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Current protocols in bioinformatics Pub Date : 2019-06-19 DOI: 10.1002/cpbi.62
{"title":"Issue Information TOC","authors":"","doi":"10.1002/cpbi.62","DOIUrl":"10.1002/cpbi.62","url":null,"abstract":"<p><b>Cover</b>: In Stansfield et al. (https://doi.org/10.1002/cpbi.76) image shows composite MD plot with significant differentially interacting regions highlighted. Highlighted points display where the differential interactions are occurring in relation to unit genomic distance on the x axis and log2 fold change on the y axis. Points highlighted in yellow are moderately significant, while points highlighted in red are highly significant.\u0000\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":10958,"journal":{"name":"Current protocols in bioinformatics","volume":"66 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpbi.62","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45215573","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
R Tutorial: Detection of Differentially Interacting Chromatin Regions From Multiple Hi-C Datasets R教程:从多个Hi-C数据集检测差异相互作用的染色质区域
Current protocols in bioinformatics Pub Date : 2019-05-24 DOI: 10.1002/cpbi.76
John C. Stansfield, Duc Tran, Tin Nguyen, Mikhail G. Dozmorov
{"title":"R Tutorial: Detection of Differentially Interacting Chromatin Regions From Multiple Hi-C Datasets","authors":"John C. Stansfield,&nbsp;Duc Tran,&nbsp;Tin Nguyen,&nbsp;Mikhail G. Dozmorov","doi":"10.1002/cpbi.76","DOIUrl":"10.1002/cpbi.76","url":null,"abstract":"<p>The three-dimensional (3D) interactions of chromatin regulate cell-type-specific gene expression, recombination, X-chromosome inactivation, and many other genomic processes. High-throughput chromatin conformation capture (Hi-C) technologies capture the structure of the chromatin on a global scale by measuring all-vs.-all interactions and can provide new insights into genomic regulation. The workflow presented here describes how to analyze and interpret a comparative Hi-C experiment. We describe the process of obtaining Hi-C data from public repositories and give suggestions for pre-processing pipelines for users who intend to analyze their own raw data. We then describe the data normalization and comparative analysis process. We present three protocols describing the use of the <span>multiHiCcompare</span>, <span>diffHic</span>, and <span>FIND</span> R packages, respectively, to perform a comparative analysis of Hi-C experiments. Finally, visualization of the results and downstream interpretation of the differentially interacting regions are discussed. The bulk of this tutorial uses the R programming environment, and the processes described can be performed with most operating systems and a single computer. © 2019 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":10958,"journal":{"name":"Current protocols in bioinformatics","volume":"66 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpbi.76","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37269157","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 5
Using PconsC4 and PconsFold2 to Predict Protein Structure 利用PconsC4和pconfold2预测蛋白质结构
Current protocols in bioinformatics Pub Date : 2019-05-07 DOI: 10.1002/cpbi.75
Claudio Bassot, David Menendez Hurtado, Arne Elofsson
{"title":"Using PconsC4 and PconsFold2 to Predict Protein Structure","authors":"Claudio Bassot,&nbsp;David Menendez Hurtado,&nbsp;Arne Elofsson","doi":"10.1002/cpbi.75","DOIUrl":"10.1002/cpbi.75","url":null,"abstract":"<p>In spite of the fact that there has been a significant increase in the number of solved protein structures, structural information is missing for many proteins. Although structural information is codified in the amino acid sequence, computational prediction using only this information is still an unsolved problem. However, one successful method to model a protein's structure starting from the primary sequence is to use contact prediction derived from multiple sequence alignment (MSA). Here we use our contact predictor PconsC4 to generate a list of probable contacts between residues in the primary sequences. These contacts are then used together with the secondary structure prediction as constraints for the CONFOLD folding method. In this way, a 3D protein model can be built starting directly from the primary sequence. © 2019 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":10958,"journal":{"name":"Current protocols in bioinformatics","volume":"66 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpbi.75","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37221788","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 7
Using EMBL-EBI Services via Web Interface and Programmatically via Web Services 通过Web接口和通过Web服务编程使用EMBL-EBI服务
Current protocols in bioinformatics Pub Date : 2019-04-30 DOI: 10.1002/cpbi.74
Fábio Madeira, Nandana Madhusoodanan, Joon Lee, Adrian R.N. Tivey, Rodrigo Lopez
{"title":"Using EMBL-EBI Services via Web Interface and Programmatically via Web Services","authors":"Fábio Madeira,&nbsp;Nandana Madhusoodanan,&nbsp;Joon Lee,&nbsp;Adrian R.N. Tivey,&nbsp;Rodrigo Lopez","doi":"10.1002/cpbi.74","DOIUrl":"10.1002/cpbi.74","url":null,"abstract":"<p>The European Bioinformatics Institute (EMBL-EBI) provides access to a wide range of core databases and analysis tools that are of key importance in bioinformatics. As well as providing web interfaces to these resources, web services are available using REST and SOAP protocols that enable programmatic access and allow their integration into other applications and analytical workflows and pipelines. This article describes the various options available to researchers and bioinformaticians who would like to use our resources via the web interface employing RESTful web service clients provided in Perl, Python, and Java, or would like to use Docker containers to integrate the resources into analysis pipelines and workflows. © 2019 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":10958,"journal":{"name":"Current protocols in bioinformatics","volume":"66 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpbi.74","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37200562","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 22
Issue Information TOC 发布信息TOC
Current protocols in bioinformatics Pub Date : 2019-02-25 DOI: 10.1002/cpbi.61
{"title":"Issue Information TOC","authors":"","doi":"10.1002/cpbi.61","DOIUrl":"10.1002/cpbi.61","url":null,"abstract":"","PeriodicalId":10958,"journal":{"name":"Current protocols in bioinformatics","volume":"65 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpbi.61","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48131419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Integrating Bacterial ChIP-seq and RNA-seq Data With SnakeChunks 利用SnakeChunks整合细菌ChIP-seq和RNA-seq数据
Current protocols in bioinformatics Pub Date : 2019-02-20 DOI: 10.1002/cpbi.72
Claire Rioualen, Lucie Charbonnier-Khamvongsa, Julio Collado-Vides, Jacques van Helden
{"title":"Integrating Bacterial ChIP-seq and RNA-seq Data With SnakeChunks","authors":"Claire Rioualen,&nbsp;Lucie Charbonnier-Khamvongsa,&nbsp;Julio Collado-Vides,&nbsp;Jacques van Helden","doi":"10.1002/cpbi.72","DOIUrl":"10.1002/cpbi.72","url":null,"abstract":"<p>Next-generation sequencing (NGS) is becoming a routine approach in most domains of the life sciences. To ensure reproducibility of results, there is a crucial need to improve the automation of NGS data processing and enable forthcoming studies relying on big datasets. Although user-friendly interfaces now exist, there remains a strong need for accessible solutions that allow experimental biologists to analyze and explore their results in an autonomous and flexible way. The protocols here describe a modular system that enable a user to compose and fine-tune workflows based on SnakeChunks, a library of rules for the Snakemake workflow engine. They are illustrated using a study combining ChIP-seq and RNA-seq to identify target genes of the global transcription factor FNR in <i>Escherichia coli</i>, which has the advantage that results can be compared with the most up-to-date collection of existing knowledge about transcriptional regulation in this model organism, extracted from the RegulonDB database. © 2019 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":10958,"journal":{"name":"Current protocols in bioinformatics","volume":"66 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpbi.72","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36982680","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Utilizing iVariantGuide for Variant Assessment of Next-Generation Sequencing 利用iVariantGuide进行下一代测序的变异评估
Current protocols in bioinformatics Pub Date : 2019-02-12 DOI: 10.1002/cpbi.73
Sophia R. Chaudhry, Michael A. Tainsky
{"title":"Utilizing iVariantGuide for Variant Assessment of Next-Generation Sequencing","authors":"Sophia R. Chaudhry,&nbsp;Michael A. Tainsky","doi":"10.1002/cpbi.73","DOIUrl":"10.1002/cpbi.73","url":null,"abstract":"<p>Molecular genetic testing provides the capability for personalized prediction, diagnosis, and pharmacological treatments of disease and disorders. Variant assessment of next-generation sequencing (NGS) is a crucial component of genetic testing for clinicians to counsel patients on risk and management. The iVariantGuide application is a dynamic Web-based application made for the tertiary analysis of NGS. Along with variant assessment, iVariantGuide provides a unique interactive pathway impact analysis of genetic variants, as well as a unique Gene Ontology (GO) analysis. Here we provide a step-by-step guide on how to utilize iVariantGuide, employing a publicly available NGS dataset consisting of a cohort of germline DNAs from high-risk serous ovarian cancer (OVCA) patients. The application will be used to exhibit the ease in filtering down to a set of compelling novel variants and their impact on biological pathways and GO terms. © 2019 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":10958,"journal":{"name":"Current protocols in bioinformatics","volume":"65 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpbi.73","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36942178","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Visualizing Post-Translational Modifications in Protein Interaction Networks Using PTMOracle 利用PTMOracle可视化蛋白质相互作用网络中的翻译后修饰
Current protocols in bioinformatics Pub Date : 2019-01-17 DOI: 10.1002/cpbi.71
Aidan P. Tay, Angelita Liang, Marc R. Wilkins, Chi Nam Ignatius Pang
{"title":"Visualizing Post-Translational Modifications in Protein Interaction Networks Using PTMOracle","authors":"Aidan P. Tay,&nbsp;Angelita Liang,&nbsp;Marc R. Wilkins,&nbsp;Chi Nam Ignatius Pang","doi":"10.1002/cpbi.71","DOIUrl":"10.1002/cpbi.71","url":null,"abstract":"<p>Post-translational modifications (PTMs) of proteins act as key regulators of protein activity, including the regulation of protein-protein interactions (PPIs). However, exploring functional links between PTMs and PPIs can be difficult. PTMOracle is a Cytoscape app that facilitates the co-visualization and co-analysis of PTMs in the context of PPI networks. PTMOracle also allows extensive data to be integrated and co-analyzed, allowing the role of domains, motifs, and disordered regions to be considered. Here, we describe several PTMOracle protocols investigating complex PTM-associated relationships and their role in PPIs. This is assisted by OraclePainter for coloring proteins by the modifications present and visualizing these in the context of networks, by OracleTools for cross-matching PTMs with sequence feature for all nodes in the network, and by OracleResults for exploring specific proteins and visualizing their PTMs in the context of protein sequences. This unit aims to demonstrate how PTMOracle can be used to systematically explore network visualizations and generate testable hypotheses regarding the functional role of PTMs in PPIs, and how the results can be analyzed to better understand the regulatory role of PTMs in PPIs. © 2019 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":10958,"journal":{"name":"Current protocols in bioinformatics","volume":"66 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpbi.71","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36915860","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Discovering Transcriptional Regulatory Elements From Run-On and Sequencing Data Using the Web-Based dREG Gateway 使用基于web的dREG网关从运行和测序数据中发现转录调控元件
Current protocols in bioinformatics Pub Date : 2018-12-27 DOI: 10.1002/cpbi.70
Tinyi Chu, Zhong Wang, Shao-Pei Chou, Charles G. Danko
{"title":"Discovering Transcriptional Regulatory Elements From Run-On and Sequencing Data Using the Web-Based dREG Gateway","authors":"Tinyi Chu,&nbsp;Zhong Wang,&nbsp;Shao-Pei Chou,&nbsp;Charles G. Danko","doi":"10.1002/cpbi.70","DOIUrl":"10.1002/cpbi.70","url":null,"abstract":"<p>Transcription is a chromatin mark that can be used effectively to identify the location of active enhancers and promoters, collectively known as transcriptional regulatory elements (TREs). We recently introduced dREG, a tool for the identification of TREs using run-on and sequencing (RO-seq) assays, including global run-on and sequencing (GRO-seq), precision run-on and sequencing (PRO-seq), and chromatin run-on and sequencing (ChRO-seq). In this protocol, we present step-by-step instructions for running dREG on an arbitrary run-on and sequencing dataset. Users provide dREG with bigWig files (in which each read is represented by a single base) representing the location of RNA polymerase in a cell or tissue sample of interest, and dREG returns a list of genomic regions that are predicted to be active TREs. Finally, we demonstrate the use of dREG regions in discovering transcription factors controlling response to a stimulus and predicting their target genes. Together, this protocol provides detailed instructions for running dREG on arbitrary run-on and sequencing data. © 2018 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":10958,"journal":{"name":"Current protocols in bioinformatics","volume":"66 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpbi.70","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36818039","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 22
Using OmicsNet for Network Integration and 3D Visualization 使用OmicsNet进行网络集成和三维可视化
Current protocols in bioinformatics Pub Date : 2018-12-17 DOI: 10.1002/cpbi.69
Guangyan Zhou, Jianguo Xia
{"title":"Using OmicsNet for Network Integration and 3D Visualization","authors":"Guangyan Zhou,&nbsp;Jianguo Xia","doi":"10.1002/cpbi.69","DOIUrl":"10.1002/cpbi.69","url":null,"abstract":"<p>OmicsNet is a novel web-based tool for creating and visualizing complex biological networks in 3D space. By coupling a comprehensive knowledgebase with the powerful WebGL technology, OmicsNet allows researchers to intuitively explore molecular interactions and regulatory relationships among genes, transcription factors, microRNAs, and metabolites. OmicsNet fills an important gap by facilitating multi-omics integration and systems biology. This article contains three basic protocols covering the key features of OmicsNet, including how to create biological networks from a single or multiple list(s) of molecules, how to integrate or enrich different types of networks, and how to navigate the 3D visualization system to obtain biological insights. The OmicsNet web server is freely available at https://www.omicsnet.ca. © 2018 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":10958,"journal":{"name":"Current protocols in bioinformatics","volume":"65 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpbi.69","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36788390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 39
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