Difference between revisions of "QLanners Week 14"
From LMU BioDB 2017
(Moved information from accidents created week 13 page to this new week 14 page.) |
(reformatted what we want to sort by each database) |
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| Line 20: | Line 20: | ||
*Sequence Logo | *Sequence Logo | ||
*Frequency Matrix | *Frequency Matrix | ||
| + | |||
| + | Breakdown of what we want from all other databases:<br> | ||
| + | '''NCBI:''' | ||
| + | *Gene ID | ||
| + | *Locus Tag | ||
| + | *Also Known As | ||
| + | <br> | ||
| + | '''Ensembl:''' | ||
| + | *Gene ID | ||
| + | *Description/Function | ||
| + | *DNA Sequence | ||
| + | <br> | ||
| + | '''UniProt:''' | ||
| + | *Gene ID | ||
| + | *Protein Sequence | ||
| + | *Similar Proteins | ||
| + | <br> | ||
| + | '''SGD:''' | ||
| + | *Gene ID | ||
| + | *Expression | ||
| + | *Regulation | ||
| + | *Interaction | ||
| + | *Gene Ontology | ||
Revision as of 23:26, 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)
- Interactions with other genes
- Consensus Sequence (JASPAR)
- Expression (SGD)
- 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
SGD:
- Gene ID
- Expression
- Regulation
- Interaction
- Gene Ontology
