scholarly journals MACPET: model-based analysis for ChIA-PET

Biostatistics ◽  
2019 ◽  
Vol 21 (3) ◽  
pp. 625-639
Author(s):  
Ioannis Vardaxis ◽  
Finn Drabløs ◽  
Morten B Rye ◽  
Bo Henry Lindqvist
Keyword(s):  
Binding Sites ◽  
Present Model ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Model Based Clustering ◽  
Model Based ◽  
Motif Occurrence ◽  
Calling Algorithm ◽  
Genomic Regions ◽  
Model Based Analysis

Summary We present model-based analysis for ChIA-PET (MACPET), which analyzes paired-end read sequences provided by ChIA-PET for finding binding sites of a protein of interest. MACPET uses information from both tags of each PET and searches for binding sites in a two-dimensional space, while taking into account different noise levels in different genomic regions. MACPET shows favorable results compared with MACS in terms of motif occurrence and spatial resolution. Furthermore, significant binding sites discovered by MACPET are involved in a higher number of significant three-dimensional interactions than those discovered by MACS. MACPET is freely available on Bioconductor. ChIA-PET; MACPET; Model-based clustering; Paired-end tags; Peak-calling algorithm.

scholarly journals MACPET: Model-based Analysis for ChIA-PET

2018 ◽  
Author(s):  
Ioannis Vardaxis ◽  
Finn Drabløs ◽  
Morten B. Rye ◽  
Bo Henry Lindqvist
Keyword(s):  
Binding Sites ◽  
Present Model ◽  
Dimensional Space ◽  
Two Dimensional ◽  
Noise Levels ◽  
Model Based ◽  
False Discovery ◽  
Motif Occurrence ◽  
Genomic Regions ◽  
Model Based Analysis

AbstractWe present Model-based Analysis for ChIA-PET (MACPET) which analyzes paired-end read sequences provided by ChIA-PET for finding binding sites of a protein of interest. MACPET uses information from both tags of each PET and searches for binding sites in a two-dimensional space, while taking into account different noise levels in different genomic regions. MACPET shows favorable results compared to MACS in terms of motif occurrence, spatial resolution and false discovery rate. Significant binding sites discovered by MACPET are involved in a higher number of significant 3D interactions than those discovered by MACS. MACPET is freely available on Bioconductor.

scholarly journals A Three-Phase Fundamental Diagram from Three-Dimensional Traffic Data

Axioms ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 17
Author(s):  
Maria Laura Delle Delle Monache ◽  
Karen Chi ◽  
Yong Chen ◽  
Paola Goatin ◽  
Ke Han ◽  
...  
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Time Estimation ◽  
Travel Time Estimation ◽  
Traffic Data ◽  
Fundamental Diagram ◽  
Model Based Clustering ◽  
Three Phase ◽  
Characterization Of Solutions ◽  
Two Phases

This paper uses empirical traffic data collected from three locations in Europe and the US to reveal a three-phase fundamental diagram with two phases located in the uncongested regime. Model-based clustering, hypothesis testing and regression analyses are applied to the speed–flow–occupancy relationship represented in the three-dimensional space to rigorously validate the three phases and identify their gaps. The finding is consistent across the aforementioned different geographical locations. Accordingly, we propose a three-phase macroscopic traffic flow model and a characterization of solutions to the Riemann problems. This work identifies critical structures in the fundamental diagram that are typically ignored in first- and higher-order models and could significantly impact travel time estimation on highways.

Design and Marker-Based Validation of a Biplane Fluoroscopy System for Studying the Foot and Ankle

2012 ◽  
Author(s):  
Joseph M. Iaquinto ◽  
Richard Tsai ◽  
Michael J. Fassbind ◽  
David R. Haynor ◽  
Bruce J. Sangeorzan ◽  
...  
Keyword(s):  
Precise Measurement ◽  
Three Dimensional ◽  
The Body ◽  
Initial Evaluation ◽  
Foot And Ankle ◽  
Research Groups ◽  
The Past ◽  
Model Based ◽  
Biplane Fluoroscopy ◽  
Model Based Analysis

The ability to accurately measure three dimensional (3D) bone kinematics is key to understanding the motion of the joints of the body, and how such motion is altered by injury, disease, and treatment. Precise measurement of such kinematics is technically challenging. Biplane fluoroscopy is ideally suited to measure bone motion. Such systems have been developed in the past for both radiographic stereo-photogrammetric analysis (RSA) [1] and the more challenging model-based analysis [2]. Research groups have studied the knee [3,4], shoulder [5] and ankle [6] motion with similar techniques. The work presented here is an initial evaluation of the performance of our system, i.e., a validation that this in-house system can detect magnitudes of motion on-par with other existing systems.

Research on Combinational Reasoning of Directional Relations Based on Double Projections Model in Three-Dimensional Space

2011 ◽  
Vol 186 ◽  
pp. 61-65
Author(s):  
Yong Shan Liu ◽  
Wei Jie Gu
Keyword(s):  
Matrix Model ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Model Based ◽  
Computational Performance ◽  
Minimum Bounding Rectangle ◽  
Directional Relations ◽  
Three Dimensional Space

The xoy and xoz planes are divided into nine areas in three-dimensional space respectively by the MBR (Minimum Bounding Rectangle), which are produced by the reference objects’ projection to their planes. The intersecting situations between the projection of target objects and the two of reference objects are expressed by two 3×3 matrices. Then, a directional relations matrix model based on double projections is put forward. A combinational reasoning method is proposed by using the computational performance of matrices based on this model. Moreover, a combinational reasoning experiment is given and the result matches the reality.

scholarly journals Miswired enhancer logic drives translocation positive rhabdomyosarcoma

2019 ◽  
Author(s):  
Berkley E. Gryder ◽  
Marco Wachtel ◽  
Kenneth Chang ◽  
Osama El Demerdash ◽  
Nicholas G. Aboreden ◽  
...  
Keyword(s):  
Muscle Development ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Logic Gates ◽  
Physical Interaction ◽  
Rna Seq ◽  
Super Enhancer ◽  
Infinite Loop ◽  
Genomic Regions ◽  
Three Dimensional Space

AbstractCore regularity transcription factors (CR TFs) define cell identity and lineage through an exquisitely precise and logical order during embryogenesis and development. These CR TFs regulate one another in three-dimensional space via distal enhancers that serve as logic gates embedded in their TF recognition sequences. Aberrant chromatin organization resulting in miswired circuitry of enhancer logic is a newly recognized feature in many cancers. Here, we report that PAX3-FOXO1 expression is driven by a translocated FOXO1 distal super enhancer (SE). Using 4C-seq, a technique detecting all genomic regions that interact with the translocated FOXO1 SE, we demonstrate its physical interaction with the PAX3 promotor only in the presence of the oncogenic translocation. Furthermore, RNA-seq and ChIP-seq in tumors bearing rare PAX translocations implicate enhancer miswiring is a pervasive feature across all FP-RMS tumors. HiChIP of enhancer mark H3K27ac showed extended connectivity between the distal FOXO1 SE and additional intra-domain enhancers and the PAX3 promoter. We show by CRISPR-paired-ChIP-Rx that PAX3-FOXO1 transcription is diminished when this network of enhancers is selectively ablated. Therefore, our data reveal a mechanism of a translocated hijacked enhancer which disrupts the normal CR TF logic during skeletal muscle development (PAX3 to MYOD to MYOG), replacing it with an infinite loop logic that locks rhabdomyosarcoma cells in an undifferentiated proliferating stage.

scholarly journals Representación gráfica de las funciones complejas con el Mathematica

2018 ◽  
pp. 52-56
Keyword(s):  
Complex Variable ◽  
Dimensional Space ◽  
Complex Function ◽  
Three Dimensional ◽  
Graphical Display ◽  
Model Based ◽  
Complex Functions ◽  
Complex Valued ◽  
Three Dimensional Space

Representación gráfica de las funciones complejas con el Mathematica Graphical display of complex functions with Mathematica Ricardo Velezmoro y Robert Ipanaqué Universidad Nacional de Piura, Urb. Miraflores s/n, Castilla, Piura, Perú. DOI: https://doi.org/10.33017/RevECIPeru2015.0008/ Resumen La representación gráfica de las funciones de valor complejo, de una variable compleja, es un tema de mucho interés dado que la gráfica de una función de este tipo tendría que ser dibujada en un espacio tetra dimensional. Este artículo presenta una propuesta para representar tales gráficas mediante el uso de un modelo basado en una submersión, del espacio tetra dimensional en el espacio tridimensional; para luego, con ayuda del Mathematica llegar a obtener una representación de las mencionadas gráficas en una pantalla 2D. Adicionalmente, se implementarán algunos comandos en el Mathematica, los mismos que permitirán realizar las representaciones de variados e interesantes ejemplos. Descriptores: función compleja, visualización, submersión Abstract The graphical display of complex-valued functions of a complex variable is a subject of much interest since the graph of such a function would have to be drawn in a four-dimensional space. This article presents a proposal to display such graphs using a model based on a submersion, from four-dimensional space to three-dimensional space; then, with the help of Mathematica arrive at a representation of the graphs mentioned in a 2D screen. Additionally, some commands are implemented in Mathematica, the same that will make representations varied and interesting examples. Keywords: complex function, visualization, submersion

scholarly journals The zinc finger protein CLAMP promotes long-range chromatin interactions that mediate dosage compensation of the Drosophila male X-chromosome

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
William Jordan ◽  
Erica Larschan
Keyword(s):  
Long Range ◽  
Zinc Finger ◽  
X Chromosome ◽  
Dosage Compensation ◽  
Binding Sites ◽  
Zinc Finger Protein ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Active Chromatin ◽  
Finger Protein

Abstract Background Drosophila dosage compensation is an important model system for defining how active chromatin domains are formed. The male-specific lethal dosage compensation complex (MSLc) increases transcript levels of genes along the length of the single male X-chromosome to equalize with that expressed from the two female X-chromosomes. The strongest binding sites for MSLc cluster together in three-dimensional space largely independent of MSLc because clustering occurs in both sexes. CLAMP, a non-sex specific, ubiquitous zinc finger protein, binds synergistically with MSLc to enrich the occupancy of both factors on the male X-chromosome. Results Here, we demonstrate that CLAMP promotes the observed three-dimensional clustering of MSLc binding sites. Moreover, the X-enriched CLAMP protein more strongly promotes longer-range three-dimensional interactions on the X-chromosome than autosomes. Genome-wide, CLAMP promotes three-dimensional interactions between active chromatin regions together with other insulator proteins. Conclusion Overall, we define how long-range interactions which are modulated by a locally enriched ubiquitous transcription factor promote hyper-activation of the X-chromosome to mediate dosage compensation.

scholarly journals Estimated cut-off values for pemphigus severity classification according to pemphigus disease area index (PDAI), autoimmune bullous skin disorder intensity score (ABSIS), and anti-desmoglein 1 autoantibodies

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Farnam Mohebi ◽  
Soheil Tavakolpour ◽  
Amir Teimourpour ◽  
Roja Toosi ◽  
Hamidreza Mahmoudi ◽  
...  
Keyword(s):  
Skin Disorder ◽  
Scoring Systems ◽  
Physician Global Assessment ◽  
Disease Area ◽  
Area Index ◽  
Model Based Clustering ◽  
Cut Point ◽  
Model Based ◽  
Intensity Score ◽  
Model Based Analysis

Abstract Background Pemphigus is a potentially fatal disease if left untreated. Valid scoring systems and defined cut-off values for classification of patients would help with better management through specified pharmaceutical and non-pharmaceutical treatments. Methods In this study, pemphigus patients who were receiving immunosuppressive treatments and had recent disease relapse were recruited for examination of pemphigus disease area index(PDAI), autoimmune bullous skin disorder intensity score (ABSIS), physician global assessment (PGA), autoimmune bullous disease quality of life (ABQoL), anti-desmoglein 1 (anti-Dsg1), and anti-Dsg3 autoantibody titers from December-2017 to February-2018. Cut-off values were estimated using model-based clustering classification and the 25th and 75th percentiles approach, performed separately for the exclusive cutaneous, exclusive mucosal, and mucocutaneous groups. Results In the 109 included patients, the 25th and 75th percentiles cut-offs were 6.2 and 27 for PDAI score, and 4 and 29.5 for ABSIS score. The model-based analysis resulted in two groups (cut-point:15) for PDAI score, and three groups (cut-points:6.4 and 31.5) for ABSIS score. The groups were significantly different for the PDAI, ABSIS, PGA, and ABQoL values. Based on anti-Dsg1 autoantibody values, the model-based analysis cut-point was 128 and the 25th and 75th percentiles cut-offs were 98 and 182. Anti-Dsg3 autoantibody values did not differentiate between pemphigus severity classes. Conclusions Estimated cut-off values based on the anti-Dsg1 level, PDAI, and ABSIS scoring systems could be used to classify patients into different severity grades for better management and prognosis.

scholarly journals Computer methods of analysis of chromosome contacts in the cell nucleus based on sequencing technology data

2017 ◽  
Vol 63 (5) ◽  
pp. 418-422 ◽  
Author(s):  
Y.L. Orlov ◽  
O. Thierry ◽  
A.G. Bogomolov ◽  
A.V. Tsukanov ◽  
E.V. Kulakova ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Gene Transcription ◽  
Cell Nucleus ◽  
Binding Sites ◽  
Dimensional Space ◽  
Genome Structure ◽  
Three Dimensional ◽  
Gene Location ◽  
Interphase Cell ◽  
Eukaryotic Genes

The study spatial chromosome structure and chromosome folding in the interphase cell nucleus is an important challenge of world science. Detection of eukaryotic genome regions that physically interact with each other could be done by modern sequencing technologies. A basic method of chromosome folding by total sequencing of contacting DNA fragments is HI-C. Long-range chromosomal interactions play an important role in gene transcription and regulation. The study of chromosome interactions, 3D (three-dimensional) genome structure and its effect on gene transcription allows revealing fundamental biological processes from a viewpoint of structural regulation and are important for cancer research. The technique of chromatin immunoprecipitation and subsequent sequencing (ChIP-seq) make possible to determine binding sites of transcription factors that regulate expression of eukaryotic genes; genome transcription factors binding maps have been. The ChIA-PET technology allows exploring not only target protein binding sites, but also pairs of such sites on proximally located and interacting with each other chromosomes co-located in three-dimensional space of the cell nucleus. Here we discuss the principles of the construction of genomic maps and matrices of chromosome contacts according to ChIA-PET and Hi-C data that capture the chromosome conformation and overview existing software for 3D genome analysis including in house programs of gene location analysis in topological domains.

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