SWIM: a computational tool to unveiling crucial nodes in complex biological networks
暂无分享,去创建一个
Giulio Pavesi | Lorenzo Farina | Paola Paci | Giulia Fiscon | Aymone Gurtner | Teresa Colombo | G. Pavesi | T. Colombo | L. Farina | P. Paci | A. Gurtner | G. Fiscon | Aymone Gurtner
[1] Graziano Pesole,et al. Cscan: finding common regulators of a set of genes by using a collection of genome-wide ChIP-seq datasets , 2012, Nucleic Acids Res..
[2] N. Matsubara,et al. Frequent mutation of the E2F-4 cell cycle gene in primary human gastrointestinal tumors. , 1997, Cancer research.
[3] Chao Cheng,et al. E2F4 regulatory program predicts patient survival prognosis in breast cancer , 2014, Breast Cancer Research.
[4] Carme Camps,et al. hsa-miR-210 Is Induced by Hypoxia and Is an Independent Prognostic Factor in Breast Cancer , 2008, Clinical Cancer Research.
[5] M E J Newman,et al. Community structure in social and biological networks , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[6] Mads Thomassen,et al. Gene expression meta-analysis identifies metastatic pathways and transcription factors in breast cancer , 2008, BMC Cancer.
[7] Mason A. Porter,et al. Communities in Networks , 2009, ArXiv.
[8] P. Neven,et al. Expression of the BRCA1-interacting protein Brip1/BACH1/FANCJ is driven by E2F and correlates with human breast cancer malignancy , 2008, Oncogene.
[9] D. Hanahan,et al. Hallmarks of Cancer: The Next Generation , 2011, Cell.
[10] R. Sharan,et al. Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells. , 2003, Genome research.
[11] Y. Benjamini,et al. Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .
[12] Yang Liu,et al. Loss-of-function mutations of an inhibitory upstream ORF in the human hairless transcript cause Marie Unna hereditary hypotrichosis , 2009, Nature Genetics.
[13] S. Maity,et al. Stable Expression of a Dominant Negative Mutant of CCAAT Binding Factor/NF-Y in Mouse Fibroblast Cells Resulting in Retardation of Cell Growth and Inhibition of Transcription of Various Cellular Genes* , 2000, The Journal of Biological Chemistry.
[14] H. Hirai,et al. Expression levels of NF-Y target genes changed by CDKN1B correlate with clinical prognosis in multiple cancers. , 2009, Genomics.
[15] Roger Guimerà,et al. Cartography of complex networks: modules and universal roles , 2005, Journal of statistical mechanics.
[16] A. Gartel,et al. FOX(M1) News—It Is Cancer , 2013, Molecular Cancer Therapeutics.
[17] Graziano Pesole,et al. Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes , 2009, Nucleic Acids Res..
[18] Alan M. Frieze,et al. Random graphs , 2006, SODA '06.
[19] Albert-László Barabási,et al. Statistical mechanics of complex networks , 2001, ArXiv.
[20] M. T. McCabe,et al. EZH2 as a potential target in cancer therapy. , 2014, Epigenomics.
[21] Roland L. Dunbrack,et al. Aurora A kinase (AURKA) in normal and pathological cell division , 2012, Cellular and Molecular Life Sciences.
[22] William Stafford Noble,et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.
[23] M. C. Palumbo,et al. Integrated Network Analysis Identifies Fight-Club Nodes as a Class of Hubs Encompassing Key Putative Switch Genes That Induce Major Transcriptome Reprogramming during Grapevine Development[W][OPEN] , 2014, Plant Cell.
[24] Albert-László Barabási,et al. Error and attack tolerance of complex networks , 2000, Nature.
[25] Giulia Piaggio,et al. NF-Y Dependent Epigenetic Modifications Discriminate between Proliferating and Postmitotic Tissue , 2008, PloS one.
[26] Marina Meila,et al. The uniqueness of a good optimum for K-means , 2006, ICML.
[27] M. Padi,et al. The CHR promoter element controls cell cycle-dependent gene transcription and binds the DREAM and MMB complexes , 2011, Nucleic acids research.
[28] Chiara Vecchi,et al. Dynamic Recruitment of NF-Y and Histone Acetyltransferases on Cell-cycle Promoters* , 2003, Journal of Biological Chemistry.
[29] Lorenzo Farina,et al. Computational analysis identifies a sponge interaction network between long non-coding RNAs and messenger RNAs in human breast cancer , 2014, BMC Systems Biology.
[30] C. Perou,et al. In Vitro and In Vivo Analysis of B-Myb in Basal-Like Breast Cancer , 2008, Oncogene.
[31] F. Martelli,et al. Transcription factor NF-Y induces apoptosis in cells expressing wild-type p53 through E2F1 upregulation and p53 activation. , 2010, Cancer research.
[32] Tzu-chin Wu,et al. p53 dysfunction by xeroderma pigmentosum group C defects enhance lung adenocarcinoma metastasis via increased MMP1 expression. , 2010, Cancer Research.
[33] R. Mantovani,et al. NF-Y and the transcriptional activation of CCAAT promoters , 2012, Critical reviews in biochemistry and molecular biology.
[34] David G Johnson,et al. E2F4 and E2F1 Have Similar Proliferative Properties but Different Apoptotic and Oncogenic Properties In Vivo , 2000, Molecular and Cellular Biology.
[35] Vishwanath R. Iyer,et al. Wide-ranging functions of E2F4 in transcriptional activation and repression revealed by genome-wide analysis , 2011, Nucleic acids research.
[36] A. Almasan,et al. E2F4 Function in G2 Maintaining G2-arrest to Prevent Mitotic Entry with Damaged DNA , 2007, Cell cycle.
[37] Brock A. Humphries,et al. The microRNA-200 family: small molecules with novel roles in cancer development, progression and therapy , 2015, Oncotarget.
[38] J. Deng,et al. The B subunit of the CCAAT box binding transcription factor complex (CBF/NF-Y) is essential for early mouse development and cell proliferation. , 2003, Cancer research.
[39] Ying Zhang,et al. OCT4 increases BIRC5 and CCND1 expression and promotes cancer progression in hepatocellular carcinoma , 2013, BMC Cancer.
[40] A. Jemal,et al. Global cancer statistics , 2011, CA: a cancer journal for clinicians.
[41] Santo Fortunato,et al. Community detection in graphs , 2009, ArXiv.
[42] J. Neely,et al. A practical guide to understanding Kaplan-Meier curves , 2010, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.
[43] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[44] Manuele Bicego,et al. The Grapevine Expression Atlas Reveals a Deep Transcriptome Shift Driving the Entire Plant into a Maturation Program[W][OA] , 2012, Plant Cell.
[45] Daniele Merico,et al. A balance between NF-Y and p53 governs the pro- and anti-apoptotic transcriptional response , 2008, Nucleic acids research.
[46] M. Coumar,et al. Treat cancers by targeting survivin: just a dream or future reality? , 2013, Cancer treatment reviews.
[47] C. Glass,et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.
[48] Wenbin Chen,et al. Identifying miRNA/mRNA negative regulation pairs in colorectal cancer , 2015, Scientific Reports.
[49] A. Jemal,et al. Global Cancer Statistics , 2011 .
[50] R. Guimerà,et al. Functional cartography of complex metabolic networks , 2005, Nature.
[51] Elisa Ficarra,et al. MicroRNA–mRNA interactions underlying colorectal cancer molecular subtypes , 2015, Nature Communications.
[52] Minoru Kanehisa,et al. KEGG as a reference resource for gene and protein annotation , 2015, Nucleic Acids Res..
[53] Sonja J. Prohaska,et al. The CHR site: definition and genome-wide identification of a cell cycle transcriptional element , 2014, Nucleic acids research.
[54] G. Macino,et al. PVT1: A Rising Star among Oncogenic Long Noncoding RNAs , 2015, BioMed research international.
[55] Kyung S. Lee,et al. Recent Advances and New Strategies in Targeting Plk1 for Anticancer Therapy. , 2015, Trends in pharmacological sciences.
[56] H. Yoshida,et al. Nuclear transcription factor Y and its roles in cellular processes related to human disease. , 2013, American journal of cancer research.
[57] J. Shendure,et al. Discovering functional transcription-factor combinations in the human cell cycle. , 2005, Genome research.
[58] G. Pavesi,et al. A high definition look at the NF-Y regulome reveals genome-wide associations with selected transcription factors , 2016, Nucleic acids research.
[59] A. Jemal,et al. Global cancer statistics, 2012 , 2015, CA: a cancer journal for clinicians.
[60] Joshua M. Stuart,et al. The Cancer Genome Atlas Pan-Cancer analysis project , 2013, Nature Genetics.
[61] Xiaoyi Gao,et al. Human population structure detection via multilocus genotype clustering , 2007, BMC Genetics.
[62] G. Collins. The next generation. , 2006, Scientific American.
[63] C. Sotiriou,et al. Global MicroRNA Expression Profiling Identifies MiR-210 Associated with Tumor Proliferation, Invasion and Poor Clinical Outcome in Breast Cancer , 2011, PloS one.
[64] B. Fahrenkrog,et al. Negative regulation of apoptosis in yeast. , 2008, Biochimica et biophysica acta.
[65] Paulo J. G. Lisboa,et al. Finding reproducible cluster partitions for the k-means algorithm , 2013, BMC Bioinformatics.
[66] Charlotte M. Deane,et al. Revisiting Date and Party Hubs: Novel Approaches to Role Assignment in Protein Interaction Networks , 2009, PLoS Comput. Biol..
[67] Lan V. Zhang,et al. Evidence for dynamically organized modularity in the yeast protein–protein interaction network , 2004, Nature.
[68] C. Croce,et al. MicroRNA signatures in human cancers , 2006, Nature Reviews Cancer.
[69] Qiong Shao,et al. MicroRNA miR-21 overexpression in human breast cancer is associated with advanced clinical stage, lymph node metastasis and patient poor prognosis. , 2008, RNA.
[70] Pablo Tamayo,et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[71] Likang Zheng,et al. MicroRNA-203 Regulates Growth and Metastasis of Breast Cancer , 2015, Cellular Physiology and Biochemistry.
[72] K. Khanna,et al. Targeting homologous recombination, new pre-clinical and clinical therapeutic combinations inhibiting RAD51. , 2015, Cancer treatment reviews.
[73] Xing Li,et al. High expression of microRNA-183/182/96 cluster as a prognostic biomarker for breast cancer , 2016, Scientific Reports.
[74] Graziano Pesole,et al. PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments , 2013, Nucleic Acids Res..
[75] C. Croce,et al. MicroRNA gene expression deregulation in human breast cancer. , 2005, Cancer research.
[76] Massimo Marchiori,et al. Error and attacktolerance of complex network s , 2004 .