Functional Analysis

Gaf Domain

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 Analysis

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

String returned no results.

Pfam didn't work...http://www.sanger.ac.uk/cgi-bin/Pfam/getblast?id=2103981H86007039eB664

Profunc http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=ay41&code=073806

Interpro 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.

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

[http://www.cisred.org/mouse3/mouse3/pattern?pattern_id=295&m=399392&pattern_name=295%20(POU2F1__Pax-6)&g=&c=

pou2f1-pax6]

aire-foxj2

pax6-pax6

pou1f1-pax6

ipf1-pou1f1