Family Report
Overview
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
and clicking the Site report help link.
- Navigate to the desired section of the report by opening the
table of contents
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:
.
- Links to display additional text within the page are indicated
by a yellow bubble, such as the show abstract link shown
here:
.
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Family Information |
Describes the characteristics of the family. |
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Related family entries |
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Orthologous relationships |
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Displays the hierarchical relationship as described in the TRANSFAC
transcription factor classification. |
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Transcription FactorClass Description |
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Provides a description for the main entries in the TRANSFAC
transcription factor classification. |
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Parent entries |
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Lists parents of the family, in other words families the family is
a member of, with hyperlinks to the corresponding Family
Reports. |
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Child entries |
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Lists children of the family, in other words members of the family,
with hyperlinks to the corresponding Family or Locus Reports. |
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Pathways & Interactions |
Displays pathways and reactions the family is associated with. |
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Pathways |
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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. |
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Interactions |
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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. |
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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. |
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Regulation of gene expression by the family |
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TRANSFAC Factor Classification |
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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. |
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Genes bound by the family |
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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. |
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Binding Region (ChIP-chip) |
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Links to the Browse by TF feature, which allows users access to
Chip-chip sequences bound by the family. |
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Consensus Binding Sequence |
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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. |
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Identifiers |
Displays the identifiers associated with the family. |
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BKL Accessions |
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Lists the identifier for the family of the page. |
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Annotations |
Displays free-text annotations added by curators to provide
additional details about the family. |
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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. |
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References |
Displays list of references cited in the Family Report. |
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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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