Protein and Function Databases Tutorial 9 Protein and Function Databases
UniProt - SwissProt/TrEMBL PROSITE Pfam Gene Onltology DAVID Protein and Function Databases UniProt - SwissProt/TrEMBL PROSITE Pfam Gene Onltology DAVID
Glossary Domain A structural unit which can be found in multiple protein contexts.
Glossary Repeat A short unit which is unstable in isolation but forms a stable structure when multiple copies are present. Family A collection of related proteins.
UniProt http://www.uniprot.org/ The Universal Protein Resource (UniProt) is a central repository of protein sequence, function, classification and cross reference. It was created by joining the information contained in swiss-Prot and TrEMBL.
Protein search Uniprot input Reviewed protein
Uniprot output Sequence download Accession number Protein status organism length
Information for one protein General information annotations
GO annotation (MF, BP, CC) General keywords GO annotation (MF, BP, CC)
Alternative splicing isoforms Features in the sequence
Sequences References
Alignment for two or more proteins
MSA
Blast
Pfam http://pfam.sanger.ac.uk/ Pfam is a database of multiple alignments of protein domains or conserved protein regions.
What kind of domains can we find in Pfam? Trusted Domains Repeats Fragment Domains Nested Domains Disulfide bonds Important residues (e.g active sites) Trans membrane domains
What kind of domains can we find in Pfam? Context domains: are those that despite not scoring above the family threshold are expected to be real, based on the other domains found in the protein. Signal peptides: (indicate a protein that will be secreted) Low complexity regions Coiled Coils: (two or three alpha helices that wind around each other)
Pfam input
Domains Domain range and score
Description Structure info Gene Ontology Links
Prosite http://www.expasy.org/tools/scanprosite ProSite is a database of protein domains and motifs that can be searched by either regular expression patterns or sequence profiles.
Search Results Domains architecture
Gene Ontology (GO) It is a database of biological processes, http://www.geneontology.org/ It is a database of biological processes, molecular functions and cellular components. GO does not contain sequence information nor gene or protein description. GO is linked to gene and protein databases. The GO database is structured as a tree
Search by AmiGO
Three principal branches http://www.geneontology.org/amigo/
Directed Acyclic Graph GO structure is a Directed Acyclic Graph
GO sources ISS Inferred from Sequence/Structural Similarity IDA Inferred from Direct Assay IPI Inferred from Physical Interaction TAS Traceable Author Statement NAS Non-traceable Author Statement IMP Inferred from Mutant Phenotype IGI Inferred from Genetic Interaction IEP Inferred from Expression Pattern IC Inferred by Curator ND No Data available IEA Inferred from electronic annotation
Results for alpha-synuclein
DAVID Functional Annotation Bioinformatics Microarray Analysis DAVID Functional Annotation Bioinformatics Microarray Analysis Identify enriched biological themes, particularly GO terms Discover enriched functional-related gene/protein groups Cluster redundant annotation terms Explore gene names in batch
annotation classification ID conversion
Functional annotation Upload Annotation options