Genome browser tutorial

We can visualize this region by selecting human and hg19 from the drop-down for species and genome assembly, and then typing in the gene name SHH in the textbox.

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Our browser auto-fills gene names as users type, based a variety of gene annotations, including refSeq, UCSC and ensemble gene sets. After clicking the submit button, the Hi-C interactions in GM for the queried gene are shown on the right panel. For Hi-C data with multiple resolutions bin sizesthere is another dropdown menu for users to choose the appropriate size according to their needs.

To make the Hi-C interaction more visible, users can conveniently adjust the color bar on the same page. Under the heatmap, we also imbed the UCSC genome browser for the same region, so that the users can explore both the chromatin interaction and other "omics" data simultaneously. In this region, there is a known enhancer marked by green bar that regulate the SHH gene We observe that this known enhancer and the promoter of SHH are located within the same TAD and the long range interaction between them is also evident in the Hi-C map, marked by the black arrow You can also conveniently check the expression for the queried the genes across over cell types profiled by the ENCODE project.

Simply click the "Check gene expression on the top right corner of this page. Identify Linkage between Genes, Enhancers and SNPs Although displaying Hi-C data as a heatmap is informative to visualize large genome structures such as TADs, it is not intuitive to show interactions between two specific loci.


For example, many users are interested in using Hi-C data to explore enhancer-promoter interactions. To facilitate users with this goal, we implemented the following three methods in our 3D Genome browser: Virtual 4C: Circular chromosomal conformation capture 4C is a chromatin ligation-based method that surveys for one-vs-many interactions in the genome, that is, to measure the interaction frequencies between a bait locus of interest and any other loci.

In our browser, we use the queried region as bait either a gene name or a SNP IDand extract a row of Hi-C data centered on the bait region, hence, virtual 4C. ChIA-PET: another implementation of chromatin ligation-based method, which detects long-range interactions between genomic regions that are enriched for a feature either histone modification or transcription factor binding. Between each pair of distal-proximal DHSs, you can compute a Pearson correlation based their tissue-specificity. We incorporated these three methods in our browser.

In the below figure, we show an example by querying rs, a SNPs that has been associated with coronary heart disease By integrating multiple lines of evidence, our browser provides a valuable resource for investigators to create hypotheses connecting distal non-coding variant, distal regulatory elements and their target gene.

Type in the gene name "Galnt7" and query its surrounding kb. Click "Go". The exact interaction loci are listed at the bottom of this page. By check the "Show all interactions OR only interactions for queried gene", you can convert between showing all the interactions in this region, or ONLY show interactions with the queried gene. This function is particularly useful when there are lots of interactions in this region.

Further, checking "Show interaction as arcs OR as shaded area" will give you differnt style for displaying the interactions. Just choose the Hi-C source data from the dropdown menu and then type in a gene name or region. In the example, we are querying myc gene in GM and K cell types at 10kb resolution. The Hi-C interaction maps for the chosen two cell types are displayed below.

The green circles indicate two potential GM cell-type specific interactions.

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This allows investigators to use our tool to analyze un-published data. The new binary file enables the remote access of contact matrix hosted on any HTTP-supported servers. It also greatly increases the query speed, as the index directly points queries to the region of interest rather than searching through the whole matrix.

The BUTLR format also dramatically reduces the storage space of contact matrix files, not only through the binarization but also through the omission of redundant values. The tutorial is being updated with the new version of the 3D Genome Browser. If you have any questions or concerns, please feel free to contact us.It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations.

The Browser is a graphical viewer optimized to support fast interactive performance and is an open-source, web-based tool suite built on top of a MySQL database for rapid visualization, examination, and querying of the data at many levels. The Saved Sessions feature of the Browser has been around for quite some time, but many of our users have not made full use of it. It offers a great way to keep track of your thinking on a particular topic.

This tutorial demonstrates the visibility controls on the Genome Browser, showing the affect on BED tracks, wiggle tracks and Conservation tracks. It also discusses supertracks and composite tracks. This tutorial describes the isPCR tool and demonstrates how to use it for predicting the size and location of PCR products and visualizing the genomic location on the genome.

It also demonstrates how to use the Browser to obtain DNA sequences from the genome. There is also a discussion about changes to the genome assemblies from one version to another, and of two ways to navigate between different assemblies of the human genome in the Browser.

This tutorial demonstrates the Data Integrator, a tool that allows combination and intersection of data from up to five primary tables. In the example, data are extracted showing SNPs, genes and phenotypes from a genomic region. This tutorial shows how to obtain coordinates of genes, then input those coordinates into the Genome Browser for display. The regions do not have to be continuous in the genome.

This tutorial will demonstrate how to find the tables in the UCSC database that are associated with the data tracks in the Genome Browser graphical viewer. This tutorial demonstrates how to find all the single nucleotide polymorphisms in a gene using the UCSC Genome Browser. This tutorial shows how to find all the single nucleotide polymorphisms upstream from genes using the UCSC Genome Browser.

This tutorial shows how to use the UCSC genome browser to find a list of genes in a given genomic region. Course Features. This tutorial series address some common questions gathered from community. Demonstrations of interesting features of the Browser users may not have found on your own.

genome browser tutorial

Lessons of this Course. Recent courses.

genome browser tutorial

Machine learning Neuromatch Academy. View the course. The neuroinformatics of neuroanatomy INCF.Search the Genome Browser help pages:. Search the entire Genome Browser website:. Browse the Genome Browser mailing list. As vertebrate genome sequences near completion and research re-focuses on their analysis, the issue of effective sequence display becomes critical: it is not helpful to have 3 billion letters of genomic DNA shown as plain text! As an alternative, the UCSC Genome Browser provides a rapid and reliable display of any requested portion of genomes at any scale, together with dozens of aligned annotation tracks known genes, predicted genes, ESTs, mRNAs, CpG islands, assembly gaps and coverage, chromosomal bands, mouse homologies, and more.

genome browser tutorial

Half of the annotation tracks are computed at UCSC from publicly available sequence data. The remaining tracks are provided by collaborators worldwide.

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Users can also add their own custom tracks to the browser for educational or research purposes. The Genome Browser stacks annotation tracks beneath genome coordinate positions, allowing rapid visual correlation of different types of information. The user can look at a whole chromosome to get a feel for gene density, open a specific cytogenetic band to see a positionally mapped disease gene candidate, or zoom in to a particular gene to view its spliced ESTs and possible alternative splicing.

The Genome Browser itself does not draw conclusions; rather, it collates all relevant information in one location, leaving the exploration and interpretation to the user. The Genome Browser supports text and sequence based searches that provide quick, precise access to any region of specific interest.

Secondary links from individual entries within annotation tracks lead to sequence details and supplementary off-site databases. To control information overload, tracks need not be displayed in full. Tracks can be hidden, collapsed into a condensed or single-line display, or filtered according to the user's criteria.

Zooming and scrolling controls help to narrow or broaden the displayed chromosomal range to focus on the exact region of interest. Clicking on an individual item within a track opens a details page containing a summary of properties and links to off-site repositories such as PubMed, GenBank, Entrez, and OMIM.

The page provides item-specific information on position, cytoband, strand, data source, and encoded protein, mRNA, genomic sequence and alignment, as appropriate to the nature of the track.

A blue navigation bar at the top of the browser provides links to several other tools and data sources.

For instance, under the "View" menu, the "DNA" link enables the user to view the raw genomic DNA sequence for the coordinate range displayed in the browser window. This DNA can encode track features via elaborate text formatting options.

The browser data represents an immense collaborative effort involving thousands of people from the international biomedical research community.Sequence data from numerous genomic projects are pouring out of the sequence centers and into public databases at an unprecedented rate.

The sequencing projects flooding the free, online databases, such as the Entrez Genome Browser [ncbi. For researchers not trained in the relatively new field of bioinformatics - which applies information technology and computer programming to the field of molecular biology - the complexity of the information flooding the public databases can be overwhelming.

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Moreover, there is a shortage of bioinformatics experts, making it difficult for some researchers to even form a collaboration that would allow them to use the freely available sequence data in their studies. This has led a number of federal research centers and institutes to increase the amount of Web-based training that will allow any molecular biologist to use the public databases to advance genomic research.

The latest tutorials, funded by the National Human Genome Research Institute, one of the 27 institutes and centers that make up the NIH, provide essential training on the use of model organism genome databases. The tutorials were developed by OpenHelix, LLC, which already has published several free training sessions [openhelix.

Publicly available genome data from an array of model organisms, such as yeast, worms and mice, is widely used to gain critical insights into human biology. NHGRI funded the tutorials to empower the average researcher and encourage even greater exploration of these publicly available genome resources. The first tutorials focus on GBrowse [gmod.

Tutorials will also be freely available in the coming weeks on the Zebrafish Information [zfin. Each narrated tutorial, which can be viewed online or downloaded to a user's computer, introduces the resource and shows researchers how to use its features and functions. Resources connected to each tutorial, including PowerPoint slides, handouts, and user exercises are also available.

The model organism tutorials are available at OpenHelix [openhelix. Although the human genome sequence is not the focus of the newly funded tutorials, there are numerous publicly available databases that provide both the sequence itself, or data from genome-wide association studies, as well as online tutorials.

One such database is the Genome Browser [genome.

genome browser tutorial

The UCSC Bioinformatics group is also funding a free tutorial that is available through OpenHelix on how to navigate their genome browser, which has data from many model organisms that can be compared to the human genome.

NCBI also hosts a set of interactive tutorials of how their databases were used in recent discoveries called Coffee Break [ncbi. With more than genetic risk factors for common diseases found as a result of genome wide association studies, or GWAS, over the last two years, there is also a rising demand for data from NCBI's dbGaP database of Genotypes and Phenotypes.

So, while you may not have a bioinformatician at your disposal, Dr. Good emphasized that "any scientist from any discipline or anyone else who wants to pursue their ideas can easily take advantage of these important databases. Our hope is that anyone can use these resources to make the breakthroughs that could dramatically change our understanding of biology or lead to better treatments for disease.Also available is an introduction to additional tools available, including Gene Sorter and VisiGene.

UCSC Genome Browser is a research tool that integrates the work of hundreds of scientists worldwide into a graphical display of genome sequences and aligned annotations. The Genome Browser—originally developed to assist in the initial assembly of the human genome — now features a rich set of annotations on a multitude of genomes. That data resides in the databases—sometimes even long before publication of the project papers ensues. The approximately 60 minute tutorials highlight and explain all the features and functionality needed to start using the Genome Browser and its tools effectively.

The tutorial also includes a step-by-step movie which walks the user through an exercise using the tools of the Genome Browser.

Also included with each tutorial is a suite of training materials, including PowerPoint slides used as a basis for the tutorial, with a suggested script for the slides, slide handouts, and exercises.

These materials can be used as reference for users or as a ready-made presentation for training others on the use of the Genome Browser. In addition, OpenHelix is contracted by resource providers to provide comprehensive, long-term training and outreach programs.

Director and HHMI investigator David Haussler leads a team of scientists, engineers and students in the study and comparative analysis of mammalian and model organism genomes. The Genome Browser—originally developed to assist in the initial assembly of the human genome—now features a rich set of annotations on a multitude of mammalian and model organism genomes. The UCSC Bioinformatics Group continues to uphold its original mission to provide free, unrestricted public access to genome data on the Web.

Search for:.Video tutorials are an effective way for researchers to quickly learn how to use online tools offered by biological databases.

At MaizeGDB, we have developed a number of video tutorials that demonstrate how to use various tools and explicitly outline the caveats researchers should know to interpret the information available to them.

Researchers who rely upon online data resources demand that these resources function intuitively. At the same time, researchers wish to expertly interact with the data available, but do not have much time to learn how to effectively and efficiently use some of the more complex tools available to them.

In addition, not all researchers interacting with the data provided are aware of the caveats that should be known to properly interpret the data presented. Biological databases are required to satisfy different needs simultaneously in an integrated fashion. Database personnel must not only strive to continually create and recreate intuitive interfaces, but also train researchers to expertly use the more complex tools and datasets offered.

Where possible, we update the interface and tools to increase ease of use. In cases where the complexity of the biological problem itself creates a complicated tool, we put effort into education and outreach. Each curator works in a different location: L. The curators regularly interact with a diverse group of active maize researcher at their home location.

These direct interactions have two distinct outcomes for researchers: first, they receive clear explanations on how to use non-intuitive aspects of the web site or its features. Second, researchers learn about tools and functionalities offered by MaizeGDB that they otherwise might not discover.

UCSC genome browser tutorial

At the same time, these interactions allow the curators to identify needs expressed by many researchers and articulate those needs to the MaizeGDB Team so that a plan for meeting stated needs can be developed and implemented. Researchers attending on-site outreach workshops fill out evaluations of the quality and usefulness of the visit. Although the evaluations are very positive, the number of people that can be reached through these local events is limited. In order to reach a wider audience, we recently began to create video tutorials that are accessible directly from the MaizeGDB home page.

To identify areas that may be universally more difficult for researchers and thus would warrant the creation of a video tutorial, we compiled web site feedback gathered using the Request Tracker software 2 and cataloged the questions asked via all types of interactions.

Such documentation is maintained internally.

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The bulk of questions asked over the past 3 years concern how the genome of inbred line B73 was sequenced, how this sequence can be accessed and used, and caveats for interacting with the data. For B73, we have created a total of five different video tutorials on the topic of how best to access and make use of the genome sequence.

In the course of developing tutorial videos for the outreach web site, we have developed a set of guidelines for video creation:. The creators of the videos must have expert knowledge of the subject matter. Thus, personal interactions with the data generators, i.

Sequence Viewer: Download Transcripts, Exons and Proteins

Feedback from researchers who use MaizeGDB must be obtained and implemented before deployment of any video to gauge whether the video addresses expressed needs. We have gone back to people that have provided feedback, and to additional maize researchers and asked them how we can improve the tutorials before its official deployment.

This activity has resulted in improvements to the tutorials each and every time.Host a Genome Browser Workshop! Do you suspect that there is a lot more to the Genome Browser than you have been using? Timeslots are available to host a Genome Browser workshop at your institution.

Thanks to the funding support of NHGRI, we are able to offer hands-on Genome Browser training onsite at your institution at very affordable prices, tailored to your audience's level of expertise. Host — NOTE: virtual tutorials are available while coronavirus limits travel.

Use the Host link to contact us. For more information or to submit a request to host a workshop, please visit our sign-up page. Can't host? Catch one of our training sessions in your area:. Our video tutorials address some common questions we've gathered from our mailing list. Along the way we try to show you interesting features of the Browser you may not have found on your own.

Visit our YouTube channel or use the links below. JavaScript is disabled in your web browser You must have JavaScript enabled in your web browser to use the Genome Browser. Map Do you suspect that there is a lot more to the Genome Browser than you have been using? Video tutorials Finding a list of genes in a region. How-to: Genome Browser Gateway. Step-by-step tutorial presented at ABRF annual meeting - how to convert files and display high-throughput sequencing results.

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