Difference between revisions of "QLanners Week 14"

Revision as of 23:48, 30 November 2017

Used the gene HSF1, which is a transcription factor, to determine which fields should be pulled from each database.

General info we want about each gene:

• Gene ID from each database
• Description/Function (ensembl)
• DNA Sequence (ensembl)
• Protein Sequence (UniProt)
• Locus tag (NCBI)
• Also Known As (NCBI)
• Consensus Sequence (JASPAR)
• Regulation (SGD)
• Interaction (SGD)
• Similar Proteins (UniProt)
• Gene Ontology (SGD - see if we can find it on UniProt)

We decided that from JASPAR we will pull:

• Gene ID (this will be the matrix id
• Sequence Logo
• Frequency Matrix
• also get class and family

Breakdown of what we want from all other databases:
NCBI:

• Gene ID
• Locus Tag
• Also Known As
• Also get RefSeq IDs for chromosome, mRNA, and protein.

Ensembl:

• Gene ID
• Description/Function
• DNA Sequence
• also get chromosomal location, about this gene

UniProt:

• Gene ID (Note that for UniProt, it will be a protein ID, and that there are two different ones that you need to get. — Kdahlquist (talk) 15:36, 30 November 2017 (PST)
• Protein Sequence
• Similar Proteins
• Protein Type/Name
• Please get the species from UniProt as well, even though we know it is going to be yeast.

SGD:

• Gene ID
  • Standard Name, i.e., HSF1
  • Systematic Name, i.e., YGL073W
  • SGD ID, i.e., S000003041
• Regulation
• Interaction
• Gene Ontology