Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data
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Frank Emmert-Streib | Ricardo de Matos Simoes | Sabine Dalleau | Kate E. Williamson | F. Emmert-Streib | K. Williamson | R. D. Simoes | S. Dalleau
[1] R. Albert. Scale-free networks in cell biology , 2005, Journal of Cell Science.
[2] Ralf Herwig,et al. ConsensusPathDB: toward a more complete picture of cell biology , 2010, Nucleic Acids Res..
[3] Frank Emmert-Streib,et al. Influence of Statistical Estimators of Mutual Information and Data Heterogeneity on the Inference of Gene Regulatory Networks , 2011, PloS one.
[4] Y. Benjamini,et al. Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .
[5] Franziska Michor,et al. Combination of a Novel Gene Expression Signature with a Clinical Nomogram Improves the Prediction of Survival in High-Risk Bladder Cancer , 2012, Clinical Cancer Research.
[6] J. Falck,et al. Cytochrome P450 ω-hydroxylase promotes angiogenesis and metastasis by upregulation of VEGF and MMP-9 in non-small cell lung cancer , 2011, Cancer Chemotherapy and Pharmacology.
[7] Gianluca Bontempi,et al. minet: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information , 2008, BMC Bioinformatics.
[8] Sumio Sugano,et al. Identification of DMC1, a novel gene in the TOC region on 17q25.1 that shows loss of expression in multiple human cancers , 2001, Journal of Human Genetics.
[9] H. Ozen. Bladder cancer. , 1998, Current opinion in oncology.
[10] Matthias Dehmer,et al. B-cell lymphoma gene regulatory networks: biological consistency among inference methods , 2013, Front. Genet..
[11] Joaquim Bellmunt,et al. Identification of prefoldin amplification (1q23.3-q24.1) in bladder cancer using comparative genomic hybridization (CGH) arrays of urinary DNA , 2013, Journal of Translational Medicine.
[12] Insuk Lee,et al. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality , 2007, BMC Bioinformatics.
[13] Kathy Pritchard-Jones,et al. Frequent Long-Range Epigenetic Silencing of Protocadherin Gene Clusters on Chromosome 5q31 in Wilms' Tumor , 2009, PLoS genetics.
[14] Frank Emmert-Streib,et al. Inferring the conservative causal core of gene regulatory networks , 2010, BMC Systems Biology.
[15] Frank Emmert-Streib,et al. Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma , 2012, BMC Systems Biology.
[16] D. Hanahan,et al. Hallmarks of Cancer: The Next Generation , 2011, Cell.
[17] Ying-Li Lin,et al. Clinical significance of protocadherin-8 (PCDH8) promoter methylation in bladder cancer , 2013, The Journal of international medical research.
[18] K. Polyak,et al. Tumor heterogeneity: causes and consequences. , 2010, Biochimica et biophysica acta.
[19] Kevin Kontos,et al. Information-Theoretic Inference of Large Transcriptional Regulatory Networks , 2007, EURASIP J. Bioinform. Syst. Biol..
[20] David P Wood. Re: Expression Signature of E2F1 and its Associated Genes Predict Superficial to Invasive Progression of Bladder Tumors. , 2011, The Journal of urology.
[21] T. Hubbard,et al. A census of human cancer genes , 2004, Nature Reviews Cancer.
[22] Edsger W. Dijkstra,et al. A note on two problems in connexion with graphs , 1959, Numerische Mathematik.
[23] Gos Micklem,et al. Supporting Online Material Materials and Methods Figs. S1 to S50 Tables S1 to S18 References Identification of Functional Elements and Regulatory Circuits by Drosophila Modencode , 2022 .
[24] Young Nyun Park,et al. Tudor domain-containing protein 4 as a potential cancer/testis antigen in liver cancer. , 2011, The Tohoku journal of experimental medicine.
[25] T. Speed,et al. Summaries of Affymetrix GeneChip probe level data. , 2003, Nucleic acids research.
[26] Damian Szklarczyk,et al. STRING v9.1: protein-protein interaction networks, with increased coverage and integration , 2012, Nucleic Acids Res..
[27] Colin N. Dewey,et al. RNA-Seq gene expression estimation with read mapping uncertainty , 2009, Bioinform..
[28] Chris Wiggins,et al. ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context , 2004, BMC Bioinformatics.
[29] Christie S. Chang,et al. The BioGRID interaction database: 2013 update , 2012, Nucleic Acids Res..
[30] B. Oliver,et al. Microarrays, deep sequencing and the true measure of the transcriptome , 2011, BMC Biology.
[31] Garrett M. Dancik,et al. Transcriptional signatures of Ral GTPase are associated with aggressive clinicopathologic characteristics in human cancer. , 2012, Cancer research.
[32] V. Velculescu,et al. Mutational analysis of gene families in human cancer. , 2005, Current opinion in genetics & development.
[33] T. Speed,et al. GOstat: find statistically overrepresented Gene Ontologies within a group of genes. , 2004, Bioinformatics.
[34] Robert Gentleman,et al. matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements , 2004, Bioinform..
[35] Yusuke Nakamura,et al. Identification of Myc-associated protein with JmjC domain as a novel therapeutic target oncogene for lung cancer , 2007, Molecular Cancer Therapeutics.
[36] Torben F. Ørntoft,et al. Emmprin and Survivin Predict Response and Survival following Cisplatin-Containing Chemotherapy in Patients with Advanced Bladder Cancer , 2007, Clinical Cancer Research.
[37] G. Altay,et al. Structural influence of gene networks on their inference: analysis of C3NET. , 2011 .
[38] N. Seki,et al. LY6K is a novel molecular target in bladder cancer on basis of integrate genome-wide profiling , 2010, British Journal of Cancer.
[39] Gabriele Ausiello,et al. MINT: the Molecular INTeraction database , 2006, Nucleic Acids Res..
[40] Y L Lin,et al. Clinical and Prognostic Significance of Protocadherin-10 (PCDH10) Promoter Methylation in Bladder Cancer , 2012, The Journal of international medical research.
[41] Gianluca Bontempi,et al. On the Impact of Entropy Estimation on Transcriptional Regulatory Network Inference Based on Mutual Information , 2008, EURASIP J. Bioinform. Syst. Biol..
[42] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[43] Gabriele Sales,et al. graphite - a Bioconductor package to convert pathway topology to gene network , 2012, BMC Bioinformatics.
[44] Adam A. Margolin,et al. Reverse engineering of regulatory networks in human B cells , 2005, Nature Genetics.
[45] G. Parmigiani,et al. The Consensus Coding Sequences of Human Breast and Colorectal Cancers , 2006, Science.
[46] Frank Emmert-Streib,et al. Bagging Statistical Network Inference from Large-Scale Gene Expression Data , 2012, PloS one.
[47] Edwin Wang,et al. Signaling network assessment of mutations and copy number variations predict breast cancer subtype-specific drug targets. , 2013, Cell reports.
[48] M. Gerstein,et al. Relating whole-genome expression data with protein-protein interactions. , 2002, Genome research.
[49] V. Karantza,et al. Keratins in health and cancer: more than mere epithelial cell markers , 2011, Oncogene.
[50] Derek Y. Chiang,et al. MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery , 2010, Nucleic acids research.
[51] Steve Horvath,et al. WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.
[52] Yun Yen,et al. Human RIF1 encodes an anti-apoptotic factor required for DNA repair. , 2009, Carcinogenesis.
[53] Zhong Liu,et al. Long non-coding RNA expression profile in human gastric cancer and its clinical significances , 2013, Journal of Translational Medicine.
[54] B. Snel,et al. The yeast coexpression network has a small‐world, scale‐free architecture and can be explained by a simple model , 2004, EMBO reports.
[55] A. E. EATON. Did Flowers Exist during the Carboniferous Epoch? , 1879, Nature.
[56] Li Li,et al. Mapping and Genome Sequence Analysis of Chromosome 5 Regions Involved in Bladder Cancer Progression , 2001, Laboratory Investigation.
[57] Ivan Molineris,et al. A new computational approach to analyze human protein complexes and predict novel protein interactions , 2007, Genome Biology.
[58] B. Challacombe,et al. Recent advances in diagnosis and treatment of transitional cell carcinoma of the bladder. , 2013, International journal of surgery.
[59] Zhong Liu,et al. Clinical significance of the low expression of FER1L4 in gastric cancer patients , 2014, Tumor Biology.
[60] Gábor Csárdi,et al. The igraph software package for complex network research , 2006 .
[61] C. Daub,et al. BMC Systems Biology , 2007 .
[62] R. Alba. A graph‐theoretic definition of a sociometric clique† , 1973 .
[63] Matthias Dehmer,et al. Interfacing cellular networks of S. cerevisiae and E. coli: Connecting dynamic and genetic information , 2013, BMC Genomics.
[64] Terje Espevik,et al. The GOLD domain-containing protein TMED7 inhibits TLR4 signalling from the endosome upon LPS stimulation , 2012, Nature Communications.
[65] Carsten Janke,et al. Tubulin glycylases are required for primary cilia, control of cell proliferation and tumor development in colon , 2014, The EMBO journal.
[66] Andreas Holzinger,et al. Functional and genetic analysis of the colon cancer network , 2014, BMC Bioinformatics.
[67] Albert,et al. Emergence of scaling in random networks , 1999, Science.
[68] Matthias Dehmer,et al. The gene regulatory network for breast cancer: integrated regulatory landscape of cancer hallmarks , 2014, Front. Genet..
[69] D. Kwiatkowski,et al. Targeting molecular aberrations in urothelial carcinoma: are we almost there? , 2013, American Society of Clinical Oncology educational book. American Society of Clinical Oncology. Annual Meeting.
[70] Jan Albrecht,et al. Increased expression of a glutamine transporter SNAT3 is a marker of malignant gliomas , 2004, Neuroreport.
[71] Jens-Peter Volkmer,et al. Anti-CD47 antibody–mediated phagocytosis of cancer by macrophages primes an effective antitumor T-cell response , 2013, Proceedings of the National Academy of Sciences.
[72] Xiang-Sun Zhang,et al. NOA: a novel Network Ontology Analysis method , 2011, Nucleic acids research.
[73] Martin Vingron,et al. IntAct: an open source molecular interaction database , 2004, Nucleic Acids Res..
[74] Melanie I. Stefan,et al. Molecules for memory: modelling CaMKII , 2007, BMC Systems Biology.
[75] Mogens Kruhøffer,et al. Gene Expression in the Urinary Bladder , 2004, Cancer Research.
[76] I S Kohane,et al. Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. , 1999, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.
[77] Hanno Steen,et al. Development of human protein reference database as an initial platform for approaching systems biology in humans. , 2003, Genome research.
[78] J. Collins,et al. Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles , 2007, PLoS biology.
[79] Karim Chamie,et al. Recurrence of high‐risk bladder cancer: A population‐based analysis , 2013, Cancer.
[80] G. Yousef,et al. Clinical utility of kallikrein-related peptidases (KLK) in urogenital malignancies , 2013, Thrombosis and Haemostasis.
[81] Eun-Jung Kim,et al. Predictive value of progression-related gene classifier in primary non-muscle invasive bladder cancer , 2010, Molecular Cancer.
[82] A Semjonow,et al. Cytogenetic analysis of multifocal bladder cancer supports a monoclonal origin and intraepithelial spread of tumor cells. , 2001, Cancer research.
[83] The Cancer Genome Atlas Research Network. Comprehensive molecular characterization of urothelial bladder carcinoma , 2014, Nature.
[84] C. Pál,et al. The evolutionary dynamics of eukaryotic gene order , 2004, Nature Reviews Genetics.
[85] In-Sun Chu,et al. Expression signature of E2F1 and its associated genes predict superficial to invasive progression of bladder tumors. , 2010, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.
[86] Steven J. M. Jones,et al. Comprehensive molecular characterization of urothelial bladder carcinoma , 2014, Nature.
[87] P. Geurts,et al. Inferring Regulatory Networks from Expression Data Using Tree-Based Methods , 2010, PloS one.
[88] Mark Newman,et al. Networks: An Introduction , 2010 .