Course No. 2 "Gene Resources: From Transcription Factor Binding Sites to Function"


 
 

Problem 1

Topics to be covered

1. Genomic and transcript related information

  • chromosome location
  • genomic, mRNA and protein sequence
  • alternative splice products and gene structure (exon-intron locations)
  • SNPs in the gene and which ones are known to be associated with a phenotype

2. Protein related information

  • protein function
  • pathways and downloading all genes in that pathway

3. Publications

  • publications documenting experiments that add to our understanding of the HRAS gene

4. Regulation of expression

  • known transcription factor binding sites

 

Retrieve entries related to "HRAS" in Entrez Gene. Identify the entry for the human HRAS gene. What is the chromosome location of this gene on the human genome? What are the alternate gene symbols and designations? Click on the HRAS link to access the full Entrez Gene report.

I. Publications 

Obtain a list of publications documenting experiments that add to our understanding of the HRAS gene.

II. Genomic and transcript related information

How can you obtain genomic, mRNA and protein sequences?

Is the RefSeq mRNA record reviewed? How many alternatively spliced products have been annotated for the gene? 

Change the display from "Full Report" to "Gene Table" to obtain exon-intron locations for each transcript variant. Go back to the Full Report.

Identify the variations annotated on this gene by clicking on the SNP: GeneView link from the Links menu. How many coding SNPs are displayed? To display clinically associated SNPs, click on the box "Clinical Source" and then click on the "refresh" button. To determine whether known SNPs in the coding region of a gene are associated with any phenotype, access the OMIM record by clicking on the 
 icon in the "Clinically Associated" column in the SNP report. Open the Table of Contents menu and click on the Table View link below the Allelic Variants link.  Compare the missense changes from the SNP report with those listed in this table.

III. Protein related information

What is the function of this protein? Name the pathways it is involved in. Obtain a list of all genes in one of the pathways using the Biosystems link.


IV. Regulation of expression

Access the Genecards (http://www.genecards.org) database. Type "HRAS" in the search box, select the "symbol only" option and click on the Search button. Then click on the HRAS link. Scroll down to the Regulatory elements section and then click on the SABiosciences Regulatory transcription factor binding sites link.  View More Transcription Factors link will provide additional transcription factor binding sites. 

 

Alternatively, to predict transcription factor binding sites in your DNA sequence, first download 1000 nucleotide upstream gene sequence.  In order to predict transcription factor binding sites from the upstream sequence, let us first download 1000 nucleotide upstream sequence.  Go back to the HRAS Gene record. Scroll to the section(s) labeled “NCBI Reference Sequences (RefSeq)” and click on the GeneBank link for the RefSeq Gene record.  Use “Change region shown” to obtain 1000 nucleotide upstream region and click on the FASTA link to get the sequence in FASTA format.  Access the resource Promo http://alggen.lsi.upc.es/cgi-bin/promo_v3/promo/promoinit.cgi?dirDB=TF_8.3.   Paste 1000 nucleotide upstream DNA sequence and click on the Submit button.  Click on Select Species. Select “Only Human factors” and “Only Human Sites.” Select SearchSites link under Step 2. Paste the FASTA sequence and click on the submit button.  Click on the Data link to get a tabular output.

 

 

Questions, Comments:  Medha Bhagwat, PhD