Characteristic Topological Features of Promoter Capture Hi-C Interaction Networks

Current Hi-C technologies for chromosome conformation capture allow to understand a broad spectrum of functional interactions between genome elements. Although significant progress has been made into analysis of Hi-C data to identify the biologically significant features, many questions still remain open. In this paper we describe analysis methods of Hi-C (specifically PCHi-C) interaction networks that are strictly focused on topological properties of these networks. The main questions we are trying to answer are: (1) can topological properties of interaction networks for different cell types alone be sufficient to distinguish between these types, and what the most important of such propert…

Disconnected Graph Layout and the Polyomino Packing Approach

Conference name: GD: International Symposium on Graph Drawing 9th International Symposium Date of Conference: 23–26 September 2001 We review existing algorithms and present a new approach for layout of disconnected graphs. The new approach is based on polyomino representation of components as opposed to rectangles. The parameters of our algorithm and their influence on the drawings produced as well as a variation of the algorithm for multiple pages are discussed. We also analyze our algorithm both theoretically and experimentally and compare it with the existing ones. The new approach produces much more compact and uniform drawings than previous methods. © Springer-Verlag Berlin Heidelberg …

Graph-based network analysis of transcriptional regulation pattern divergence in duplicated yeast gene pairs

The genome and interactome of Saccharomyces cerevisiae have been characterized extensively over the course of the past few decades. However, despite many insights gained over the years, both functional studies and evolutionary analyses continue to reveal many complexities and confounding factors in the construction of reliable transcriptional regulatory network models. We present here a graph-based technique for comparing transcriptional regulatory networks based on network motif similarity for gene pairs. We construct interaction graphs for duplicated transcription factor pairs traceable to the ancestral whole-genome duplication as well as other paralogues in Saccharomyces cerevisiae. We c…

How to draw combinatorial map? From graphs and edges to corner rotations and permutations

In this article we consider combinatorial maps approach to graphs on surfaces, and how between them can be establish terminological uniformity in favor of combinatorial maps in way rotations are set as base structural elements and all other notions are derived from them. We set this approach as rotational prevalence principle. We consider simplest way how to draw combinatorial map, and ask how this approach in form of rotational prevalence could be used in graphs drawing practice and wider in algorithms. We try to show in this paper that the use of corners in the place of halfedges is much more natural than that of halfedges. Formally there is no difference between both choices, but corner …

Layout algorithms of graph-like diagrams for GRADE windows graphic editors

We propose a set of layout operations ensuring flexible and convenient interactive editing of communication diagrams and nested entity-relationship models having textual labels on connections. The set includes several procedures for incremental diagram layout. Tools for fully automatic layout and for direct manual painting of graphic primitives are also integrated in a single system. In this way we have filled to some extent the gap between both extremal levels of editing.

Graph-based characterisations of cell types and functionally related modules in promoter capture Hi-C Data

Topological structure analysis of chromatin interaction networks.

Abstract Background Current Hi-C technologies for chromosome conformation capture allow to understand a broad spectrum of functional interactions between genome elements. Although significant progress has been made into analysis of Hi-C data to identify biologically significant features, many questions still remain open, in particular regarding potential biological significance of various topological features that are characteristic for chromatin interaction networks. Results It has been previously observed that promoter capture Hi-C (PCHi-C) interaction networks tend to separate easily into well-defined connected components that can be related to certain biological functionality, however, …

Network motif-based analysis of regulatory patterns in paralogous gene pairs

Current high-throughput experimental techniques make it feasible to infer gene regulatory interactions at the whole-genome level with reasonably good accuracy. Such experimentally inferred regulatory networks have become available for a number of simpler model organisms such as S. cerevisiae, and others. The availability of such networks provides an opportunity to compare gene regulatory processes at the whole genome level, and in particular, to assess similarity of regulatory interactions for homologous gene pairs either from the same or from different species. We present here a new technique for analyzing the regulatory interaction neighborhoods of paralogous gene pairs. Our central focu…

Intelligent system for electrical heating control based on optical precipitation sensor

Abstract The paper presents testing results of the SCADA system IntelHeat introduced at the Latvian Railways for automated heating control of railway points during winters with the purpose of electricity saving by optimized real-time assignment of heating levels. The system is based on innovative optical sensors of precipitation detecting rain and snow particles using diffuse and specular reflection channels. The results of trial exploitation demonstrated the ability of the IntelHeat system to manage points heating flexibly in accordance with changes of weather conditions and correspondence with archived meteorological data.