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Review
. 2014 Jul 1;107:19.9.1-36.
doi: 10.1002/0471142727.mb1909s107.

The UCSC Genome Browser: What Every Molecular Biologist Should Know

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Free PMC article
Review

The UCSC Genome Browser: What Every Molecular Biologist Should Know

Mary E Mangan et al. Curr Protoc Mol Biol. .
Free PMC article

Abstract

Electronic data resources can enable molecular biologists to quickly get information from around the world that a decade ago would have been buried in papers scattered throughout the library. The ability to access, query, and display these data makes benchwork much more efficient and drives new discoveries. Increasingly, mastery of software resources and corresponding data repositories is required to fully explore the volume of data generated in biomedical and agricultural research, because only small amounts of data are actually found in traditional publications. The UCSC Genome Browser provides a wealth of data and tools that advance understanding of genomic context for many species, enable detailed analysis of data, and provide the ability to interrogate regions of interest across disparate data sets from a wide variety of sources. Researchers can also supplement the standard display with their own data to query and share this with others. Effective use of these resources has become crucial to biological research today, and this unit describes some practical applications of the UCSC Genome Browser.

Keywords: ENCODE; SNP; UCSC Genome Browser; comparative genomics; custom tracks; primers; variations.

Figures

Figure 19.9.1
Figure 19.9.1
(A) The UCSC Genome Browser organizes the display of genomic information with the official or reference genome sequence as the framework, positioning additional data as “annotation tracks” in the appropriate genomic location to provide context for understanding any genomic region. Default tracks for the human genome assembly February 2009 (GRCh37/hg19) are shown. (B) An underlying MySQL database stores genomic sequence data, annotation track details, and auxiliary information which can then be visualized with the graphical Genome viewer interface, or queried and downloaded using the Table Browser interface.
Figure 19.9.1
Figure 19.9.1
(A) The UCSC Genome Browser organizes the display of genomic information with the official or reference genome sequence as the framework, positioning additional data as “annotation tracks” in the appropriate genomic location to provide context for understanding any genomic region. Default tracks for the human genome assembly February 2009 (GRCh37/hg19) are shown. (B) An underlying MySQL database stores genomic sequence data, annotation track details, and auxiliary information which can then be visualized with the graphical Genome viewer interface, or queried and downloaded using the Table Browser interface.
Figure 19.9.2
Figure 19.9.2
The Gateway query box provides the entry point for basic text queries of the UCSC Genome Browser and offers access to the Genome viewer. Details and links about the current genome assembly for that species are provided. Helpful formatting notes are offered to guide additional queries.
Figure 19.9.3
Figure 19.9.3
Overview of a region of the UCSC Genome Browser viewer. The position of the TP53 (uc002gij.3) gene that was clicked from the results is indicated with the arrow (labeled “clicked”). The browser adds a highlight box around the clicked item to help you identify it on the viewer. The arrow (labeled “details”) indicates the bar to click for details about the track data. Zooming out (or in) allows users to change the range overview (“zoom out” arrow).
Figure 19.9.4
Figure 19.9.4
The neighborhood of the TP53 gene includes a second gene, WRAP53, denoted on the right. The Publications track is highlighted. The Publications track connects this genomic region to instances of that sequence that appear in scientific journal articles.
Figure 19.9.5
Figure 19.9.5
A portion of the track controls menu area is shown. An open menu for a single track offers a variety of display visibility choices. “Hide” removes the track from view; “dense” collapses all the data into a single line; “squish” uses half-sized graphics; “pack” efficiently positions each item (several may share a line if room permits); and “full” puts each data item on a separate line. In the case of a “Super-track” that combines several tracks into a coordinated set, the choices will be “show” and “hide” for the set. However, each component track will still retain the full options. The full options will be available on the hyperlinked description page for the super-track. Choices for the visibility will depend on the data type and one’s needs. An oval indicates a clickable hyperlink that provides details about the data contents of the track or the super-track.
Figure 19.9.6
Figure 19.9.6
The data associated with Publications track are shown. The viewer will display a large list of publications aligned to the region that is discussed in the paper. The first author and year of publication are displayed in the view (arrow labeled “Author and Year”). Mousing over an item opens an information popup with the title of the article (circled in the figure).
Figure 19.9.7
Figure 19.9.7
(A) Focus on the ENCODE Regulation super-track area (a histone mark track, a DNase hypersensitivity track, and a transcription factor track, boxed in red). (B) The Super-track show/hide menu adjusts the set of tracks as a group (Figure 19.9.5), but the sub-track controls accessed from the “ENCODE Regulation…” hyperlink offer additional options for setting viewing choices of the component tracks. ENCODE Regulation sub-track Layered H3K27ac settings page offers various strategies for adjusting the view. (C) The default view of the H3K27ac shows all the available cell line histogram signal data (upper). When only one of the cell lines is selected, the browser reflects the choice with yellow graphics only. (D) The Txn Factor ChIP track shows signals from various experiments with different transcription factor antibodies (names to the left of a signal) and in different cell lines (letter codes to the right of a signal; red boxed area).
Figure 19.9.7
Figure 19.9.7
(A) Focus on the ENCODE Regulation super-track area (a histone mark track, a DNase hypersensitivity track, and a transcription factor track, boxed in red). (B) The Super-track show/hide menu adjusts the set of tracks as a group (Figure 19.9.5), but the sub-track controls accessed from the “ENCODE Regulation…” hyperlink offer additional options for setting viewing choices of the component tracks. ENCODE Regulation sub-track Layered H3K27ac settings page offers various strategies for adjusting the view. (C) The default view of the H3K27ac shows all the available cell line histogram signal data (upper). When only one of the cell lines is selected, the browser reflects the choice with yellow graphics only. (D) The Txn Factor ChIP track shows signals from various experiments with different transcription factor antibodies (names to the left of a signal) and in different cell lines (letter codes to the right of a signal; red boxed area).
Figure 19.9.7
Figure 19.9.7
(A) Focus on the ENCODE Regulation super-track area (a histone mark track, a DNase hypersensitivity track, and a transcription factor track, boxed in red). (B) The Super-track show/hide menu adjusts the set of tracks as a group (Figure 19.9.5), but the sub-track controls accessed from the “ENCODE Regulation…” hyperlink offer additional options for setting viewing choices of the component tracks. ENCODE Regulation sub-track Layered H3K27ac settings page offers various strategies for adjusting the view. (C) The default view of the H3K27ac shows all the available cell line histogram signal data (upper). When only one of the cell lines is selected, the browser reflects the choice with yellow graphics only. (D) The Txn Factor ChIP track shows signals from various experiments with different transcription factor antibodies (names to the left of a signal) and in different cell lines (letter codes to the right of a signal; red boxed area).
Figure 19.9.7
Figure 19.9.7
(A) Focus on the ENCODE Regulation super-track area (a histone mark track, a DNase hypersensitivity track, and a transcription factor track, boxed in red). (B) The Super-track show/hide menu adjusts the set of tracks as a group (Figure 19.9.5), but the sub-track controls accessed from the “ENCODE Regulation…” hyperlink offer additional options for setting viewing choices of the component tracks. ENCODE Regulation sub-track Layered H3K27ac settings page offers various strategies for adjusting the view. (C) The default view of the H3K27ac shows all the available cell line histogram signal data (upper). When only one of the cell lines is selected, the browser reflects the choice with yellow graphics only. (D) The Txn Factor ChIP track shows signals from various experiments with different transcription factor antibodies (names to the left of a signal) and in different cell lines (letter codes to the right of a signal; red boxed area).
Figure 19.9.8
Figure 19.9.8
(A) Common SNPs or All SNPs can be shown. The variations from dbSNP can be viewed on the browser using different tracks. A “Common SNPs” track may be the right choice for some investigations. Other times the “All SNPs” track is suitable. Each of these can be further filtered or set for other visualization needs using the corresponding settings pages. (B) Examination of the region of interest and corresponding SNP information may provide useful additional information about variations that affect function. SNPs in the coding regions and in the regulatory regions may offer leads to pursue with further benchwork. Tracks can be dragged to new locations for easier viewing. Here the SNP track has been dragged to be placed beneath the genes track.
Figure 19.9.8
Figure 19.9.8
(A) Common SNPs or All SNPs can be shown. The variations from dbSNP can be viewed on the browser using different tracks. A “Common SNPs” track may be the right choice for some investigations. Other times the “All SNPs” track is suitable. Each of these can be further filtered or set for other visualization needs using the corresponding settings pages. (B) Examination of the region of interest and corresponding SNP information may provide useful additional information about variations that affect function. SNPs in the coding regions and in the regulatory regions may offer leads to pursue with further benchwork. Tracks can be dragged to new locations for easier viewing. Here the SNP track has been dragged to be placed beneath the genes track.
Figure 19.9.9
Figure 19.9.9
Track description information is available via hyperlinks on the browser main page or via gray vertical bars on the left side of the browser graphic for that track. They may contain configuration options or filters to customize the data for the display. Here, the 46-Species conservation track offers choices for which species to display. Conservation sets are available for many reference genomes, with the most species mapped to the most recent human and mouse assemblies. New collections are added as new genomes become available for the analyses.
Figure 19.9.10
Figure 19.9.10
(A) First exon area of the human HOXA7 gene, with comparative data for several fish indicated. (B) Zoom in to a sufficient level and then click in the fish species region of the Conservation track to view the alignment. (C) Clicking on the conservation area in the display yields the actual alignment data for human and the species that were selected. More details on the display characteristics can be found on the lower portion of the page. Nucleotides of translated codons are in capital letters and colored blue.
Figure 19.9.10
Figure 19.9.10
(A) First exon area of the human HOXA7 gene, with comparative data for several fish indicated. (B) Zoom in to a sufficient level and then click in the fish species region of the Conservation track to view the alignment. (C) Clicking on the conservation area in the display yields the actual alignment data for human and the species that were selected. More details on the display characteristics can be found on the lower portion of the page. Nucleotides of translated codons are in capital letters and colored blue.
Figure 19.9.10
Figure 19.9.10
(A) First exon area of the human HOXA7 gene, with comparative data for several fish indicated. (B) Zoom in to a sufficient level and then click in the fish species region of the Conservation track to view the alignment. (C) Clicking on the conservation area in the display yields the actual alignment data for human and the species that were selected. More details on the display characteristics can be found on the lower portion of the page. Nucleotides of translated codons are in capital letters and colored blue.
Figure 19.9.11
Figure 19.9.11
Overview of the Table Browser interface with steps highlighted (arrows). Many choices for data type, genomic regions, operations and output of the data are available. To quickly reset any previous choices, filters, or other aspects, click the reset link near the bottom of the form (red box).
Figure 19.9.12
Figure 19.9.12
A variety of output choices are available to obtain results from the Table Browser. Additionally the data can be sent directly to the Galaxy or GREAT tools for further exploration.
Figure 19.9.13
Figure 19.9.13
(A) The Table Browser interface offers the opportunity to specify data types for the output by selecting fields from the list of available items. (B) Output shows samples of the selected items.
Figure 19.9.13
Figure 19.9.13
(A) The Table Browser interface offers the opportunity to specify data types for the output by selecting fields from the list of available items. (B) Output shows samples of the selected items.
Figure 19.9.14
Figure 19.9.14
The Table Browser will accept lists of identifiers as appropriate for specific tables. Here, rsIDs from dbSNP as gleaned from the literature (A) can be pasted directly into the Table Browser to limit the search (B).
Figure 19.9.14
Figure 19.9.14
The Table Browser will accept lists of identifiers as appropriate for specific tables. Here, rsIDs from dbSNP as gleaned from the literature (A) can be pasted directly into the Table Browser to limit the search (B).
Figure 19.9.15
Figure 19.9.15
(A) Using the “selected fields from primary and related tables” option, the output of the Table Browser can be configured to join data from several tables. This will include tables linked to the first query tables, which are available to add to the query lower on the selection page. (B) Output from main table and linked tables.
Figure 19.9.15
Figure 19.9.15
(A) Using the “selected fields from primary and related tables” option, the output of the Table Browser can be configured to join data from several tables. This will include tables linked to the first query tables, which are available to add to the query lower on the selection page. (B) Output from main table and linked tables.
Figure 19.9.16
Figure 19.9.16
For certain tables (notably those associated with the UCSC Genes track and its main table, knownGene) several layers of linked tables (presented diagrammatically in panel A) may contain information of interest. They can be joined together with successive steps to provide a table of data from the linked tables (B). Here, the Gene Ontology (GO) data are pulled from a different table, “go”, that is available for linkage from several different assembly-specific databases.
Figure 19.9.16
Figure 19.9.16
For certain tables (notably those associated with the UCSC Genes track and its main table, knownGene) several layers of linked tables (presented diagrammatically in panel A) may contain information of interest. They can be joined together with successive steps to provide a table of data from the linked tables (B). Here, the Gene Ontology (GO) data are pulled from a different table, “go”, that is available for linkage from several different assembly-specific databases.
Figure 19.9.17
Figure 19.9.17
Users may add data of their own to the Genome Browser via the Custom Tracks feature. (A) Access the Custom Tracks feature by selecting the button on the Gateway page. This button is also available on the main browser graphic display page and on the Table Browser interface. (B) Data may be uploaded by a variety of methods, including finding a file on a local computer (Browse…), pasting in a URL for a Web-accessible file, or pasting in the data directly (i.e., paste URLs or data). Several different file formats are accepted (top). (C) All custom tracks that have been uploaded are available under the “manage custom tracks” button on the main browser page (replaces “add custom tracks” when custom tracks have been added).
Figure 19.9.17
Figure 19.9.17
Users may add data of their own to the Genome Browser via the Custom Tracks feature. (A) Access the Custom Tracks feature by selecting the button on the Gateway page. This button is also available on the main browser graphic display page and on the Table Browser interface. (B) Data may be uploaded by a variety of methods, including finding a file on a local computer (Browse…), pasting in a URL for a Web-accessible file, or pasting in the data directly (i.e., paste URLs or data). Several different file formats are accepted (top). (C) All custom tracks that have been uploaded are available under the “manage custom tracks” button on the main browser page (replaces “add custom tracks” when custom tracks have been added).
Figure 19.9.17
Figure 19.9.17
Users may add data of their own to the Genome Browser via the Custom Tracks feature. (A) Access the Custom Tracks feature by selecting the button on the Gateway page. This button is also available on the main browser graphic display page and on the Table Browser interface. (B) Data may be uploaded by a variety of methods, including finding a file on a local computer (Browse…), pasting in a URL for a Web-accessible file, or pasting in the data directly (i.e., paste URLs or data). Several different file formats are accepted (top). (C) All custom tracks that have been uploaded are available under the “manage custom tracks” button on the main browser page (replaces “add custom tracks” when custom tracks have been added).
Figure 19.9.18
Figure 19.9.18
(A) Custom tracks are available for display in the main browser graphic in the same way as resident tracks and may be controlled via pull-down menus in the same way (red box). (B) Custom Tracks are also available in the Table Browser (red box) and can be queried in the same fashion as resident tracks.
Figure 19.9.18
Figure 19.9.18
(A) Custom tracks are available for display in the main browser graphic in the same way as resident tracks and may be controlled via pull-down menus in the same way (red box). (B) Custom Tracks are also available in the Table Browser (red box) and can be queried in the same fashion as resident tracks.
Figure 19.9.19
Figure 19.9.19
Track Hub selection page. The cursor arrow indicates the location of the file on the data provider’s server that contains instructions for the hub.
Figure 19.9.20
Figure 19.9.20
Track Hub miRcode displayed on hg19 with the UCSC Genes track. Note the new blue-bar track group below the Browser graphic. One of the two miRcode tracks is displayed at “dense” visibility.
Figure 19.9.21
Figure 19.9.21
Text files supporting the miRcode Track Hub. (A) The primary page, http://www.mircode.org/ucscHub/hub.txt, defines the label for the Hub blue-bar group, shortLabel miRcode microRNA sites and includes other information required to display the Hub. (B) http://www.mircode.org/ucscHub/genomes.txt page can have the names of multiple genome assemblies. Here, only hg19 is referenced. (C) The trackDb.txt page is in the hg19 directory and details the configuration of each track. Here, two tracks are defined which determine the tracks in the track controls (shortLabel) of the new blue bar group (Fig. 19.9.20). The bigDataUrl tag identifies the bigBed file that contains the data. It must be in the same directory as the text page, http://www.mircode.org/ucscHub/hg19.

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