CluGene: A Bioinformatics Framework for the Identification of Co-Localized, Co-Expressed and Co-Regulated Genes Aimed at the Investigation of Transcriptional Regulatory Networks from High-Throughput Expression Data
暂无分享,去创建一个
Nicola Senin | Andrea Crisanti | Tania Dottorini | A. Crisanti | N. Senin | Pietro Palladino | T. Dottorini | Pietro Palladino | Tania Persampieri | Roberta Spaccapelo | R. Spaccapelo | Tania Persampieri
[1] P. Michalak. Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes. , 2008, Genomics.
[2] Yuri Y. Shevelyov,et al. Large clusters of co-expressed genes in the Drosophila genome , 2002, Nature.
[3] J. Collado-Vides,et al. Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes , 2008, Proceedings of the National Academy of Sciences.
[4] H. Stein,et al. Down-regulation of BOB.1/OBF.1 and Oct2 in classical Hodgkin disease but not in lymphocyte predominant Hodgkin disease correlates with immunoglobulin transcription. , 2001, Blood.
[5] M. Busslinger,et al. The promoter of the CD19 gene is a target for the B-cell-specific transcription factor BSAP , 1992, Molecular and cellular biology.
[6] Louxin Zhang,et al. Genome-scale analysis of positional clustering of mouse testis-specific genes , 2005, BMC Genomics.
[7] Nicola Senin,et al. Gepoclu: a software tool for identifying and analyzing gene positional clusters in large-scale gene expression analysis , 2011, BMC Bioinformatics.
[8] H. Stein,et al. Hodgkin and reed-sternberg cells represent an expansion of a single clone originating from a germinal center B-cell with functional immunoglobulin gene rearrangements but defective immunoglobulin transcription. , 2000, Blood.
[9] Mathieu Raffinot,et al. Gene teams: a new formalization of gene clusters for comparative genomics , 2003, Comput. Biol. Chem..
[10] C. Lawrence,et al. Human-mouse genome comparisons to locate regulatory sites , 2000, Nature Genetics.
[11] G. Church,et al. A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression , 2000, Nature Genetics.
[12] J. A. Chan,et al. The B-cell transcription factors BSAP, Oct-2, and BOB.1 and the pan-B-cell markers CD20, CD22, and CD79a are useful in the differential diagnosis of classic Hodgkin lymphoma. , 2003, American journal of clinical pathology.
[13] S. Pileri,et al. Monoclonal antibodies PG-B6a and PG-B6p recognize, respectively, a highly conserved and a formol-resistant epitope on the human BCL-6 protein amino-terminal region. , 1996, The American journal of pathology.
[14] Hans-Peter Kriegel,et al. A Density-Based Algorithm for Discovering Clusters in Large Spatial Databases with Noise , 1996, KDD.
[15] Michael Ruogu Zhang,et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. , 1998, Molecular biology of the cell.
[16] H Stein,et al. A monoclonal antibody (MUM1p) detects expression of the MUM1/IRF4 protein in a subset of germinal center B cells, plasma cells, and activated T cells. , 2000, Blood.
[17] Jean YH Yang,et al. Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.
[18] X. Dai,et al. Nuclear colocalization of transcription factor target genes strengthens coregulation in yeast , 2011, Nucleic acids research.
[19] R. Siebert,et al. Mutation of an IKK phosphorylation site within the transactivation domain of REL in two patients with B-cell lymphoma enhances REL's in vitro transforming activity , 2007, Oncogene.
[20] Xin He,et al. Identifying Conserved Gene Clusters in the Presence of Homology Families , 2005, J. Comput. Biol..
[21] William Stafford Noble,et al. Assessing computational tools for the discovery of transcription factor binding sites , 2005, Nature Biotechnology.
[22] A. Sharpe,et al. The ikaros gene is required for the development of all lymphoid lineages , 1994, Cell.
[23] Nick Gilbert,et al. The role of chromatin structure in regulating the expression of clustered genes , 2005, Nature Reviews Genetics.
[24] Eugene V Koonin,et al. Evolution of genome architecture. , 2009, The international journal of biochemistry & cell biology.
[25] J. V. Moran,et al. Initial sequencing and analysis of the human genome. , 2001, Nature.
[26] C. Pál,et al. The evolutionary dynamics of eukaryotic gene order , 2004, Nature Reviews Genetics.
[27] E. J. Williams,et al. Coexpression of neighboring genes in the genome of Arabidopsis thaliana. , 2004, Genome research.
[28] S. Brunak,et al. SignalP 4.0: discriminating signal peptides from transmembrane regions , 2011, Nature Methods.
[29] D. W. Rogers,et al. A genome-wide analysis in Anopheles gambiae mosquitoes reveals 46 male accessory gland genes, possible modulators of female behavior , 2007, Proceedings of the National Academy of Sciences.
[30] D. Kalaitzidis,et al. The c-Rel transcription factor and B-cell proliferation: a deal with the devil , 2004, Oncogene.
[31] B. Maher. ENCODE: The human encyclopaedia , 2012, Nature.
[32] N. L. Johnson,et al. Multivariate Analysis , 1958, Nature.
[33] A. Strasser,et al. Mice lacking the c-rel proto-oncogene exhibit defects in lymphocyte proliferation, humoral immunity, and interleukin-2 expression. , 1995, Genes & development.
[34] Ramón Díaz-Uriarte,et al. IDconverter and IDClight: Conversion and annotation of gene and protein IDs , 2007, BMC Bioinformatics.
[35] G. Stormo. Consensus patterns in DNA. , 1990, Methods in enzymology.
[36] Wyeth W. Wasserman,et al. In silico identification of metazoan transcriptional regulatory regions , 2003, Naturwissenschaften.
[37] G. Lenz,et al. Defective octamer-dependent transcription is responsible for silenced immunoglobulin transcription in Reed-Sternberg cells. , 2001, Blood.
[38] T. Gilmore,et al. Histone acetyltransferase p300 is a coactivator for transcription factor REL and is C-terminally truncated in the human diffuse large B-cell lymphoma cell line RC-K8. , 2010, Cancer letters.
[39] Hans-Peter Kriegel,et al. OPTICS: ordering points to identify the clustering structure , 1999, SIGMOD '99.
[40] A. Crisanti,et al. Regulation of Anopheles gambiae male accessory gland genes influences postmating response in female , 2013, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.
[41] P. Bucher,et al. Searching for regulatory elements in human noncoding sequences. , 1997, Current opinion in structural biology.
[42] D. Botstein,et al. Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[43] L. Pham,et al. Constitutive NF-kappaB and NFAT activation in aggressive B-cell lymphomas synergistically activates the CD154 gene and maintains lymphoma cell survival. , 2005, Blood.
[44] G. Lenz,et al. Frequent expression of the B-cell-specific activator protein in Reed-Sternberg cells of classical Hodgkin's disease provides further evidence for its B-cell origin. , 1999, Blood.
[45] J. Lawrence,et al. Shared Strategies in Gene Organization among Prokaryotes and Eukaryotes , 2002, Cell.
[46] D. Pe’er,et al. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data , 2003, Nature Genetics.
[47] J. Delabie,et al. The transcription factor PU.1, necessary for B-cell development is expressed in lymphocyte predominance, but not classical Hodgkin's disease. , 2001, The American journal of pathology.
[48] E. Wagner,et al. Complete block of early B cell differentiation and altered patterning of the posterior midbrain in mice lacking Pax5 BSAP , 1994, Cell.
[49] P. Gaulard,et al. Small lymphocytic lymphoma, marginal zone B-cell lymphoma, and mantle cell lymphoma exhibit distinct gene-expression profiles allowing molecular diagnosis. , 2004, Blood.
[50] G. Church,et al. Identifying regulatory networks by combinatorial analysis of promoter elements , 2001, Nature Genetics.
[51] B. Koop,et al. Human and rodent DNA sequence comparisons: a mosaic model of genomic evolution. , 1995, Trends in genetics : TIG.
[52] V. Diehl,et al. Oct-2 and Bob-1 deficiency in Hodgkin and Reed Sternberg cells. , 2001, Cancer research.
[53] A. Osbourn,et al. Operons , 2009, Cellular and Molecular Life Sciences.
[54] Juan F. García,et al. Analysis of Octamer-Binding Transcription Factors Oct2 and Oct1 and their coactivator BOB.1/OBF.1 in Lymphomas , 2002, Modern Pathology.
[55] Terence P Speed,et al. Lineage-specific expansion of proteins exported to erythrocytes in malaria parasites , 2006, Genome Biology.
[56] Gerald M Rubin,et al. Evidence for large domains of similarly expressed genes in the Drosophila genome , 2002, Journal of biology.
[57] Gary D. Stormo,et al. DNA binding sites: representation and discovery , 2000, Bioinform..
[58] T. Golub,et al. Molecular profiling of diffuse large B-cell lymphoma identifies robust subtypes including one characterized by host inflammatory response. , 2004, Blood.
[59] A. Krogh,et al. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.
[60] M. Vasef,et al. Expression profiling of transcription factors Pax-5, Oct-1, Oct-2, BOB.1, and PU.1 in Hodgkin's and non-Hodgkin's lymphomas: a comparative study using high throughput tissue microarrays , 2006, Modern Pathology.
[61] W. Miller,et al. Long human-mouse sequence alignments reveal novel regulatory elements: a reason to sequence the mouse genome. , 1997, Genome research.
[62] M. Fraga,et al. Differential Diagnosis of Classic Hodgkin Lymphoma , 2010, International journal of surgical pathology.
[63] Hamada,et al. Expression of the PAX5/BSAP transcription factor in haematological tumour cells and further molecular characterization of the t(9;14)(p13;q32) translocation in B‐cell non‐Hodgkin's lymphoma , 1998, British journal of haematology.
[64] Laurie J. Heyer,et al. Exploring expression data: identification and analysis of coexpressed genes. , 1999, Genome research.
[65] Xin He,et al. Detecting gene clusters under evolutionary constraint in a large number of genomes , 2009, Bioinform..
[66] International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome , 2001, Nature.
[67] Travis Harrison,et al. A Host-Targeting Signal in Virulence Proteins Reveals a Secretome in Malarial Infection , 2004, Science.
[68] David J. Arenillas,et al. oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes , 2005, Nucleic acids research.
[69] Peter A. C. 't Hoen,et al. CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes , 2008, BMC Bioinformatics.
[70] Sergei Vassilvitskii,et al. k-means++: the advantages of careful seeding , 2007, SODA '07.
[71] H. Stein,et al. Loss of PU.1 expression is associated with defective immunoglobulin transcription in Hodgkin and Reed-Sternberg cells of classical Hodgkin disease. , 2002, Blood.
[72] Hanah Margalit,et al. Chromosomal organization is shaped by the transcription regulatory network. , 2005, Trends in genetics : TIG.
[73] P. Papathanos,et al. Transcription Regulation of Sex-Biased Genes during Ontogeny in the Malaria Vector Anopheles gambiae , 2011, PloS one.
[74] K. Al-Kuraya,et al. The biological and clinical impact of inhibition of NF‐κB‐initiated apoptosis in diffuse large B cell lymphoma (DLBCL) , 2011, The Journal of pathology.
[75] Christopher J. Tonkin,et al. Dissecting Apicoplast Targeting in the Malaria Parasite Plasmodium falciparum , 2003, Science.