Difference between revisions of "QLanners Week 14"
From LMU BioDB 2017
(added another item from uniprot) |
Kdahlquist (talk | contribs) (update SGD gene IDs) |
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'''SGD:''' | '''SGD:''' | ||
*Gene ID | *Gene ID | ||
| + | ** ''Standard Name'', i.e., ''HSF1'' | ||
| + | ** ''Systematic Name'', i.e., ''YGL073W'' | ||
| + | ** ''SGD ID'', i.e., ''S000003041'' | ||
*Regulation | *Regulation | ||
*Interaction | *Interaction | ||
*Gene Ontology | *Gene Ontology | ||
Revision as of 23:32, 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
- Sequence Logo
- Frequency Matrix
Breakdown of what we want from all other databases:
NCBI:
- Gene ID
- Locus Tag
- Also Known As
Ensembl:
- Gene ID
- Description/Function
- DNA Sequence
UniProt:
- Gene ID
- Protein Sequence
- Similar Proteins
- Protein Type/Name
SGD:
- Gene ID
- Standard Name, i.e., HSF1
- Systematic Name, i.e., YGL073W
- SGD ID, i.e., S000003041
- Regulation
- Interaction
- Gene Ontology
