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TGD Help: Locus Page Help
Overview
The locus page is the portal to all information in
TGD related to a particular gene: literature, sequences, protein
annotations, its genomic location, and more. Locus pages will be updated as new information becomes available for a given gene.
Organization of the Locus Page
If information has been published about a gene, the page will be divided into two sections, such as for PDD1.
The upper half, titled CURATED INFORMATION, contains annotation TGD curators have attributed to the
gene as it has been described in the literature. The lower half, titled PROVISIONAL ANNOTATION,
contains TGD's automatic annotation of the preliminary TIGR gene model that we
have determined corresponds to the published gene. Since conflicts
may exist between the sequence described for the published gene and
the TIGR gene model, TGD is not integrating these two halves of the
page at this time. When the TIGR gene models have been finalized, TGD will begin to reconcile
differences between the published and predicted sequences, so that we
can integrate the information on these pages.
The CURATED INFORMATION section lists the following information for a gene that has been published in the literature:
- Standard Name is the published name of the gene that has been accepted by the Tetrahymena thermophila community.
- Alias may be a published name of the gene that has yet to be accepted by the Tetrahymena thermophila community or may be a non-standard name of the gene. When multiple names are published for a gene, one name is designated the standard name and the other published names are retained under Alias.
- Sequence ID is the TGDID, a unique identifier within TGD that is specific for a single item in the database.
- Feature Type indicates the type of the feature displayed on the locus page . Feature types currently include: Gene, which is used for those genes that have information published about them, and ORF (Open Reading Frame; corresponds to a stretch of DNA that could potentially be translated into a polypeptide or RNA), which is currently being used to distinguish the preliminary gene calls.
- Description contains a concise summary or description of the function and biological context of each gene
product.
- Genome Browser (GBrowse), developed by the Generic Model Organism Database (GMOD) project, is an interactive genome browser that can be customized to show selected chromosomal features as well as display user provided annotations. For help with GBrowse see the TGD general tutorial and GBrowse Help
- Literature Curation displays the most recent publication in TGD about the gene, along with any other genes (represented as gene names or TGDIDs) associated with this paper. There is also a link to additional references, and their associated genes.
- Gene Ontology (GO) annotations.
The Gene Ontology (GO) Annotations (Molecular Function, Biological Process, and Cellular Component) describe a gene's molecular functions, its role in biological processes, and its localization in cellular components or molecular complexes. Each annotation links to a page showing all Tetrahymena genes annotated to the term. The GO annotations use a controlled vocabulary, facilitating searches within TGD and across other databases.
- Retrieve Sequences provides links to the gene's sequence records at NCBI.
- Primary TGDID is a unique identifier within TGD that is specific for a single item in the database.
The PROVISIONAL ANNOTATION section lists the following information specific to automatic annotation of TIGR's preliminary gene models:
- Alias is an alternative unique identifier for TIGR's preliminary gene model given by TGD. These identifiers were given the prefix Pre(liminary)Tt to reinforce its preliminary nature.
- Sequence ID is the unique identifier for TIGR's preliminary gene model given by TIGR.
- Description is a brief description of the product of the gene model that was provided by automatic annotation by TIGR.
- Feature Type indicates the type of the feature displayed on the locus page . TIGR's preliminary gene models have the feature type ORF (Open Reading Frame; corresponds to a stretch of DNA that could potentially be translated into a polypeptide or RNA).
- Homologs. The table in this section displays the top BLAST
hits (based on E-values) resulting from a BLASTP comparison of TIGR's preliminary
gene models against various model organism databases. The the
organisms we performed our comparisons with are:
- Saccharomyces cerevisiae (SGD)
- Drosophila melanogaster (FlyBase)
- Caenorhabditis elegans (WormBase)
- Homo sapiens (IPI(HUMAN))
- Dictyostelium discoideum (DictyBase)
- Paramecium tetraurelia (ParameciumDB)
- Plasmodium falciparum (PlasmoDB)
- Toxoplasma gondii (ToxoDB)
- Cryptosporidium parvum (CryptoDB)
If no BLAST hit below 1.0e-02 was found for the gene in an organism, no results are shown for that organism.
The columns in the table indicate the following: the database that was BLASTed against, the unique identifier in the database for the hits, the description of the BLAST hit, the E-value (Expect threshold, a BLAST parameter that reflects the number of matches expected to be found by chance), % Aligned (% of length of the query protein over which it aligns with the hit protein), Source Range (the range of the query sequence, expressed as amino acid coordinates, over which it is aligned with the target sequence in the BLAST alignment) and the Target Range (the range of the target sequence, expressed as amino acid coordinates, over which it is aligned with the query sequence in the BLAST alignment).
- Genome Browser (GBrowse). See the description above.
- Domain Information displayed was determined by querying TIGR's preliminary gene models against InterPro, a database that integrates many different databases, such as PROSITE, PRINTS, Pfam, ProDom, SMART, and TIGRFAM. The gene models were queried using InterProScan, "a tool that combines different protein signature recognition methods into one resource". Additional information regarding InterProScan is available in an InterProScan Readme. The domain information includes a domain description and the InterPro ID of the hit. The InterPro ID is hyperlinked to more information about this domain in InterPro.
- Gene Ontology (GO) annotations displayed were determined by querying TIGR's preliminary gene models against InterPro using InterProScan. For more information regarding InterPro or InterProScan see the description for Domain Information above, and for more information regarding GO annotations see the description in CURATED INFORMATION above.
- Protein Physical Properties displayed includes the protein length and molecular weight of the protein along with a hyperlink to a separate Protein Information Page where additional protein information is displayed.
- Retrieve Sequences. Using the pull down menu you can view either the coding sequence or the ORF translation of the preliminary gene model.
- Primary TGDID is a unique identifier within TGD that is specific for a single item in the database.
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