1,721,380 research outputs found
Genome wide survey of microRNA-Transcription Factor regulatory circuits in human
Full text linkIn this work, we describe a computational framework for the genome-wide identification and characterization of mixed transcriptional/post-transcriptional regulatory circuits in humans. We concentrated in particular on feed-forward loops (FFL), in which a master transcription factor regulates a microRNA, and together with it, a set of joint target protein coding genes. The circuits were assembled with a two step procedure. We first constructed separately the transcriptional and post-transcriptional components of the human regulatory network by looking for conserved over-represented motifs in human and mouse promoters, and 3'-UTRs. Then, we combined the two subnetworks looking for mixed feed-forward regulatory interactions, finding a total of 638 putative (merged) FFLs. In order to investigate their biological relevance, we filtered these circuits using three selection criteria: (I) GeneOntology enrichment among the joint targets of the FFL, (II) independent computational evidence for the regulatory interactions of the FFL, extracted from external databases, and (III) relevance of the FFL in cancer. Most of the selected FFLs seem to be involved in various aspects of organism development and differentiation. We finally discuss a few of the most interesting cases in detail
TOWARDS A CLASSIFICATION OF FUSION RULE ALGEBRAS IN RATIONAL CONFORMAL FIELD-THEORIES
No full textWe review the main topics concerning Fusion Rule Algebras (FRA) of Rational Conformal Field Theories. After an exposition of their general properties, we examine known results on the complete classification for low number of fields (less-than-or-equal-to 4). We then turn our attention to FRA's generated polynomially by one (real) fundamental field, for which a classification is known. Attempting to generalize this result, we describe some connections between FRA's and Graph Theory. The possibility to get new results on the subject following this "graph" approach is briefly discussed
ORTHOGONAL-POLYNOMIAL STRUCTURES AND FUSION ALGEBRAS OF RATIONAL CONFORMAL FIELD-THEORIES
No full textA large class of fusion algebras, isomorphic to rings of orlhogonal polynomials in one real variable, is studied. It includes all SU(2) WZW and all minimal model fusion algebras. All the algebras in this class having structure constants limited to 0 or I are classified. Two series consistent with both modular and duality constraints are found. Numerical searches for structure constants also larger than 1 seem to indicate that the whole classification is exhausted by the two aforementioned series and an additional one. Relations of these structures with the SU(2) group are discussed
Graph theory analysis of genomic problems: community analysis of fragile sites correlations and of pseudogenes alignments
No full textGraph theory offers the ideal framework to model biological systemic properties. Recently these methods were successfully applied in proteomics and in the study of metabolic networks. In this paper we want to show that these same tools are equally powerful also to address genomic problems, like alignment networks or the networks obtained by looking at suitable correlators of chromosomic features. We shall in particular address two examples. In the first example we shall study human common fragile sites (CFS), a class of “hyper-sensitive” segments of DNA. The interest in CFS is motivated by their largely debated role in cancerogenesis. In order to functionally characterize them we developed a novel genome-wide approach based on graph theory and Gene Ontology vocabulary. We obtain a few non-trivial results fitting with largely accepted knowledge and a more recently advanced proposal about the role of CFS in tumor cell biology. The second application is a preliminary work on a potential new type of transcriptional regulatory mechanism. It involves pseudogenes which are non-functional copies of genes. This mechanism should imply similarity between the upstream sequences of genes and pseudogenes. We constructed the upstream similarity network in the budding yeast S. Cerevisiae. Network properties suggest that pseudogenes-mediated regulation could be a common feature in eukaryotic organisms
Numerical determination of the operator-product-expansion coefficients in the 3D Ising model from off-critical correlators
Full text linkWe propose a general method for the numerical evaluation of operator product expansion coefficients in three dimensional conformal field theories based on the study of the conformal perturbation of two point functions in the vicinity of the critical point. We test our proposal in the three dimensional Ising model, looking at the magnetic perturbation of the (r)σ(0) (r)ε(0) and (r)ε(0) correlators from which we extract the values of C=1.07(3) and Cεεε=1.45(30). Our estimate for C agrees with those recently obtained using conformal bootstrap methods, while C, as far as we know, is new and could be used to further constrain conformal bootstrap analyses of the 3d Ising universality class
Conformal perturbation of off-critical correlators in the 3D Ising universality class
Full text linkThanks to the impressive progress of conformal bootstrap methods we have now very precise estimates of both scaling dimensions and operator product expansion coefficients for several 3D universality classes. We show how to use this information to obtain similarly precise estimates for off-critical correlators using conformal perturbation. We discuss in particular the σ(r)σ(0),(r)ε(0) and σ(r)ε(0) two-point functions in the high and low temperature regimes of the 3D Ising model and evaluate the leading and next to leading terms in the s=trΔt expansion, where t is the reduced temperature. Our results for σ(r)σ(0) agree both with Monte Carlo simulations and with a set of experimental estimates of the critical scattering function
The critical equation of state of the two-dimensional Ising model
No full textWe compute the 2n-point coupling constants in the high-temperature phase of the two-dimensional Ising model by using transfer-matrix techniques. This provides the first few terms of the expansion of the effective potential (Helmholtz free energy) and of the equation of state in terms of the renormalized magnetization. By means of a suitable parametric representation, we determine an analytic extension of these expansions, providing the equation of state in the whole critical region in the t, h plane
Improved lattice actions for SU(N) × SU(N) chiral models
No full textA multiparameter family of tree level improved actions for SU(N) × SU(N) 2-d chiral models is proposed and the ratios of the scales Λ are calculated. For N = 2 the mass gap is evaluated by a strong coupling expansion and used to select improved actions with larger scaling region. Moreover the non universal O(g2) corrections are shown to be not negligible even for improved actions. © 1983
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