Complex Report

Overview

Complex Reports contain information about complexes of molecules (proteins and small molecules) that play regulatory roles in signaling pathways.

Each Complex Report is similarly organized and comprises different blocks for properties curated and references cited in the Report. Other BKL Reports mentioned in the Complex Report are hyperlinked to the corresponding Reports. For example, protein and small molecules subunits of the complex are listed on the Complex Report, with links to their corresponding Locus and Small Molecule Reports, respectively.

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

Anatomy of a Complex Report

The general structure of a Complex Report is described below.

• Access help by clicking the help menu    and clicking the Site report help link.
  
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• 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.
  
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• Links to external resources are indicated by a blue bubble, such as the PubMedID link shown here:    .
  
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• Links to display additional text within the page are indicated by a yellow bubble, such as the show abstract link shown here:    .
  

Complex Information Describes the characteristics of the complex. Composition of the complex Subunits Identifies the subunits of the complex, with hyperlinks to the corresponding Locus and Small Molecule Reports. Also includes numbers that indicate how many molecules of each subunit comprise the complex, when the information is provided in the scientific literature. Modified forms Lists the number of known modified forms for the complex.

Pathways & Interactions Displays pathways and interactions the complex is associated with.   Pathways Identifies pathways and chains the complex 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. Interactions Displays reactions the complex is associated with. Identifies reactions the complex is involved in, with hyperlinks to the corresponding Reaction Reports. Click here for detailed information about Reactions in BKL.

Transcriptional Regulation Describes the protein binding to DNA and other transcriptional regulation activities attributed to the protein.   Regulation of gene expression Binding Sites/Regulated Genes A tabular display of genes the protein 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-seq or similar experiments) A tabular list of ChIP experiments that identified binding sites within the region of the gene, with links to the corresponding ChIP experiment report. Consensus Binding Sequence Lists the matrix logo for the matrices the protein interacts with, with hyperlinks to the corresponding TRANSFAC Matrix Reports. The first five entries are shown, click [ more ...] to view all entries. Interacting transcription factors Interacting factors Lists transcription factors that interact with the protein, hyperlinked to the corresponding Locus Reports.

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 complex.   This block displays comments from the curator common to the complex, separated by topic. For a list of topics covered in Annotations, click here.

References Displays list of references cited in the Complex 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.