UserGuide:Gene Page

From WormBaseWiki
Jump to: navigation, search

Gene Summary Page

The Gene Summary page provides concise information on gene identification, genetic location, function, gene ontology, available alleles, cDNAs, protein similarities, and papers that cite the gene. Most of these classes contain multiple subclasses with their descriptions and hypertext links to pages containing detailed information on particular subclasses, where available.

The following is a brief description of classes and subclasses on the Gene Summary page:

IDENTIFICATION

Brief ID: Provides a concise description that allows one to rapidly assess the gene function, expression pattern, what the gene product is, etc. Clicking on the "details" link displays a more detailed gene description, if it is available.

Species: Species of origin.

Common name: A CGC approved gene name. Genetic nomenclature for C. elegans can be found here:

Other names: Names by which the gene may also have been referred (e.g., name assigned to the gene by the sequencing consortium).

Origin: Provides the source of information from which Locus data was extracted.

Other sequence(s): Links to GenBank sequence entry(ies).

NCBI LocusLink: "LocusLink" provides a single query interface to curated sequence and descriptive information about genetic loci. It presents information on official nomenclature, aliases, sequence accessions, phenotypes, EC numbers, MIM numbers, UniGene clusters, homology, map locations, and related web sites.

"AceView" shows the alignment of mRNAs and ESTs to the genome sequence, and the genes and (alternative) transcripts reconstructed from these alignments. The genes can be viewed aligned on the genome, and as spliced mRNA variants, decorated with BLASTp homologies, PFAM and PSORT motifs Stops and Met in the 3 frames, and all supporting mRNAs and ESTs. Text descriptions of the gene and its mRNAs (with useful links) are also shown.

Gene model: Provides links to the Sequence report (Gene model) and Protein report (Protein) pages as well as SwissProt database entries, WormPep amino acid sequences and spliced/unspliced nucleotide sequences. Also contains brief information on protein similarities and domain structure.

Putative C. briggsae ortholog: Provides a link to the putative C. briggsae ortholog as well as to graphical and text alignments of the corresponding C. elegans and C. briggsae genomic regions (View Synteny).

Literature citations: Links to all papers in which the gene was cited.

Note: Specifies whether the gene has been defined mutationally (links to locus page) and has been linked to any gene models. May contain other remarks such as corrections of gene structure or the annotation method.

LOCATION

Genetic Position: Links to genetic map and mapping data.

Genomic Position: Links to physical map via genome browser. Display can be customized to include different tracks.

Part of Operon: Specifies if the gene is a part of an operon and links it to the operon report page.

Physically Mapped Clones: Links to Clone Report pages for clones to which the gene was mapped.

Genomic Environs: Graphical view of the physical map. Clicking on the image redirects you to the physical map page like Genomic Position link does.

FUNCTION

Mutant Phenotype: Mutant phenotypes for studied alleles are presented. Publications from which the data were extracted are cited.

RNAi Phenotype: Phenotype(s) produced by dsRNA interference. These could be derived from either large-scale RNAi screens or experiments that targeted the gene specifically, or both.

Anatomic Expression Pattern: Documents gene expression based on GFP reporters, antibodies, in situ hybridization, etc. These could include subcellular localization.

Affymetrix Microarray Expression Data: Gene expression analysis based on microarray experiments using Affymetrix chips.

SMD Microarray Expression Data: Gene expression analysis based on microarray experiments using Stanford Microarray chips.

Microarray Topology Map: Links to the three-dimensional expression map that displays correlations of gene expression profiles as distances in two dimensions and gene density in the third dimension. The gene expression map can be used as a gene discovery tool to identify genes that are co-regulated with known sets of genes or to uncover previously unknown genetic functions.

For more information on the topology map, visit: http://cmgm.stanford.edu/~kimlab/topomap/c._elegans_topomap.htm

Protein Domains: List of detected Pfam and InterPro sequence motifs.

GENE ONTOLOGY CLASSIFICATION

The goal of the Gene Ontology project is to produce a dynamic controlled vocabulary that can be applied to all organisms even as knowledge of gene and protein roles in cells is accumulating and changing. The three organizing principles of GO are biological process, cellular component and molecular function.

Biological Process: Describes broad biological goals, such as mitosis or purine metabolism, that are accomplished by ordered assemblies of molecular functions.

Cellular Component: Describes subcellular structures, locations, and macromolecular complexes such as nucleus, telomere, and origin recognition complex.

Molecular Function: Describes the tasks performed by individual gene products; examples are transcription factor and DNA helicase. For more information on GO, visit:

http://geneontology.org

ALLELES

Reference Allele: Most often the mutation that has been studied in greatest detail. Usually, though not always, the reference allele is the allele with the strongest and most obvious effects. As a result, in a few cases the reference allele is a gain-of-function allele, but most often it is the strongest known loss-of-function allele. In cases where both viable and lethal alleles are available, it will usually be the strongest viable allele. Also known as canonical allele.

Alleles: Other known alleles of the gene.

Strains: Genetic strains that are available from CGC.

SIMILARITIES

List of best BLAST matches using the longest protein product as a query. Links to identified sequences are provided together with brief descriptions, E-values and consensus length.

REAGENTS

Transgene Strains: Strains carrying chromosomally integrated arrays. These could be reporter arrays, overexpression arrays, arrays carrying a mutated gene, etc.

Primer Pairs: List of primers that amplify part of the gene or complete gene. Usually are designed by the ORFeome project or are used in SMD Microarrays.

Matching cDNA: List of available cDNA clones.

BIBLIOGRAPHY

List of literature that cited the gene. This list could contain both published papers and unpublished results such as meeting abstracts.