Documentation: Genetic Data
These data provide a range of basic information about the gene in question,
to enable firm identification and thus provide a sound basis for more detailed
consideration. The various IDs specify the gene, its transcript(s) and the protein
it encodes.
Contents
Gene Name
Mouse Ensembl ID
Human Ensembl ID
PPID
UniProt
UniGene
Gene Class
Gene Name
The common gene name.
Mouse Ensembl ID
The Ensembl ID for the mouse version of the gene. The ID acts as a link to the
Ensembl readout for the gene.
Ensembl is an annotated genome database covering a variety of eukaryotic genomes.
Ensembl IDs are unique identifiers for their genes. The database is a joint
project between the European Bioinformatics Institute (EBI) and the Wellcome
Trust Sanger Institute (WTSI). The full Ensembl database can be found at www.ensembl.org,
where it is freely available.
Human Ensembl ID
The Ensembl ID for the human version of the gene. The ID acts as a link to the
Ensembl readout for the gene.
Ensembl is an annotated genome database covering a variety of eukaryotic genomes.
Ensembl IDs are unique identifiers for their genes. The database is a joint
project between the European Bioinformatics Institute (EBI) and the Wellcome
Trust Sanger Institute (WTSI). The full Ensembl database can be found at www.ensembl.org,
where it is freely available.
PPID
The PPID for the protein encoded by the gene. The PPID acts as a link to the
PPID readout for the protein.
The PPID (Protein-Protein Interaction Database) is an on-line database of protein-protein
interactions. The PPID for any gene is a unique identifier for that gene. The
database has been used to build an interaction map of the synaptic proteome.
It also fulfils a more prosaic function by displaying a wide variety of different
names for each gene, in an attempt to resolve some of the confusion surrounding
multiple gene names in the literature. The PPID database can be found at www.ppid.org;
registration is required, but the database is freely available.
Figure 1: Sample PPID linkage chart, showing actin's
interactions
UniProt
The UniProt ID for the protein encoded by the gene. The UniProt acts as a link
to the UniProt readout for the protein.
UniProt is an annotated database of protein sequences. UniProt IDs are unique
identifiers for protein sequences. The database is maintained collaboratively
by the Swiss Institute for Bioinformatics (SIB) and the European Bioinformatics
Institute (EBI). It is freely available at www.ebi.ac.uk/swissprot.
UniGene
The UniGene ID for the transcript encoded by the gene. The UniGene acts as a
link to the UniGene readout for this transcript.
UniGene is an online database of expressed sequence tags (ESTs), grouped into
gene-oriented clusters. The UniGene ID thus acts as an identifier for a given
sequence of mRNA, which is constructed from the exons of the gene in question.
The UniGene database can be found at www.ncbi.nlm.nih.gov/UniGene,
where it is freely available.
Class
The class of molecule into which the protein encoded by the gene falls. The
class acts as a link to a list of all the molecules of that class in the database.
Information about classes is derived from 16236029,
'Collins MO, Husi H, Yu L, Brandon JM, Anderson CN, Blackstock WP, Choudhary
JS, Grant SG, "Molecular characterization and comparison of the components and
multiprotein complexes in the postsynaptic proteome", J Neurochem, 2005 Oct
17. This paper describes various proteomic strategies designed to obtain a
definitive list of the proteins in the post-synaptic density (PSD). It then
classifies these proteins, principally according to their function. The same
classification system is used here. The categories are listed in the table below.
Protein Classes
|
Channels and Receptors |
Ca2+ ATPases
Ca2+ release channels
Glutamate receptors
Na+ channel
Na+/K+ ATPases
Voltage-dependent anion channels
Voltage-gated K+ channel
Voltage- and ligand-gated Ca2+ channel
Other channels and receptors
Other ligand receptors |
| MAGUKs / Adaptors / Scaffolders |
PDZ-domain-containing scaffolders
Non-PDZ-domain-containing scaffolders
14-3-3 |
| Signalling Molecules and Enzymes |
Adenylate/Guanylate Cyclase
ATP Synthases
Development
Heat Shock / Chaperones / Chaperonins
NADH-Ubiquinone Oxidoreductase
Phosphodiesterases
Polyubiquitin
Proteases
Secreted / Secretory Signalling
Other signaling molecules
Other enzymes |
| Transcription and Translation |
Elongation factors
Ribosomal proteins
Transcription elements |
| Cytoskeletal and Cell Adhesion |
Actin / ARP
Actinin
Catenins
Cell Recognition Molecules
Keratins
MAPs
Myelin
Spectrin
Tubulin
Other Cell Adhesion Molecules
Other Cytoskeletal Proteins |
| Synaptic Vesicles / Protein Transport |
Clathrin
Motor proteins
Synaptic Vesicle
Transporters |
| G-proteins and Modulators |
G-proteins
Modulators |
| Ser/Thr Kinases |
|
| Tyr Kinases |
|
| Protein Phosphatases |
|
| Novel |
|
