Difference between revisions of "JP Mar 17 16"
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Wrote our first status report after our oral presentation on the 15th. | Wrote our first status report after our oral presentation on the 15th. | ||
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GO Slim: | GO Slim: | ||
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Want to map the whole transcriptome (relative expressions?) GO Slim terms and compare to gene of interest (relative expression?) GO Slim terms. | Want to map the whole transcriptome (relative expressions?) GO Slim terms and compare to gene of interest (relative expression?) GO Slim terms. | ||
| − | + | Wrote a code to extract gene id from a list of given gene names. Needed to manually search the gene id for the translated POUFs. | |
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| + | Resources: | ||
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| + | Generic GO term Mapper: | ||
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| + | http://go.princeton.edu/cgi-bin/GOTermMapper | ||
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| + | using the goslim_generic.obo from the OWLTools page: http://www.geneontology.org/ontology/subsets/goslim_generic.obo | ||
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| + | *nothing | ||
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| + | Using generic human given by website | ||
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| + | *this looks promising | ||
| − | Map2Slim option in OWLTools: "Given a GO slim file, and a current ontology (in one or more files), the Map2Slim script will map a gene association file (containing annotations to the full GO) to the terms in the GO slim. | + | |
| + | Map2Slim option in OWLTools: "Given a GO slim file, and a current ontology (in one or more files), the Map2Slim script will map a gene association file (containing annotations to the full GO) to the terms in the GO slim. | ||
| + | |||
| + | *this doesn't work on school computers | ||
http://geneontology.org/page/go-slim-and-subset-guide | http://geneontology.org/page/go-slim-and-subset-guide | ||
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| + | CateGOrizer | ||
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| + | http://www.animalgenome.org/bioinfo/tools/catego/ | ||
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| + | g: | ||
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| + | http://biit.cs.ut.ee/gprofiler/gconvert.cgi | ||
Latest revision as of 18:54, 17 March 2016
Wrote our first status report after our oral presentation on the 15th.
GO Slim:
Want to map the whole transcriptome (relative expressions?) GO Slim terms and compare to gene of interest (relative expression?) GO Slim terms.
Wrote a code to extract gene id from a list of given gene names. Needed to manually search the gene id for the translated POUFs.
Resources:
Generic GO term Mapper:
http://go.princeton.edu/cgi-bin/GOTermMapper
using the goslim_generic.obo from the OWLTools page: http://www.geneontology.org/ontology/subsets/goslim_generic.obo
- nothing
Using generic human given by website
- this looks promising
Map2Slim option in OWLTools: "Given a GO slim file, and a current ontology (in one or more files), the Map2Slim script will map a gene association file (containing annotations to the full GO) to the terms in the GO slim.
- this doesn't work on school computers
http://geneontology.org/page/go-slim-and-subset-guide
CateGOrizer
http://www.animalgenome.org/bioinfo/tools/catego/
g:
