Help: Query Results
SOURCE contains two types of pages, Gene Reports and CloneReports.
GeneReports display information about genes including
functional, structural and expression data. GeneReports give an
overview of a gene's biology by describing its protein function, the tissue sources
of cDNA clones associated with the gene, links to microarray
experiments that included the queried gene, and the mapping of the
gene within the human genome. CloneReports display information about
a given cDNA clone (also known as an Expressed Sequence
Tag or EST) including putative ID, the size of the insert, vector
information, and links to BLAST searches and genome browsing tools. Users can
switch between the two types of reports by clicking on the button at
the top of each report page.
The gene information results of a SOURCE Query are arranged in a table. The general format for a well characterized clone is as follows.
Within the title of the Gene Information table is the unique CloneID followed by a header containing the gene's common name, with links to additional sources for summarized gene data.
These include GeneCards, and the Online Mendelian Inheritance in Man (OMIM) project.
- UniGene Section
The first section of the table lists the data compiled from the UniGene project. The first row within this section is the UniGene Build Number, identifying the date (essentially the edition) of UniGene from which the data in this table's section was obtained. The second row within this section contains the UniGene Cluster ID. The third row contains pooled expression data from the clones within this UniGene cluster. The relative abundance of the cluster's expression has been calculated for each tissue type in which it has been identified. The top ten tissues, ranked according to normalized clone abundance, are listed with an additional link to a graphical representation of the cluster's frequency of expresssion in all tissue libaries within the database. The next row within the UniGene section is a link to Gene-to-Tag Mapping from the Serial Analysis of Gene Expression (SAGE ) project at NCBI. The final row within this section contains links to the lists of microarray experiments at Stanford University which contained cDNAs within this UniGene cluster.
- SwissProt Section
The second section within the SOURCE table contains information obtained from the SwissProt database. Information within this section is entirely dependent on whether the clone of interest has been mapped to a known gene product. The SwissProt Accession Number links to the NiceProt View from SWISS-PROT. The rows following the accession number are derived from the "Comments" section within the NiceProt View. These may include information on the protein's function, subcellular localization, alternative products, tissue specificity, developmental stage, and domain similarity.
This section is for annotation provided by groups such as LocusLink and
Proteome and for controlled vocabularies such as Gene Ontology (GO). For controlled vocabularies, the table contains:
The evidence codes have the following meanings:
- the type of ontology
- the term
- a coded representation of the evidence for this annotation
- the source of the annotation
|IMP||inferred from mutant phenotype|
|IGI||inferred from genetic interaction|
|IPI||inferred from physical interaction|
|ISS||inferred from sequence or structural
|IDA||inferred from direct assay|
|IEP||inferred from expression pattern|
|IEA||inferred from electronic annotation|
|TAS||traceable author statement|
|NAS||non-traceable author statement|
- RHdb and GeneMap99
The final section within the SOURCE query results table is information from RHdb and GeneMap99, containing Radiation Hybrid Accession numbers, the human chromosome number, and physical position of the clone.
The cDNA information results of a SOURCE Query are arranged in a table. The contents of this table are obtained from NCBI's database of "Expressed Sequence Tags" (dbEST).
Within the title of the cDNA Information table is the unique CloneID.
- cDNA Clone Identifier
This table section contains information on the specific clone, including the source for obtaining it, the organism cloned from, the size of the insert, as well as the vector it in contained in.
- 3' and 5' EST Information
This table section contains EST information, including the dbEST accession number, the GenBank accession number and the documented history of the clone at both GenBank and dbEST. There are also links to perform new BLASTN and BLASTX searches at NCBI.
Because of the varying levels of EST, gene, and protein characterization, as well as the nature of the various databases that SOURCE is compiled from, results may differ from the formats described above. Although all query results should contain UniGene cluster info, queries of CloneIDs from poorly characterized genes may return Gene information results lacking additional data in the title header (gene common name, GeneCard, and OMIM links), and the Swiss-Prot and GeneMap99 sections (or both) may be absent. Queries for CloneIDs that begin with HBC or ATCC will not have any cDNA information.
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