodent and human hepatocellular carcinomas. Journal of cellular biochemistry. 2006, 99 (3): 671-678. 10.1002/jcb.20982.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tsai WC, Hsu PW, Lai TC, Chau GY, Lin CW, Chen CM, Lin CD, Liao YL, Wang JL, Chau YP, et al: MicroRNA-122, a tumor suppressor microRNA that regulates intrahepatic metastasis of hepatocellular carcinoma. Hepatology. 2009, 49 (5): 1571-1582. 10.1002/hep.22806.
Article
CAS
PubMed
Google Scholar
Hsu SH, Wang B, Kota J, Yu J, Costinean S, Kutay H, Yu L, Bai S, La Perle K, Chivukula RR, et al: Essential metabolic, anti-inflammatory, and anti-tumorigenic functions of miR-122 in liver. The Journal of clinical investigation. 2012, 122 (8): 2871-2883. 10.1172/JCI63539.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tsai WC, Hsu SD, Hsu CS, Lai TC, Chen SJ, Shen R, Huang Y, Chen HC, Lee CH, Tsai TF, et al: MicroRNA-122 plays a critical role in liver homeostasis and hepatocarcinogenesis. The Journal of clinical investigation. 2012, 122 (8): 2884-2897. 10.1172/JCI63455.
Article
PubMed Central
CAS
PubMed
Google Scholar
Xu H, He JH, Xiao ZD, Zhang QQ, Chen YQ, Zhou H, Qu LH: Liver-enriched transcription factors regulate microRNA-122 that targets CUTL1 during liver development. Hepatology. 2010, 52 (4): 1431-1442. 10.1002/hep.23818.
Article
CAS
PubMed
Google Scholar
Csak T, Bala S, Lippai D, Satishchandran A, Catalano D, Kodys K, Szabo G: microRNA-122 regulates hypoxia-inducible factor-1 and vimentin in hepatocytes and correlates with fibrosis in diet-induced steatohepatitis. Liver international: official journal of the International Association for the Study of the Liver. 2014
Google Scholar
Stadtfeld M, Apostolou E, Akutsu H, Fukuda A, Follett P, Natesan S, Kono T, Shioda T, Hochedlinger K: Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells. Nature. 2010, 465 (7295): 175-181. 10.1038/nature09017.
Article
PubMed Central
CAS
PubMed
Google Scholar
Valdmanis PN, Roy-Chaudhuri B, Kim HK, Sayles LC, Zheng Y, Chuang CH, Caswell DR, Chu K, Zhang Y, Winslow MM, et al: Upregulation of the microRNA cluster at the Dlk1-Dio3 locus in lung adenocarcinoma. Oncogene. 2013
Google Scholar
Luk JM, Burchard J, Zhang C, Liu AM, Wong KF, Shek FH, Lee NP, Fan ST, Poon RT, Ivanovska I, et al: DLK1-DIO3 genomic imprinted microRNA cluster at 14q32.2 defines a stemlike subtype of hepatocellular carcinoma associated with poor survival. The Journal of biological chemistry. 2011, 286 (35): 30706-30713. 10.1074/jbc.M111.229831.
Article
PubMed Central
CAS
PubMed
Google Scholar
Manodoro F, Marzec J, Chaplin T, Miraki-Moud F, Moravcsik E, Jovanovic JV, Wang J, Iqbal S, Taussig D, Grimwade D, et al: Loss of imprinting at the 14q32 domain is associated with microRNA overexpression in acute promyelocytic leukemia. Blood. 2014, 123 (13): 2066-2074. 10.1182/blood-2012-12-469833.
Article
CAS
PubMed
Google Scholar
Wang J, Li J, Shen J, Wang C, Yang L, Zhang X: MicroRNA-182 downregulates metastasis suppressor 1 and contributes to metastasis of hepatocellular carcinoma. BMC cancer. 2012, 12: 227-10.1186/1471-2407-12-227.
Article
PubMed Central
CAS
PubMed
Google Scholar
Li L, Tang J, Zhang B, Yang W, Liugao M, Wang R, Tan Y, Fan J, Chang Y, Fu J, et al: Epigenetic modification of MiR-429 promotes liver tumour-initiating cell properties by targeting Rb binding protein 4. Gut. 2014
Google Scholar
Murakami Y, Toyoda H, Tanaka M, Kuroda M, Harada Y, Matsuda F, Tajima A, Kosaka N, Ochiya T, Shimotohno K: The progression of liver fibrosis is related with overexpression of the miR-199 and 200 families. PloS one. 2011, 6 (1): e16081-10.1371/journal.pone.0016081.
Article
PubMed Central
CAS
PubMed
Google Scholar
Gruber AJ, Zavolan M: Modulation of epigenetic regulators and cell fate decisions by miRNAs. Epigenomics. 2013, 5 (6): 671-683. 10.2217/epi.13.65.
Article
CAS
PubMed
Google Scholar
Saito Y, Saito H: Role of CTCF in the regulation of microRNA expression. Frontiers in genetics. 2012, 3: 186-
PubMed Central
CAS
PubMed
Google Scholar
Mukhopadhyay R, Yu W, Whitehead J, Xu J, Lezcano M, Pack S, Kanduri C, Kanduri M, Ginjala V, Vostrov A, et al: The binding sites for the chromatin insulator protein CTCF map to DNA methylation-free domains genome-wide. Genome research. 2004, 14 (8): 1594-1602. 10.1101/gr.2408304.
Article
PubMed Central
CAS
PubMed
Google Scholar
Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, et al: Integration of biological networks and gene expression data using Cytoscape. Nature protocols. 2007, 2 (10): 2366-2382. 10.1038/nprot.2007.324.
Article
PubMed Central
CAS
PubMed
Google Scholar
Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T: A travel guide to Cytoscape plugins. Nature methods. 2012, 9 (11): 1069-1076. 10.1038/nmeth.2212.
Article
PubMed Central
CAS
PubMed
Google Scholar
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 research. 2003, 13 (11): 2498-2504. 10.1101/gr.1239303.
Article
PubMed Central
CAS
PubMed
Google Scholar
Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T: Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2011, 27 (3): 431-432. 10.1093/bioinformatics/btq675.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hsu SD, Tseng YT, Shrestha S, Lin YL, Khaleel A, Chou CH, Chu CF, Huang HY, Lin CM, Ho SY, et al: miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. Nucleic acids research. 2014, D78-85. 42 Database
Vergoulis T, Vlachos IS, Alexiou P, Georgakilas G, Maragkakis M, Reczko M, Gerangelos S, Koziris N, Dalamagas T, Hatzigeorgiou AG: TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support. Nucleic acids research. 2012, D222-229. 40 Database
Li JH, Liu S, Zhou H, Qu LH, Yang JH: starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic acids research. 2014, D92-97. 42 Database
Sarachana T, Zhou R, Chen G, Manji HK, Hu VW: Investigation of post-transcriptional gene regulatory networks associated with autism spectrum disorders by microRNA expression profiling of lymphoblastoid cell lines. Genome medicine. 2010, 2 (4): 23-10.1186/gm144.
Article
PubMed Central
PubMed
Google Scholar
Xiao Y, Ping Y, Fan H, Xu C, Guan J, Zhao H, Li Y, Lv Y, Jin Y, Wang L, et al: Identifying dysfunctional miRNA-mRNA regulatory modules by inverse activation, cofunction, and high interconnection of target genes: a case study of glioblastoma. Neuro-oncology. 2013, 15 (7): 818-828. 10.1093/neuonc/not018.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bandyopadhyay S, Mitra R: TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples. Bioinformatics. 2009, 25 (20): 2625-2631. 10.1093/bioinformatics/btp503.
Article
CAS
PubMed
Google Scholar
Li XH, Qu JQ, Yi H, Zhang PF, Yi HM, Wan XX, He QY, Ye X, Yuan L, Zhu JF, et al: Integrated analysis of differential miRNA and mRNA expression profiles in human radioresistant and radiosensitive nasopharyngeal carcinoma cells. PloS one. 2014, 9 (1): e87767-10.1371/journal.pone.0087767.
Article
PubMed Central
PubMed
Google Scholar
Kramer A, Green J, Pollard J, Tugendreich S: Causal analysis approaches in Ingenuity Pathway Analysis. Bioinformatics. 2014, 30 (4): 523-530. 10.1093/bioinformatics/btt703.
Article
PubMed Central
PubMed
Google Scholar
FASTX-Toolkit: FASTQ/A short-reads pre-processing tools. [http://hannonlab.cshl.edu/fastx_toolkit/]
Chen CJ, Servant N, Toedling J, Sarazin A, Marchais A, Duvernois-Berthet E, Cognat V, Colot V, Voinnet O, Heard E, et al: ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data. Bioinformatics. 2012, 28 (23): 3147-3149. 10.1093/bioinformatics/bts587.
Article
CAS
PubMed
Google Scholar
Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome biology. 2009, 10 (3): R25-10.1186/gb-2009-10-3-r25.
Article
PubMed Central
PubMed
Google Scholar
Griffiths-Jones S: The microRNA Registry. Nucleic acids research. 2004, D109-111. 32 Database
Kozomara A, Griffiths-Jones S: miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic acids research. 2014, D68-73. 42 Database
Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A: Rfam 11.0: 10 years of RNA families. Nucleic acids research. 2013, D226-232. 41 Database
Friedlander MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S, Rajewsky N: Discovering microRNAs from deep sequencing data using miRDeep. Nature biotechnology. 2008, 26 (4): 407-415. 10.1038/nbt1394.
Article
PubMed
Google Scholar
Friedlander MR, Mackowiak SD, Li N, Chen W, Rajewsky N: miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic acids research. 2012, 40 (1): 37-52. 10.1093/nar/gkr688.
Article
PubMed Central
PubMed
Google Scholar