Family Report


Family Reports contain information about families and subfamilies of proteins that play regulatory roles in signaling pathways or transcription factors. Family entries can be species-specific (type: "family"), i.e. they comprise related proteins (paralogs) from one species, or they can be species-inspecific, i.e. they comprise homologous proteins (orthologs) from several species (type: "orthofamily").

Each Family Report is similarly organized and comprises different blocks for properties curated and references cited in the Report. Other BKL Reports mentioned in the Family Report are hyperlinked to the corresponding Reports. For example, individual members of the family or subfamily are listed on the Family Report, with links to their corresponding Locus Reports.

Family Reports may be accessed through the BKL Tools or through hyperlinks on BKL reports.

Anatomy of a Family Report

The general structure of a Family Report is described below.

  • Access help by clicking the help menu  help  and clicking the Site report help link.

  • Navigate to the desired section of the report by opening the table of contents  toc

Points of navigation within the report are indicated by the following visual cues.

  • Links to additional reports within the BKL are presented as regular text links.

  • Links to external resources are indicated by a blue bubble, such as the PubMedID link shown here:  external link  .

  • Links to display additional text within the page are indicated by a yellow bubble, such as the show abstract link shown here:  expand content  .

Family Information Describes the characteristics of the family. help
Related family entries
Orthologous relationships
Displays the hierarchical relationship as described in the TRANSFAC transcription factor classification.
Transcription FactorClass Description
Provides a description for the main entries in the TRANSFAC transcription factor classification.
Parent entries
Lists parents of the family, in other words families the family is a member of, with hyperlinks to the corresponding Family Reports.
Child entries
Lists children of the family, in other words members of the family, with hyperlinks to the corresponding Family or Locus Reports.

Pathways & Interactions Displays pathways and reactions the family is associated with.  
Identifies pathways and chains the family functions in, with hyperlinks to the corresponding Pathway Reports. In cases where a manually-drawn pathway map is available for the associated pathway, hyperlinks are provided to the map. Click here for details about pathways and chains described in BKL.
Identifies reactions the family is involved in (i.e. events acting on the family, or events triggered by the family), with hyperlinks to the corresponding Reaction Reports. Click here for detailed information about Reactions in BKL.

Transcriptional Regulation Describes the family binding to DNA and other gene regulation activities attributed to the family. Clicking the icon loads the gene and its regulators into the BKL Pathfinder.  
Regulation of gene expression by the family
TRANSFAC Factor Classification
Provides the transcription factor classification from the TRANSFAC transcription factor hierarchy. Includes the systematic name of the factor, a link to the systematic transcription factor classification number, a description of the factor type, as well as a link to the classification number for the factor family. Clicking on a classification number takes the user to the transcription factor hierarchy.
Genes bound by the family
A tabular display of genes the family interacts with, with hyperlinks to the corresponding Locus Reports for the genes and TRANSFAC Site Reports for the binding sites. Provides information about the location of binding within the gene, as well as the quality score for the interaction. The first five entries are shown, click [more ...] to view all entries.
Binding Region (ChIP-chip)
Links to the Browse by TF feature, which allows users access to Chip-chip sequences bound by the family.
Consensus Binding Sequence
Lists the matrix logo for the matrices the family interacts with, with hyperlinks to the corresponding TRANSFAC Matrix Reports. The first five entries are shown, click [more ...] to view all entries.

Identifiers Displays the identifiers associated with the family.  
BKL Accessions
Lists the identifier for the family of the page.

Annotations Displays free-text annotations added by curators to provide additional details about the family.  
This block displays comments from the curator, regarding particular protein domains, function, mechanisms...etc. that are common to the family, separated by topic. For a list of topics covered in Annotations, click here.

References Displays list of references cited in the Family Report.  
This block gives the full citations, with titles, that correspond to the PubMed identifiers displayed. When a PubMed identifier is not available, the Medline identifier is displayed. When neither a PubMed nor Medline identifier is available, a BIOBASE-specific number is assigned preceded by a "P". Nearly all of the reference numbers are hyperlinked to the Entrez database where the abstracts may be read. All references cited in the annotations and properties section are listed, and other references known to contain information about the protein may also be listed. The first five references are shown, click [ more ...] to view all references. View abstracts via webservice, by additionally clicking the [+] which appears.

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