메뉴 건너뛰기




Volumn 14, Issue 2, 2016, Pages 310-319

Elucidating MicroRNA Regulatory Networks Using Transcriptional, Post-transcriptional, and Histone Modification Measurements

Author keywords

[No Author keywords available]

Indexed keywords

DICER; MICRORNA; TRANSCRIPTION FACTOR;

EID: 84955338195     PISSN: None     EISSN: 22111247     Source Type: Journal    
DOI: 10.1016/j.celrep.2015.12.031     Document Type: Article
Times cited : (74)

References (55)
  • 1
    • 84903454574 scopus 로고    scopus 로고
    • Integrative identification of deregulated miRNA/TF-mediated gene regulatory loops and networks in prostate cancer
    • Afshar A.S., Xu J., Goutsias J. Integrative identification of deregulated miRNA/TF-mediated gene regulatory loops and networks in prostate cancer. PLoS ONE 2014, 9:e100806. 10.1371/journal.pone.0100806.
    • (2014) PLoS ONE , vol.9 , pp. e100806
    • Afshar, A.S.1    Xu, J.2    Goutsias, J.3
  • 2
    • 84940502214 scopus 로고    scopus 로고
    • Predicting effective microRNA target sites in mammalian mRNAs
    • Agarwal V., Bell G.W., Nam J.-W., Bartel D.P. Predicting effective microRNA target sites in mammalian mRNAs. eLife 2015, 4:e05005. 10.7554/eLife.05005.
    • (2015) eLife , vol.4 , pp. e05005
    • Agarwal, V.1    Bell, G.W.2    Nam, J.-W.3    Bartel, D.P.4
  • 3
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders S., Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010, 11:R106. 10.1186/gb-2010-11-10-r106.
    • (2010) Genome Biol. , vol.11 , pp. R106
    • Anders, S.1    Huber, W.2
  • 6
    • 84864443057 scopus 로고    scopus 로고
    • 2: from miRNA and genes expression data integrative analysis to microRNA-transcription factor mixed regulatory circuits (2012 update)
    • 2: from miRNA and genes expression data integrative analysis to microRNA-transcription factor mixed regulatory circuits (2012 update). Nucleic Acids Res. 2012, 40:W13-W21. 10.1093/nar/gks460.
    • (2012) Nucleic Acids Res. , vol.40 , pp. W13-W21
    • Bisognin, A.1    Sales, G.2    Coppe, A.3    Bortoluzzi, S.4    Romualdi, C.5
  • 7
    • 84922418997 scopus 로고    scopus 로고
    • Endogenous miRNA and target concentrations determine susceptibility to potential ceRNA competition
    • Bosson A.D., Zamudio J.R., Sharp P.A. Endogenous miRNA and target concentrations determine susceptibility to potential ceRNA competition. Mol. Cell 2014, 56:347-359. 10.1016/j.molcel.2014.09.018.
    • (2014) Mol. Cell , vol.56 , pp. 347-359
    • Bosson, A.D.1    Zamudio, J.R.2    Sharp, P.A.3
  • 8
    • 0346727524 scopus 로고    scopus 로고
    • MicroRNAs modulate hematopoietic lineage differentiation
    • Chen C.-Z., Li L., Lodish H.F., Bartel D.P. MicroRNAs modulate hematopoietic lineage differentiation. Science 2004, 303:83-86. 10.1126/science.1091903.
    • (2004) Science , vol.303 , pp. 83-86
    • Chen, C.-Z.1    Li, L.2    Lodish, H.F.3    Bartel, D.P.4
  • 9
    • 67749132423 scopus 로고    scopus 로고
    • Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps
    • Chi S.W., Zang J.B., Mele A., Darnell R.B. Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 2009, 460:479-486. 10.1038/nature08170.
    • (2009) Nature , vol.460 , pp. 479-486
    • Chi, S.W.1    Zang, J.B.2    Mele, A.3    Darnell, R.B.4
  • 10
    • 84857955708 scopus 로고    scopus 로고
    • An alternative mode of microRNA target recognition
    • Chi S.W., Hannon G.J., Darnell R.B. An alternative mode of microRNA target recognition. Nat. Struct. Mol. Biol. 2012, 19:321-327. 10.1038/nsmb.2230.
    • (2012) Nat. Struct. Mol. Biol. , vol.19 , pp. 321-327
    • Chi, S.W.1    Hannon, G.J.2    Darnell, R.B.3
  • 14
    • 84902338279 scopus 로고    scopus 로고
    • MicroRNAs shape circadian hepatic gene expression on a transcriptome-wide scale
    • Du N.-H., Arpat A.B., De Matos M., Gatfield D. MicroRNAs shape circadian hepatic gene expression on a transcriptome-wide scale. eLife 2014, 3:e02510.
    • (2014) eLife , vol.3 , pp. e02510
    • Du, N.-H.1    Arpat, A.B.2    De Matos, M.3    Gatfield, D.4
  • 15
    • 78650747491 scopus 로고    scopus 로고
    • Discovery and characterization of chromatin states for systematic annotation of the human genome
    • Ernst J., Kellis M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat. Biotechnol. 2010, 28:817-825. 10.1038/nbt.1662.
    • (2010) Nat. Biotechnol. , vol.28 , pp. 817-825
    • Ernst, J.1    Kellis, M.2
  • 16
    • 33748191291 scopus 로고    scopus 로고
    • Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE
    • Foat B.C., Morozov A.V., Bussemaker H.J. Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE. Bioinformatics 2006, 22:e141-e149. 10.1093/bioinformatics/btl223.
    • (2006) Bioinformatics , vol.22 , pp. e141-e149
    • Foat, B.C.1    Morozov, A.V.2    Bussemaker, H.J.3
  • 17
    • 77956520986 scopus 로고    scopus 로고
    • CircuitsDB: a database of mixed microRNA/transcription factor feed-forward regulatory circuits in human and mouse
    • Friard O., Re A., Taverna D., De Bortoli M., Corá 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.
    • (2010) BMC Bioinformatics , vol.11 , pp. 435
    • Friard, O.1    Re, A.2    Taverna, D.3    De Bortoli, M.4    Corá, D.5
  • 18
    • 84946197772 scopus 로고    scopus 로고
    • Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation
    • Gaidatzis D., Burger L., Florescu M., Stadler M.B. Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation. Nat. Biotechnol. 2015, 33:722-729. 10.1038/nbt.3269.
    • (2015) Nat. Biotechnol. , vol.33 , pp. 722-729
    • Gaidatzis, D.1    Burger, L.2    Florescu, M.3    Stadler, M.B.4
  • 19
    • 80455154984 scopus 로고    scopus 로고
    • Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs
    • Garcia D.M., Baek D., Shin C., Bell G.W., Grimson A., Bartel D.P. Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat. Struct. Mol. Biol. 2011, 18:1139-1146. 10.1038/nsmb.2115.
    • (2011) Nat. Struct. Mol. Biol. , vol.18 , pp. 1139-1146
    • Garcia, D.M.1    Baek, D.2    Shin, C.3    Bell, G.W.4    Grimson, A.5    Bartel, D.P.6
  • 21
    • 84874419781 scopus 로고    scopus 로고
    • SAMNet: a network-based approach to integrate multi-dimensional high throughput datasets
    • Gosline S.J., Spencer S.J., Ursu O., Fraenkel E. SAMNet: a network-based approach to integrate multi-dimensional high throughput datasets. Integr. Biol. (Camb.) 2012, 4:1415-1427. 10.1039/c2ib20072d.
    • (2012) Integr. Biol. (Camb.) , vol.4 , pp. 1415-1427
    • Gosline, S.J.1    Spencer, S.J.2    Ursu, O.3    Fraenkel, E.4
  • 23
    • 77955644289 scopus 로고    scopus 로고
    • Mammalian microRNAs predominantly act to decrease target mRNA levels
    • Guo H., Ingolia N.T., Weissman J.S., Bartel D.P. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 2010, 466:835-840. 10.1038/nature09267.
    • (2010) Nature , vol.466 , pp. 835-840
    • Guo, H.1    Ingolia, N.T.2    Weissman, J.S.3    Bartel, D.P.4
  • 24
    • 84866086842 scopus 로고    scopus 로고
    • High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints
    • Guo Y., Mahony S., Gifford D.K. High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints. PLoS Comput. Biol. 2012, 8:e1002638. 10.1371/journal.pcbi.1002638.
    • (2012) PLoS Comput. Biol. , vol.8 , pp. e1002638
    • Guo, Y.1    Mahony, S.2    Gifford, D.K.3
  • 25
    • 84883805211 scopus 로고    scopus 로고
    • The role of miRNAs in regulating gene expression networks
    • Gurtan A.M., Sharp P.A. The role of miRNAs in regulating gene expression networks. J. Mol. Biol. 2013, 425:3582-3600. 10.1016/j.jmb.2013.03.007.
    • (2013) J. Mol. Biol. , vol.425 , pp. 3582-3600
    • Gurtan, A.M.1    Sharp, P.A.2
  • 28
    • 77954517267 scopus 로고    scopus 로고
    • MicroRNAs and gene regulatory networks: managing the impact of noise in biological systems
    • Herranz H., Cohen S.M. MicroRNAs and gene regulatory networks: managing the impact of noise in biological systems. Genes Dev. 2010, 24:1339-1344. 10.1101/gad.1937010.
    • (2010) Genes Dev. , vol.24 , pp. 1339-1344
    • Herranz, H.1    Cohen, S.M.2
  • 29
    • 67149115119 scopus 로고    scopus 로고
    • Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs
    • Khan A.A., Betel D., Miller M.L., Sander C., Leslie C.S., Marks D.S. Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat. Biotechnol. 2009, 27:549-555. 10.1038/nbt.1543.
    • (2009) Nat. Biotechnol. , vol.27 , pp. 549-555
    • Khan, A.A.1    Betel, D.2    Miller, M.L.3    Sander, C.4    Leslie, C.S.5    Marks, D.S.6
  • 30
    • 84855916545 scopus 로고    scopus 로고
    • Protein-RNA interactions: new genomic technologies and perspectives
    • König J., Zarnack K., Luscombe N.M., Ule J. Protein-RNA interactions: new genomic technologies and perspectives. Nat. Rev. Genet. 2012, 13:77-83. 10.1038/nrg3141.
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 77-83
    • König, J.1    Zarnack, K.2    Luscombe, N.M.3    Ule, J.4
  • 31
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead B., Salzberg S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 2012, 9:357-359. 10.1038/nmeth.1923.
    • (2012) Nat. Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 32
    • 34247565615 scopus 로고    scopus 로고
    • The tumor suppressor microRNA let-7 represses the HMGA2 oncogene
    • Lee Y.S., Dutta A. The tumor suppressor microRNA let-7 represses the HMGA2 oncogene. Genes Dev. 2007, 21:1025-1030. 10.1101/gad.1540407.
    • (2007) Genes Dev. , vol.21 , pp. 1025-1030
    • Lee, Y.S.1    Dutta, A.2
  • 34
    • 84924629414 scopus 로고    scopus 로고
    • Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
    • Love M.I., Huber W., Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014, 15:550. 10.1186/PREACCEPT-8897612761307401.
    • (2014) Genome Biol. , vol.15 , pp. 550
    • Love, M.I.1    Huber, W.2    Anders, S.3
  • 36
    • 79952113645 scopus 로고    scopus 로고
    • Sequence analysis of chromatin immunoprecipitation data for transcription factors
    • Macisaac K.D., Fraenkel E. Sequence analysis of chromatin immunoprecipitation data for transcription factors. Methods Mol. Biol. 2010, 674:179-193. 10.1007/978-1-60761-854-6_11.
    • (2010) Methods Mol. Biol. , vol.674 , pp. 179-193
    • Macisaac, K.D.1    Fraenkel, E.2
  • 37
    • 33947431322 scopus 로고    scopus 로고
    • Disrupting the pairing between let-7 and Hmga2 enhances oncogenic transformation
    • Mayr C., Hemann M.T., Bartel D.P. Disrupting the pairing between let-7 and Hmga2 enhances oncogenic transformation. Science 2007, 315:1576-1579. 10.1126/science.1137999.
    • (2007) Science , vol.315 , pp. 1576-1579
    • Mayr, C.1    Hemann, M.T.2    Bartel, D.P.3
  • 38
    • 84858379476 scopus 로고    scopus 로고
    • MicroRNAs in stress signaling and human disease
    • Mendell J.T., Olson E.N. MicroRNAs in stress signaling and human disease. Cell 2012, 148:1172-1187. 10.1016/j.cell.2012.02.005.
    • (2012) Cell , vol.148 , pp. 1172-1187
    • Mendell, J.T.1    Olson, E.N.2
  • 39
    • 80051755369 scopus 로고    scopus 로고
    • MIRTFnet: analysis of miRNA regulated transcription factors
    • Naeem H., Küffner R., Zimmer R. MIRTFnet: analysis of miRNA regulated transcription factors. PLoS ONE 2011, 6:e22519. 10.1371/journal.pone.0022519.
    • (2011) PLoS ONE , vol.6 , pp. e22519
    • Naeem, H.1    Küffner, R.2    Zimmer, R.3
  • 40
    • 84858446579 scopus 로고    scopus 로고
    • MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship
    • Pasquinelli A.E. MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship. Nat. Rev. Genet. 2012, 13:271-282. 10.1038/nrg3162.
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 271-282
    • Pasquinelli, A.E.1
  • 41
    • 79952266465 scopus 로고    scopus 로고
    • Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
    • Pique-Regi R., Degner J.F., Pai A.A., Gaffney D.J., Gilad Y., Pritchard J.K. Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res. 2011, 21:447-455. 10.1101/gr.112623.110.
    • (2011) Genome Res. , vol.21 , pp. 447-455
    • Pique-Regi, R.1    Degner, J.F.2    Pai, A.A.3    Gaffney, D.J.4    Gilad, Y.5    Pritchard, J.K.6
  • 42
    • 84884997420 scopus 로고    scopus 로고
    • MiR-145 functions as a tumor-suppressive RNA by targeting Sox9 and adducin 3 in human glioma cells
    • Rani S.B., Rathod S.S., Karthik S., Kaur N., Muzumdar D., Shiras A.S. MiR-145 functions as a tumor-suppressive RNA by targeting Sox9 and adducin 3 in human glioma cells. Neuro-oncol. 2013, 15:1302-1316. 10.1093/neuonc/not090.
    • (2013) Neuro-oncol. , vol.15 , pp. 1302-1316
    • Rani, S.B.1    Rathod, S.S.2    Karthik, S.3    Kaur, N.4    Muzumdar, D.5    Shiras, A.S.6
  • 46
    • 34547555796 scopus 로고    scopus 로고
    • Global and local architecture of the mammalian microRNA-transcription factor regulatory network
    • Shalgi R., Lieber D., Oren M., Pilpel Y. Global and local architecture of the mammalian microRNA-transcription factor regulatory network. PLoS Comput. Biol. 2007, 3:e131. 10.1371/journal.pcbi.0030131.
    • (2007) PLoS Comput. Biol. , vol.3 , pp. e131
    • Shalgi, R.1    Lieber, D.2    Oren, M.3    Pilpel, Y.4
  • 48
    • 77956276383 scopus 로고    scopus 로고
    • DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells
    • pdb.prot5384
    • Song L., Crawford G.E. DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. Cold Spring Harb. Protoc. 2010, 2010. pdb.prot5384. 10.1101/pdb.prot5384.
    • (2010) Cold Spring Harb. Protoc. , vol.2010
    • Song, L.1    Crawford, G.E.2
  • 49
    • 84936744064 scopus 로고    scopus 로고
    • Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions
    • Sugimoto Y., König J., Hussain S., Zupan B., Curk T., Frye M., Ule J. Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions. Genome Biol. 2012, 13:R67. 10.1186/gb-2012-13-8-r67.
    • (2012) Genome Biol. , vol.13 , pp. R67
    • Sugimoto, Y.1    König, J.2    Hussain, S.3    Zupan, B.4    Curk, T.5    Frye, M.6    Ule, J.7
  • 50
    • 54549108798 scopus 로고    scopus 로고
    • MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation
    • Tay Y., Zhang J., Thomson A.M., Lim B., Rigoutsos I. MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature 2008, 455:1124-1128. 10.1038/nature07299.
    • (2008) Nature , vol.455 , pp. 1124-1128
    • Tay, Y.1    Zhang, J.2    Thomson, A.M.3    Lim, B.4    Rigoutsos, I.5
  • 51
    • 34249819336 scopus 로고    scopus 로고
    • MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals
    • Tsang J., Zhu J., van Oudenaarden A. MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals. Mol. Cell 2007, 26:753-767. 10.1016/j.molcel.2007.05.018.
    • (2007) Mol. Cell , vol.26 , pp. 753-767
    • Tsang, J.1    Zhu, J.2    van Oudenaarden, A.3
  • 52
    • 70350672533 scopus 로고    scopus 로고
    • Combinatorial network of primary and secondary microRNA-driven regulatory mechanisms
    • Tu K., Yu H., Hua Y.-J., Li Y.-Y., Liu L., Xie L., Li Y.-X. Combinatorial network of primary and secondary microRNA-driven regulatory mechanisms. Nucleic Acids Res. 2009, 37:5969-5980. 10.1093/nar/gkp638.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 5969-5980
    • Tu, K.1    Yu, H.2    Hua, Y.-J.3    Li, Y.-Y.4    Liu, L.5    Xie, L.6    Li, Y.-X.7
  • 53
    • 79954993788 scopus 로고    scopus 로고
    • MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action
    • Wen J., Parker B.J., Jacobsen A., Krogh A. MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action. RNA 2011, 17:820-834. 10.1261/rna.2387911.
    • (2011) RNA , vol.17 , pp. 820-834
    • Wen, J.1    Parker, B.J.2    Jacobsen, A.3    Krogh, A.4
  • 54
    • 84888117735 scopus 로고    scopus 로고
    • MiRNA and mRNA cancer signatures determined by analysis of expression levels in large cohorts of patients
    • Zadran S., Remacle F., Levine R.D. miRNA and mRNA cancer signatures determined by analysis of expression levels in large cohorts of patients. Proc. Natl. Acad. Sci. 2013, 110:19160-19165. 10.1073/pnas.1316991110.
    • (2013) Proc. Natl. Acad. Sci. , vol.110 , pp. 19160-19165
    • Zadran, S.1    Remacle, F.2    Levine, R.D.3
  • 55
    • 79960230895 scopus 로고    scopus 로고
    • Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data
    • Zhang C., Darnell R.B. Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. Nat. Biotechnol. 2011, 29:607-614. 10.1038/nbt.1873.
    • (2011) Nat. Biotechnol. , vol.29 , pp. 607-614
    • Zhang, C.1    Darnell, R.B.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.