scholarly journals Hierarchical chromatin organization detected by TADpole

2020 ◽  
Vol 48 (7) ◽  
pp. e39-e39
Author(s):  
Paula Soler-Vila ◽  
Pol Cuscó ◽  
Irene Farabella ◽  
Marco Di Stefano ◽  
Marc A Marti-Renom
Keyword(s):  
Rapid Development ◽  
Region Of Interest ◽  
Principal Component ◽  
Genomic Region ◽  
Genetically Engineered ◽  
Bioinformatics Analyses ◽  
Chromosome Conformation ◽  
Data Resolution ◽  
Architectural Proteins ◽  
Interaction Matrices

Abstract The rapid development of Chromosome Conformation Capture (3C-based techniques), as well as imaging together with bioinformatics analyses, has been fundamental for unveiling that chromosomes are organized into the so-called topologically associating domains or TADs. While TADs appear as nested patterns in the 3C-based interaction matrices, the vast majority of available TAD callers are based on the hypothesis that TADs are individual and unrelated chromatin structures. Here we introduce TADpole, a computational tool designed to identify and analyze the entire hierarchy of TADs in intra-chromosomal interaction matrices. TADpole combines principal component analysis and constrained hierarchical clustering to provide a set of significant hierarchical chromatin levels in a genomic region of interest. TADpole is robust to data resolution, normalization strategy and sequencing depth. Domain borders defined by TADpole are enriched in main architectural proteins (CTCF and cohesin complex subunits) and in the histone mark H3K4me3, while their domain bodies, depending on their activation-state, are enriched in either H3K36me3 or H3K27me3, highlighting that TADpole is able to distinguish functional TAD units. Additionally, we demonstrate that TADpole's hierarchical annotation, together with the new DiffT score, allows for detecting significant topological differences on Capture Hi-C maps between wild-type and genetically engineered mouse.

scholarly journals Hierarchical chromatin organization detected by TADpole

2019 ◽  
Author(s):  
Paula Soler-Vila ◽  
Pol Cuscó Pons ◽  
Irene Farabella ◽  
Marco Di Stefano ◽  
Marc A. Marti-Renom
Keyword(s):  
Rapid Development ◽  
Super Resolution ◽  
Region Of Interest ◽  
Principal Component ◽  
Genomic Region ◽  
Mouse Strains ◽  
Bioinformatics Analyses ◽  
Chromosome Conformation ◽  
Resolution Imaging ◽  
Interaction Matrices

ABSTRACTThe rapid development of chromosome conformation capture (3C-based) techniques as well as super-resolution imaging together with bioinformatics analyses has been fundamental for unveiling that chromosomes are organized into the so-called topologically associating domains or TADs. While these TADs appear as nested patterns in the 3C-based interaction matrices, the vast majority of available computational methods are based on the hypothesis that TADs are individual and unrelated chromatin structures. Here we introduce TADpole, a computational tool designed to identify and analyze the entire hierarchy of TADs in intra-chromosomal interaction matrices. TADpole combines principal component analysis and constrained hierarchical clustering to provide an unsupervised set of significant partitions in a genomic region of interest. TADpole identification of domains is robust to the data resolution, normalization strategy, and sequencing depth. TADpole domain borders are enriched in CTCF and cohesin binding proteins, while the domains are enriched in either H3K36me3 or H3k27me3 histone marks. We show TADpole usefulness by applying it to capture Hi-C experiments in wild-type and mutant mouse strains to pinpoint statistically significant differences in their topological structure.

scholarly journals 3D reconstruction of genomic regions from sparse interaction data

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Julen Mendieta-Esteban ◽  
Marco Di Stefano ◽  
David Castillo ◽  
Irene Farabella ◽  
Marc A Marti-Renom
Keyword(s):  
3D Models ◽  
Genomic Region ◽  
Gene Promoters ◽  
Chromosome Conformation ◽  
The Matrix ◽  
Chromatin Structural ◽  
A Cell ◽  
Similar Accuracy ◽  
Genomic Regions ◽  
Interaction Matrices

Abstract Chromosome conformation capture (3C) technologies measure the interaction frequency between pairs of chromatin regions within the nucleus in a cell or a population of cells. Some of these 3C technologies retrieve interactions involving non-contiguous sets of loci, resulting in sparse interaction matrices. One of such 3C technologies is Promoter Capture Hi-C (pcHi-C) that is tailored to probe only interactions involving gene promoters. As such, pcHi-C provides sparse interaction matrices that are suitable to characterize short- and long-range enhancer–promoter interactions. Here, we introduce a new method to reconstruct the chromatin structural (3D) organization from sparse 3C-based datasets such as pcHi-C. Our method allows for data normalization, detection of significant interactions and reconstruction of the full 3D organization of the genomic region despite of the data sparseness. Specifically, it builds, with as low as the 2–3% of the data from the matrix, reliable 3D models of similar accuracy of those based on dense interaction matrices. Furthermore, the method is sensitive enough to detect cell-type-specific 3D organizational features such as the formation of different networks of active gene communities.

scholarly journals 3D reconstruction of genomic regions from sparse interaction data

2020 ◽  
Author(s):  
Julen Mendieta-Esteban ◽  
Marco Di Stefano ◽  
David Castillo ◽  
Irene Farabella ◽  
Marc A Marti-Renom
Keyword(s):  
Genomic Region ◽  
Gene Promoters ◽  
Chromosome Conformation ◽  
Data Sparseness ◽  
The Matrix ◽  
Chromatin Structural ◽  
A Cell ◽  
Cell Type Specific ◽  
Genomic Regions ◽  
Interaction Matrices

AbstractChromosome Conformation Capture (3C) technologies measure the interaction frequency between pairs of chromatin regions within the nucleus in a cell or a population of cells. Some of these 3C technologies retrieve interactions involving non-contiguous sets of loci, resulting in sparse interaction matrices. One of such 3C technologies is Promoter Capture Hi-C (pcHi-C) that is tailored to probe only interactions involving gene promoters. As such, pcHi-C provides sparse interaction matrices that are suitable to characterise short- and long-range enhancer-promoter interactions. Here, we introduce a new method to reconstruct the chromatin structural (3D) organisation from sparse 3C-based datasets such as pcHi-C. Our method allows for data normalisation, detection of significant interactions, and reconstruction of the full 3D organisation of the genomic region despite of the data sparseness. Specifically, it produces reliable reconstructions, in line with the ones obtained from dense interaction matrices, with as low as the 2-3% of the data from the matrix. Furthermore, the method is sensitive enough to detect cell-type-specific 3D organisational features such as the formation of different networks of active gene communities.

scholarly journals Information Spillover Effects of Real Estate Markets: Evidence from Ten Metropolitan Cities in China

2021 ◽  
Vol 14 (6) ◽  
pp. 244
Author(s):  
Junjie Li ◽  
Li Zheng ◽  
Chunlu Liu ◽  
Zhifeng Shen
Keyword(s):  
Real Estate ◽  
Rapid Development ◽  
House Price ◽  
Principal Component ◽  
Spillover Effects ◽  
Real Estate Markets ◽  
The Real ◽  
The Real Estate ◽  
Information Interaction ◽  
Information Spillover

With the rapid development of information communication technology and the Internet, information spillover between cities in real estate markets is becoming more frequent. The influence of information spillover in real estate markets is becoming more and more prominent. However, the current research of information spillover between cities is still relatively insufficient. In view of this research gap, this paper builds a research framework on the information conduction effect in the real estate markets of 10 Chinese cities by using Baidu search data, text mining and principal component analysis and analyzes the information interaction and dynamic influence of the real estate markets in each city by using the vector autoregressive model empirically. The results show that the information interaction among the real estate markets in each city has a network pattern and there is a significant two-way information spillover effect in most cities. When the “information distance” becomes closer, the information interaction between the markets of the cities becomes closer and it is easier for cities to influence each other. The results help to explain the information spillover mechanism behind the house price spillover and to improve the ability to predict and analyze the information spillover process in real estate markets.

scholarly journals Maximal Power Tests for Detecting Defects in Meiotic Recombination

Genetics ◽  
2002 ◽  
Vol 161 (3) ◽  
pp. 1333-1337
Author(s):  
Thomas I Milac ◽  
Frederick R Adler ◽  
Gerald R Smith
Keyword(s):  
Optimal Design ◽  
Design Of Experiments ◽  
Meiotic Recombination ◽  
Region Of Interest ◽  
Genetic Distances ◽  
Genomic Region ◽  
Maximal Power ◽  
Optimal Design Of Experiments ◽  
Crossover Interference ◽  
Single Interval

Abstract We have determined the marker separations (genetic distances) that maximize the probability, or power, of detecting meiotic recombination deficiency when only a limited number of meiotic progeny can be assayed. We find that the optimal marker separation is as large as 30–100 cM in many cases. Provided the appropriate marker separation is used, small reductions in recombination potential (as little as 50%) can be detected by assaying a single interval in as few as 100 progeny. If recombination is uniformly altered across the genomic region of interest, the same sensitivity can be obtained by assaying multiple independent intervals in correspondingly fewer progeny. A reduction or abolition of crossover interference, with or without a reduction of recombination proficiency, can be detected with similar sensitivity. We present a set of graphs that display the optimal marker separation and the number of meiotic progeny that must be assayed to detect a given recombination deficiency in the presence of various levels of crossover interference. These results will aid the optimal design of experiments to detect meiotic recombination deficiency in any organism.

scholarly journals Forensic analysis on printer inks via chemometrics

2021 ◽  
Vol 1192 (1) ◽  
pp. 012029
Author(s):  
L H Mohd Zawawi ◽  
N F Mohamed Azmin ◽  
M F Abd. Wahab ◽  
S I Ibrahim ◽  
M Y Mohd Yunus
Keyword(s):  
Principal Component Analysis ◽  
Digital Media ◽  
Graphical Representation ◽  
Rapid Development ◽  
Principal Component ◽  
Component Analysis ◽  
Forensic Analysis ◽  
Criminal Cases ◽  
Trial Court ◽  
Wide Range

Abstract Printer inks are becoming necessary for utilization for wide range of purposes by society in current times with rapid development in technology and digital media area. Thus, forgery and counterfeiting becoming easier for the criminals. It is dangerous as some criminals will misused the technology by mean of addition and adulteration of parts of text or numbers on document as the inks and document can be made as an evidence in the trial court. Thus, the characterization and differentiation of the printed inks in the suspected documents (civil or criminal cases) may provide important information about the authenticity of the printer inks. The focus of this study to differentiate the chemical component of three different types of sample inks by incorporation of FTIR spectrophotometer with principal component analysis. The unique features of the ink samples were unmasked from the score plots of the principal component analysis. Thus, the graphical representation provided by the FTIR spectra with principal component analysis enabled the discrimination certain chemical in the printer inks.

scholarly journals Environmental and Ecological Risk Assessment of Trace Metal Contamination in Mangrove Ecosystems: A Case from Zhangjiangkou Mangrove National Nature Reserve, China

2016 ◽  
Vol 2016 ◽  
pp. 1-14 ◽  
Author(s):  
Jun Wang ◽  
Huihong Du ◽  
Ye Xu ◽  
Kai Chen ◽  
Junhua Liang ◽  
...  
Keyword(s):  
Risk Assessment ◽  
Trace Metals ◽  
Ecological Risk ◽  
Ecological Risk Assessment ◽  
Nature Reserve ◽  
Anthropogenic Activities ◽  
Rapid Development ◽  
Agricultural Waste ◽  
Principal Component ◽  
National Nature Reserve

Zhangjiangkou Mangrove National Nature Reserve is a subtropical wetland ecosystem in southeast coast of China, which is of dense population and rapid development. The concentrations, sources, and pollution assessment of trace metals (Cu, Cd, Pb, Cr, Zn, As, and Hg) in surface sediment from 29 sites and the biota specimen were investigated for better ecological risk assessment and environmental management. The ranges of trace metals in mg/kg sediment were as follows: Cu (10.79–26.66), Cd (0.03–0.19), Pb (36.71–59.86), Cr (9.67–134.51), Zn (119.69–157.84), As (15.65–31.60), and Hg (0.00–0.08). The sequences of the bioaccumulation of studied metals are Zn > Cu > As > Cr > Pb > Cd > Hg with few exceptions. Cluster analysis and principal component analysis revealed that the trace metals in the studied area mainly derived from anthropogenic activities, such as industrial effluents, agricultural waste, and domestic sewage. Pollution load index and geoaccumulation index were calculated for trace metals in surface sediments, which indicated unpolluted status in general except Pb, Cr, and As.

Image Texture Based Hybrid Diagnostic Tool for Kidney Disease Classification

2018 ◽  
Vol 8 (9) ◽  
pp. 1899-1908
Author(s):  
P. Sreelatha ◽  
M. Ezhilarasi
Keyword(s):  
Diagnostic Tool ◽  
Classification Accuracy ◽  
Wavelet Coefficient ◽  
Region Of Interest ◽  
Principal Component ◽  
Disease Classification ◽  
Image Texture ◽  
Support Vector ◽  
Adaptive Wavelet ◽  
Medical Diagnostic

The identification of chronic medical conditions and its associated mortality has led to the emergence of less invasive methods for medical diagnostic imaging. This work proposes a Computer Aided Diagnostic tool useful in automatic classification of kidney images as normal, simple cysts, kidney stones and the less investigated complex cystic renal cell carcinoma. The first part of the work investigates an effective despeckling algorithm with a proposed adaptive wavelet based denoising technique. Encouraging increased PSNR values ranging from 15 dB to 24 dB were obtained. Second part of work suggests a set of wavelet coefficient based feature set which showed a classification accuracy of 92.2%, better by 20.3% to 0.8% against existing methods. The final part of the work to develop a complete tool for kidney image classification combines the proposed wavelet based features with three existing statistical based feature sets yielded a classification accuracy of 96.9%. The suggested features were extracted from the region of interest from an image set. A reduced feature set of 18 from the original size of 163 was obtained using principal component analysis and applied for training a support vector machine classifier.

The Evaluation of Comprehensive Transportation System in Inner Mongolia Based on Principal Component Analysis

2014 ◽  
Vol 505-506 ◽  
pp. 782-786
Author(s):  
Chun Mei Zhang ◽  
Zhan Xin Ma ◽  
Lu Lu Zhai ◽  
Xin Yu Cui ◽  
Xiao Biao Zhao
Keyword(s):  
Principal Component Analysis ◽  
Inner Mongolia ◽  
Rapid Development ◽  
Principal Component ◽  
Component Analysis ◽  
Transportation System ◽  
Autonomous Region ◽  
Economic Output ◽  
Transportation Development ◽  
Inner Mongolia Autonomous Region

Based on the relevant data of comprehensive transportation system in Inner Mongolia Autonomous Region from 1990 to 2011, the transport equipment, transport mileage, transport capacity, and the transport share of the total economic output in four aspects are studied. Then we select 13 indicators to build the evaluation of comprehensive transportation system in Inner Mongolia Autonomous Region. Using SPSS17.0 software to perform the principal component analysis could get the evaluation of the development of comprehensive transportation system in Inner Mongolia, which has maintained rapid development in the past 22 years, especially after 2003, higher than previous years. It is in accordance with the current transportation development of Inner Mongolia Autonomous Region, next we verify the feasibility of the Principal Component Analysis (PCA) on transportation problem. The method also has theoretical significance of research on relevant aspects of other areas.

scholarly journals ANALISIS PENYIMPANGAN PENGGUNAAN LAHAN BERDASARKAN RENCANA TATA RUANG WILAYAH KABUPATEN SUMEDANG

2018 ◽  
Vol 20 (4) ◽  
pp. 399
Author(s):  
Reny Khaerani ◽  
Santun R.P. Sitorus ◽  
Omo Rusdiana
Keyword(s):  
Principal Component Analysis ◽  
Land Use ◽  
Regression Analysis ◽  
Multiple Regression Analysis ◽  
Multiple Regression ◽  
Human Resource ◽  
Spatial Planning ◽  
Rapid Development ◽  
Principal Component ◽  
Spatial Plan

Spatial plan is the result of spatial planning which is done through the process and procedure of arranging and determining based on the prevailing laws and regulations. The phenomenon that often happens is the deviation of existing land use with spatial plan. Sumedang Regency is experiencing a fairly rapid development, so there is an increase in human resource activity that implicate the widespread space needs and consequently deviation of land use is very vulnerable. The purpose of this study to determine the extent of deviation of land use occurs as well as what factors affect the occurence of irregular use of land. The analysis used in this study using GIS approach, Principal Component Analysis and Multiple Regression Analysis. The result of analysis shows that there are 25 types of deviation of existing land use and the most dominant is deviation into wetland (18,364 ha), dryland field (8,405 ha) and widened land (7,741 ha). While the factors that influence the occurence of deviation of land use are population and settlement, availability of land, infrastructure and accessibility, and sosioeconomic condition of society

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