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 [[http://compchembio.srcgenomics.uq.edu.au/tgdb/getEntrezGeneInfo.do?uid=270802&symbol=BC048403&description=cDNA%20sequence%20BC048403&aliases=E030027L10&organism=Mus%20musculus&chr=10&location=10%20D2 |270802] ]