Course No. 6 "Genome Browser"

 

Problem 2

We have the following goals in analyzing human genomic sequence:

  • Locate a human gene
  • Download the gene sequence along with its upstream sequence (to analyze promoter regions)
  • Download the cDNA sequence and its corresponding amino acid translation
  • Identify Single Nucleotide Polymorphisms (SNPs) and conserved regions in the gene
  • Identify genes in the neighborhood and homologs in other organisms
  • Find identified alternative splice variants
  • Use browsers to download results in a batch

UCSC genome browser

Retrieve the UCSC Genome Bioinformatics web page (http://genome.ucsc.edu/) and click on the “Genome Browser” link. Click on the "Click here to reset” link to reset the browser user interface settings to their defaults.  Click first on the "configure tracks and display" button. From Configure Tracks on UCSC Genome Browser select the "hide all" Tracks button and click the submit button. 

To access the RYR1 gene region and download its genomic sequence: Type RYR1 in the position/search box and select the go button.  Click on the first RYR1 gene link under the RefSeq Genes heading.  Under Genes and Gene Prediction Tracks, click on the UCSC Genes.  From the Display mode, select pack from the pull-down menu. From Label, check the box for “gene symbol,” and select the Submit button.  The gene is placed on the forward strand as seen from the direction of arrows on the gene model.  From the TrackMap, click on the RYR1 gene symbol label to the left of the UCSC Genes Track (the top one).  Under Sequence and Links to Tools and Databases, select the “Genomic Sequence” from assembly link to download the genomic sequence and/or the upstream and downstream sequence.

To view SNPs annotated on the region: Go back to the Genome Browser RYR1 display page.  Under Variation, click on the All SNPs (147) track. At the top, change the Display mode option to “pack.” Under Coloring Options, change “Splice Site” from Red to Blue and click on the Submit button.

To download SNPs in the conserved region: Click on the Tables link at the top of the page.  From Group select “Variation and Repeats.” From Track, select All SNP147. From Region select the position radio button.  From Intersection, click the “create” button. From Group, select “Comparative Genomics.” From Track, select “Conservation.” Click on the submit button.  From Output Format, select “BED-browser extensible data” and click on the “get output” button.  Adjust the upstream/downstream base location, if necessary and click on the get BED button.

 

MapViewer

Access NCBI's MapViewer (http://www.ncbi.nlm.nih.gov/mapview/) resource.  Select Homo sapiens Annotation Release 108.  Type “RYR1” in the search box and click on the Find button.  Select Gene from the Quick Filter box on the right and click on the Filter button.

Identify homologs in other organisms: Under Maps, click on the “Genes_seq” link for the reference assembly. Click on the hm link to access the HomoloGene page for the RYR1 gene. 

 

Ensembl


Access the Ensembl genome browser page (http://www.ensembl.org/index.html). Select Human genome under the Popular genomes heading.  Select Gene from the Search all categories pull down menu.  Type "RYR1" in the search box and click on the Go button. Click on the RYR1 link.  Click on the Show transcript table link if necessary.

To obtain the cDNA sequence with amino acid translation:  Click on the first transcript id ENST00000355481. From the Transcript-based displays menu (left-side of screen), select the “cDNA” link under the Sequence heading.  You can use “Configure this page” link (below the Transcript-based displays Menu) to change the display settings.  The pop-up window can be closed by clicking the checkmark in the upper right.

To download the chromosome locations for mouse homologs of multiple human genes in a batch mode: Select the Biomart link at the top of the page.  Select Ensembl Genes 87 as the database and Homo sapiens genes GRCh38.p7 as the dataset.  Click on the Filters menu, open the GENE criteria by clicking on the + sign, select the id type as “HGNC symbol” and type the gene symbols such as HFE, HRAS, OTC in the box below.  Click on the Count button at the top to check how many genes Biomart can find.  Click on the Attributes option and select the Homologs radio button. Open the GENE menu by clicking on the + sign, uncheck the boxes Ensembl Gene ID and Ensembl transcript ID and check the box Associated Gene Name.  Open the ORTHOLOGS menu by clicking on the + sign.  Scroll down to the Mouse Orthologs section.  Select the boxes next to Mouse Chromosome Start, Mouse Chromosome End, and Mouse Chromosome. Retrieve mouse homolog locations by clicking on the Results tab at the top.  Check the box for “Unique results only”.

Questions, Comments:  Medha Bhagwat, PhD