Functional Analysis: Difference between revisions
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=== Annotation-based Co-occurring Motif Pattern === | === Annotation-based Co-occurring Motif Pattern === | ||
[http://www.cisred.org/mouse3/mouse3/pattern?pattern_id=295&m=399392&pattern_name=295%20(POU2F1__Pax-6)&g=&c=pou2f1-pax6] | |||
[http://www.cisred.org/mouse3/mouse3/pattern?pattern_id=295&m=399392&pattern_name=295%20(POU2F1__Pax-6)&g=&c= | |||
[http://www.cisred.org/mouse3/pattern?pattern_id=14&c=200999&pattern_name=AIRE__FOXJ2&g=&m= aire-foxj2] | [http://www.cisred.org/mouse3/pattern?pattern_id=14&c=200999&pattern_name=AIRE__FOXJ2&g=&m= aire-foxj2] | ||
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[http://www.cisred.org/mouse3/mouse3/pattern?pattern_id=1574&m=181562&pattern_name=1574%20(IPF1__POU1F1)&g=&c= ipf1-pou1f1] | [http://www.cisred.org/mouse3/mouse3/pattern?pattern_id=1574&m=181562&pattern_name=1574%20(IPF1__POU1F1)&g=&c= ipf1-pou1f1] | ||
Revision as of 23:59, 11 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]
Results:
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.
STRING: a database of predicted functional associations between proteins. String returned no results.
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.
Pfam didn't work...http://www.sanger.ac.uk/cgi-bin/Pfam/getblast?id=2103981H86007039eB664 - protein families
Interpro returned no results - protein domain prediction.
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
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
Cis Red - The cisRED database holds conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations. regulatory elements in BC048403
