Functional Analysis: Difference between revisions
MelissaBrown (talk | contribs) No edit summary |
MelissaBrown (talk | contribs) No edit summary |
||
Line 23: | Line 23: | ||
[[Locate Analysis]] | [[Locate Analysis]] | ||
STRING: a database of predicted functional associations between proteins. String returned no results. | |||
Mammalian Orthology http://www.informatics.jax.org/searches/homology_report.cgi?_Marker_key=92352 -- Genes | Mammalian Orthology http://www.informatics.jax.org/searches/homology_report.cgi?_Marker_key=92352 -- Genes | ||
Line 28: | Line 29: | ||
Mammalian Orthology http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=homologene&dopt=HomoloGene&list_uids=17580 --Proteins | Mammalian Orthology http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=homologene&dopt=HomoloGene&list_uids=17580 --Proteins | ||
Profunc http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=ay41&code=073806 | |||
CDART http://www.ncbi.nlm.nih.gov/Structure/lexington/lexington.cgi?cmd=rps - when given a protein query sequence, CDART displays the functional domains that make up the protein and lists proteins with similar domain architectures. | |||
Returns no results for mouse sequence. | |||
InPfam didn't work...http://www.sanger.ac.uk/cgi-bin/Pfam/getblast?id=2103981H86007039eB664terpro - protein domain prediction. | |||
Interpro returned no results. | Interpro returned no results. | ||
== GEGG biochemical pathways == | == GEGG biochemical pathways == |
Revision as of 00:48, 9 June 2007
New avenues in protein function prediction http://www.proteinscience.org/cgi/content/full/15/6/1527
Sequence -> Function
- Detecting Protein Function and Protein-Protein Interactions from Genome Sequences
Edward M. Marcotte, Matteo Pellegrini, Ho-Leung Ng, Danny W. Rice, Todd O. Yeates, and David Eisenberg (30 July 1999) Science 285 (5428), 751. [DOI: 10.1126/science.285.5428.751] [1]
Structure -> Function
- Proknow
Pal D and Eisenberg D. (2005). Inference of protein function from protein structure. Structure 13, 121-130. [2]
- Profunc [3]
Laskowski R A, Watson J D, Thornton J M (2005). ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res., 33, W89-W93. [4]
Using mouse sequence:
Locate http://locate.imb.uq.edu.au LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of proteins from the RIKEN FANTOM3 mouse protein sequence set. The membrane organization is predicted by the high-throughput, computational pipeline MemO. The subcellular locations were determined by a high-throughput, immunofluorescence-based assay and by manually reviewing peer-reviewed publications. Locate Analysis
STRING: a database of predicted functional associations between proteins. String returned no results.
Mammalian Orthology http://www.informatics.jax.org/searches/homology_report.cgi?_Marker_key=92352 -- Genes
Mammalian Orthology http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=homologene&dopt=HomoloGene&list_uids=17580 --Proteins
CDART http://www.ncbi.nlm.nih.gov/Structure/lexington/lexington.cgi?cmd=rps - when given a protein query sequence, CDART displays the functional domains that make up the protein and lists proteins with similar domain architectures. Returns no results for mouse sequence.
InPfam didn't work...http://www.sanger.ac.uk/cgi-bin/Pfam/getblast?id=2103981H86007039eB664terpro - protein domain prediction.
Interpro returned no results.
GEGG biochemical pathways
KEGG pathways which involve cAMP
MicroArray Analysis
Entrez gene ID 270802 1. click link to 270802 2. click link to symatlas 3. find correlated
Symatlas is a database full of microarray data for genes in different tissues. It has the function to find correlated microarray data which brings up genes with similar expression data.
The results of a correlation search give a fair few corresponding genes with similar microarray expressions, however the presence of several olfactory receptors seemed interesting : Olfr435, Olfr57, Olfr829, Olfr30.
As the structural team have found a GAF domain on the C-terminal, i tried to find a link between olfactory receptors and the GAF domain. - related to cGMP and PDEs???
Structure of the GAF domain, a ubiquitous signaling motif and a new class of cyclic GMP receptor
cis-regulatory elements
regulatory elements in BC048403
Annotation-based Co-occurring Motif Pattern
A summary of co-cooccuring patterns is in the powerpoint file
pou2f1-pax6]