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NCBI Bioinformatics Resources: An Introduction: Find genes | proteins

From topic to gene and protein

Object: Starting with a disease, syndrome, process, or other topic, identify the associated genes and proteins.

Example: Find the genes and proteins associated with warfarin sensitivity.


PubMed information

UC Berkeley faculty, staff, students, and campus visitors should use the UC Berkeley-specific PubMed URL (http://uclibs.org/PID/11594), or click on the PubMed link from any library website. The UC-eLinks icon to access full text will be displayed for every article record:


 

Searching on a topic

In PubMed, enter search terms for the disease, syndrome, process, or other topic of interest in the search box and click Search. PubMed is a database of the biomedical literature; this search will retrieve articles from scientific journals relating to warfarin sensitivity.


Finding related genes

Under Find related data in the right-hand discovery column, select the database Gene with the option Gene, and click Find items. This will retrieve records in the database Gene that cite the current articles.

 

Note that you are taken to the database Gene. Gene records will be displayed that cite any of the articles retrieved by the original PubMed search. In this case there are eight gene records that cite at least one of the initial set of articles on warfarin sensitivity.

 

Click on a gene symbol to view the corresponding Gene record:

Gene Table of Contents

 

The Table of Contents links to sections within the Gene record:

Genomic context: chromosomal location
Genomic regions, transcripts, products: graphical view of gene features
Expression: tissues in which gene is expressed
Bibliography: related citations in PubMed
Variation: links to variants in ClinVar, dbVar
General gene information: markers, homology clone names, gene ontology
General protein information: names and accession numbers of protein products
NCBI Reference sequences: links to curated and annotated reference sequence records for the gene (accession number prefix NG), mRNA (NM) and protein (NP).

  • NG accession number links to the GenBank record, FASTA sequence, and Sequence viewer in the Nucleotide database.
  • NM accession number links to the mRNA record in the Nucleotide database.
  • NP accession number links to the protein record in the Protein database.

See all RefSeq accession numbers and molecule types


Finding related proteins

To view the protein structure, click on the NP protein accession number in the RefSeq section, which will display the record for the cytochrome P450 2C9 precursor protein reference sequence in the Protein database.

If there is a 3D structure available in the Structure database, it will be displayed under Protein 3D Structures in the right-hand discovery menu. Only experimentally determined structures are included; see What are macromolecular structures?: Experimental Methods in the Structure Help file.

To view the structures, click on See all structures:

 

The record for the protein in the Structure database will display.

 

Select a structure of interest to view the structure summary in the Molecular Modeling Database (MMDB):

Structure summary

Click on the "View in iCN3D" icon, or download the Cn3D ("See in 3D") structure viewer. Once Cn3D is installed, click Download and open the resulting file in CN3D:

Under the Style menu of the Structure viewer, the rendering conventions and color choices can be changed. Specific amino acids or amino acid sequences can be highlighted using the sequence/alignment viewer.


Saving your results

To save the structure,

  • in iCN3D, go to File > Save File and choose your preferred file type.
  • in the Cn3D viewer select File > Save As or Export as PNG, and save the file to your computer.

To save any intermediate step in the process, click on the Send to drop-down menu at the upper right and select Collections. You will be prompted to log in to or register for an NCBI account; once you are logged in, you can create a new collection or append the search to an existing collection.