Jiang J, Jia P, Shen B, Zhao Z: Top associated SNPs in prostate cancer are significantly enriched in cis-expression quantitative trait loci and at transcription factor binding sites. Oncotarget. 2014, 5 (15): 6168-6177.
Article
PubMed Central
PubMed
Google Scholar
Chen J, Zhang D, Yan W, Yang D, Shen B: Translational bioinformatics for diagnostic and prognostic prediction of prostate cancer in the next-generation sequencing era. Biomed Res Int. 2013, 2013: 901578-
PubMed Central
PubMed
Google Scholar
Chen J, Wang Y, Shen B, Zhang D: Molecular signature of cancer at gene level or pathway level? Case studies of colorectal cancer and prostate cancer microarray data. Computational and mathematical methods in medicine. 2013, 2013: 909525-
PubMed Central
PubMed
Google Scholar
Wang Y, Chen J, Li Q, Wang H, Liu G, Jing Q, Shen B: Identifying novel prostate cancer associated pathways based on integrative microarray data analysis. Computational biology and chemistry. 2011, 35 (3): 151-158. 10.1016/j.compbiolchem.2011.04.003.
Article
CAS
PubMed
Google Scholar
Berger MF, Lawrence MS, Demichelis F, Drier Y, Cibulskis K, Sivachenko AY, Sboner A, Esgueva R, Pflueger D, Sougnez C, Onofrio R, Carter SL, Park K, Habegger L, Ambrogio L, Fennell T, Parkin M, Saksena G, Voet D, Ramos AH, Pugh TJ, Wilkinson J, Fisher S, Winckler W, Mahan S, Ardlie K, Baldwin J, Simons JW, Kitabayashi N, MacDonald TY, Kantoff PW, Chin L, Gabriel SB, Gerstein MB, Golub TR, Meyerson M, Tewari A, Lander ES, Getz G, Rubin MA, Garraway LA: The genomic complexity of primary human prostate cancer. Nature. 2011, 470 (7333): 214-220. 10.1038/nature09744.
Article
PubMed Central
CAS
PubMed
Google Scholar
Grasso CS, Wu YM, Robinson DR, Cao XH, Dhanasekaran SM, Khan AP, Quist MJ, Jing X, Lonigro RJ, Brenner JC, Asangani IA, Ateeq B, Chun SY, Siddiqui J, Sam L, Anstett M, Mehra R, Prensner JR, Palanisamy N, Ryslik GA, Vandin F, Raphael BJ, Kunju LP, Rhodes DR, Pienta KJ, Chinnaiyan AM, Tomlins SA: The mutational landscape of lethal castration-resistant prostate cancer. Nature. 2012, 487 (7406): 239-243. 10.1038/nature11125.
Article
PubMed Central
CAS
PubMed
Google Scholar
Garraway LA, Lander ES: Lessons from the cancer genome. Cell. 2013, 153 (1): 17-37. 10.1016/j.cell.2013.03.002.
Article
CAS
PubMed
Google Scholar
Consortium EP, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M: An integrated encyclopedia of DNA elements in the human genome. Nature. 2012, 489 (7414): 57-74. 10.1038/nature11247.
Article
Google Scholar
Guttman M, Rinn JL: Modular regulatory principles of large non-coding RNAs. Nature. 2012, 482 (7385): 339-346. 10.1038/nature10887.
Article
PubMed Central
CAS
PubMed
Google Scholar
Brunner AL, Beck AH, Edris B, Sweeney RT, Zhu SX, Li R, Montgomery K, Varma S, Gilks T, Guo X, Foley JW, Witten DM, Giacomini CP, Flynn RA, Pollack JR, Tibshirani R, Chang HY, van de Rijn M, West RB: Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers. Genome biology. 2012, 13 (8): R75-10.1186/gb-2012-13-8-r75.
Article
PubMed Central
PubMed
Google Scholar
Ponting CP, Oliver PL, Reik W: Evolution and functions of long noncoding RNAs. Cell. 2009, 136 (4): 629-641. 10.1016/j.cell.2009.02.006.
Article
CAS
PubMed
Google Scholar
Zhang W, Zang J, Jing X, Sun Z, Yan W, Yang D, Guo F, Shen B: Identification of candidate miRNA biomarkers from miRNA regulatory network with application to prostate cancer. J Transl Med. 2014, 12: 66-10.1186/1479-5876-12-66.
Article
PubMed Central
PubMed
Google Scholar
Li Y, Vongsangnak W, Chen L, Shen B: Integrative analysis reveals disease-associated genes and biomarkers for prostate cancer progression. BMC Med Genomics. 2014, 7 (Suppl 1): S3-10.1186/1755-8794-7-S1-S3.
Article
PubMed Central
PubMed
Google Scholar
Sequence Read Archive (SRA). [http://www.ncbi.nlm.nih.gov/sra]
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
Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Huminiecki L, Kasprzyk A, Lehvaslaiho H, Lijnzaad P, Melsopp C, Mongin E, Pettett R, Pocock M, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, Clamp M: The Ensembl genome database project. Nucleic acids research. 2002, 30 (1): 38-41. 10.1093/nar/30.1.38.
Article
PubMed Central
CAS
PubMed
Google Scholar
UCSC table browser. [http://genome.ucsc.edu/cgi-bin/hgTables?command=start]
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature protocols. 2012, 7 (3): 562-578. 10.1038/nprot.2012.016.
Article
PubMed Central
CAS
PubMed
Google Scholar
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B: Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature methods. 2008, 5 (7): 621-628. 10.1038/nmeth.1226.
Article
CAS
PubMed
Google Scholar
Zhao Z, Xu J, Chen J, Kim S, Reimers M, Bacanu SA, Yu H, Liu C, Sun J, Wang Q, Jia P, Xu F, Zhang Y, Kendler KS, Peng Z, Chen X: Transcriptome sequencing and genome-wide association analyses reveal lysosomal function and actin cytoskeleton remodeling in schizophrenia and bipolar disorder. Molecular psychiatry. 2014
Google Scholar
Langfelder P, Horvath S: WGCNA: an R package for weighted correlation network analysis. BMC bioinformatics. 2008, 16: 559-
Article
Google Scholar
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature genetics. 2000, 25 (1): 25-29. 10.1038/75556.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wang J, Duncan D, Shi Z, Zhang B: WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013. Nucleic acids research. 2013, 41 (Web Server): W77-83.
Article
PubMed Central
PubMed
Google Scholar
Tang Y, Yan W, Chen J, Luo C, Kaipia A, Shen B: Identification of novel microRNA regulatory pathways associated with heterogeneous prostate cancer. Bmc Syst Biol. 2013, 7 (Suppl 3): S6-10.1186/1752-0509-7-S3-S6.
Article
PubMed Central
PubMed
Google Scholar
Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL: Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes & development. 2011, 25 (18): 1915-1927. 10.1101/gad.17446611.
Article
CAS
Google Scholar
Zhang B, Horvath S: A general framework for weighted gene co-expression network analysis. Statistical applications in genetics and molecular biology. 2005, 4: Article17-
Article
PubMed
Google Scholar
Langfelder P, Horvath S: Eigengene networks for studying the relationships between co-expression modules. Bmc Syst Biol. 2007, 1:
Google Scholar
Verone AR, Duncan K, Godoy A, Yadav N, Bakin A, Koochekpour S, Jin JP, Heemers HV: Androgen-responsive serum response factor target genes regulate prostate cancer cell migration. Carcinogenesis. 2013, 34 (8): 1737-1746. 10.1093/carcin/bgt126.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sementchenko VI, Schweinfest CW, Papas TS, Watson DK: ETS2 function is required to maintain the transformed state of human prostate cancer cells. Oncogene. 1998, 17 (22): 2883-2888. 10.1038/sj.onc.1202220.
Article
CAS
PubMed
Google Scholar
Jiang J, Cui W, Vongsangnak W, Hu G, Shen B: Post genome-wide association studies functional characterization of prostate cancer risk loci. BMC Genomics. 2013, 14 (Suppl 8): S9-10.1186/1471-2164-14-S8-S9.
Article
PubMed Central
PubMed
Google Scholar
Briggs MR, Kadonaga JT, Bell SP, Tjian R: Purification and biochemical characterization of the promoter-specific transcription factor, Sp1. Science. 1986, 234 (4772): 47-52. 10.1126/science.3529394.
Article
CAS
PubMed
Google Scholar
Courey AJ, Tjian R: Analysis of Sp1 in vivo reveals multiple transcriptional domains, including a novel glutamine-rich activation motif. Cell. 1988, 55 (5): 887-898. 10.1016/0092-8674(88)90144-4.
Article
CAS
PubMed
Google Scholar
Soutoglou E, Viollet B, Vaxillaire M, Yaniv M, Pontoglio M, Talianidis I: Transcription factor-dependent regulation of CBP and P/CAF histone acetyltransferase activity. The EMBO journal. 2001, 20 (8): 1984-1992. 10.1093/emboj/20.8.1984.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kadam S, Emerson BM: Transcriptional specificity of human SWI/SNF BRG1 and BRM chromatin remodeling complexes. Molecular cell. 2003, 11 (2): 377-389. 10.1016/S1097-2765(03)00034-0.
Article
CAS
PubMed
Google Scholar
Williams LV, Veliceasa D, Vinokour E, Volpert OV: miR-200b Inhibits Prostate Cancer EMT, Growth and Metastasis. Plos One. 2013, 8 (12):
Qin WM, Shi Y, Zhao BT, Yao CG, Jin L, Ma JX, Jin YX: miR-24 Regulates Apoptosis by Targeting the Open Reading Frame (ORF) Region of FAF1 in Cancer Cells. Plos One. 2010, 5 (2):
Mao YQ, Chen H, Lin YW, Xu X, Hu ZH, Zhu Y, Wu J, Xu XL, Zheng XY, Xie LP: microRNA-330 inhibits cell motility by downregulating Sp1 in prostate cancer cells. Oncol Rep. 2013, 30 (1): 327-333.
CAS
PubMed
Google Scholar
Porkka KP, Ogg EL, Saramaki OR, Vessella RL, Pukkila H, Lahdesmaki H, van Weerden WM, Wolf M, Kallioniemi OP, Jenster G, Visakorpi T: The miR-15a-miR-16-1 Locus is Homozygously Deleted in a Subset of Prostate Cancers. Gene Chromosome Canc. 2011, 50 (7): 499-509. 10.1002/gcc.20873.
Article
CAS
Google Scholar
Dorer DE, Nettelbeck DM: Targeting cancer by transcriptional control in cancer gene therapy and viral oncolysis. Advanced drug delivery reviews. 2009, 61 (7-8): 554-571. 10.1016/j.addr.2009.03.013.
Article
CAS
PubMed
Google Scholar
Yi X, White DM, Aisner DL, Baur JA, Wright WE, Shay JW: An alternate splicing variant of the human telomerase catalytic subunit inhibits telomerase activity. Neoplasia. 2000, 2 (5): 433-440. 10.1038/sj.neo.7900113.
Article
PubMed Central
CAS
PubMed
Google Scholar
Stasiewicz D, Staroslawska E, Brzozowska A, Mocarska A, Losicki M, Szumilo J, Burdan F: [Epidemiology and risk factors of the prostate cancer]. Polski merkuriusz lekarski : organ Polskiego Towarzystwa Lekarskiego. 2012, 33 (195): 163-167.
Google Scholar
Chen M, Zhang JT: Membrane insertion, processing, and topology of cystic fibrosis transmembrane conductance regulator (CFTR) in microsomal membranes. Molecular membrane biology. 1996, 13 (1): 33-40. 10.3109/09687689609160572.
Article
CAS
PubMed
Google Scholar
Sankpal UT, Goodison S, Abdelrahim M, Basha R: Targeting Sp1 transcription factors in prostate cancer therapy. Medicinal chemistry. 2011, 7 (5): 518-525. 10.2174/157340611796799203.
Article
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, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD: 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