Disease Report

Overview

A Disease Report is created for each disease curated to a human protein in the Proteome module, and for each disease curated to a human transcription factor in the TRANSFAC module. Each Disease Report, presented as a web page, has different blocks for Disease Title, Disease Properties, and References. The Disease Properties block contains links to Property Reports that display additional, referenced annotations supporting the observations.


Access to Disease Reports

When a human gene, protein, or antibody has been curated as being associated with a disease, a Disease Report for that disease may be accessed through the link provided in the Biomarker Associations section of the Locus Report, or from the Property Report. The Disease Property Report is accessible by clicking the [details] link on the Locus Report.

When a mouse protein has been curated as being a model for a disease, and a Disease Report exists for that disease, the Disease View Report may be accessed through the link provided in the Mutant Phenotype Property Report for the protein's Locus Report. The Mutant Phenotype Property Report is accessible by clicking the [details] link on the Locus Report. 


Please note: BKL subscribers who have licensed the PROTEOME and PGMD modules will see the full complement of information available in a Disease Report. BKL subscribers who have licensed only part of the BKL will see subsets of information, depending on the subscription. The combined Disease Report for subscribers of the complete BIOBASE Knowledge Library is described below.


Disease Reports may also be accessed through the Disease Quick Search feature and the Disease Advanced Search function within the BKL Tools.


Anatomy of a Disease Report

The general structure of a Disease Report is shown below.

  • Access help by clicking the help menu  help  and clicking the Disease 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  .


Introduction Provides a description and synonyms for the disease help
Description
A concise, one-sentence description of the protein, including relevant aspects of a protein's role or function in the cell. Title lines begin with a name phrase, followed by a description of the protein's function and/or the process or pathway in which it is involved, followed by disease information when available for human, mouse, and rat proteins. In the absence of literature-supported functional or disease information, domains and family membership are noted. Subcellular localization, regulation, splicing patterns, and expression patterns are included when pertinent or in the absence of additional information. Title lines that appear on Locus Reports originate from the Proteome Databases and are updated continually to reflect the current literature.
Synonyms
Lists synonyms for the gene and protein, including additional names and abbreviations, separated by semicolons.

Biomarker Associations Displays a tabular summary of relationships between human genes, mRNAs, and proteins and human disease processes. The first five entries are shown, and subsequent entries can be viewed ten at a time. To view subsequent entries, the user can click on the box indicating the set of ten entries they would like to see. Click [View all] to view all entries. Data may be alternately sorted by clicking on the column header. Click [details] or on a checkmark to view a tabular breakdown of the data supporting the disease-protein associations represented by that section. Click the name listed in the Gene/Protein column to open the corresponding Locus Report. Click [hide] to remove curation from view and [show] (not displayed here) to return curation to view. The number of protein-disease relationships represented by each section is shown under each gene/protein name, under each relationship heading, and next to each checkmark.
Type of Association
Categories listed here describe the types of relationship reported between the protein and a disease.
Causal
Indicates a causal relationship between the protein and the disease and can be either confirmed or hypothetical. A tabular breakdown of the data supporting the linkage with each disease (including cited references) is accessible by clicking on [details], which opens a Property Report. The MeSH description of each disease is accessible from the Property Report.
Correlative
Indicates a correlative relationship between the protein and the disease and can be either confirmed or hypothetical. A tabular breakdown of the data supporting the linkage with each disease (including cited references) is accessible by clicking on [details], which opens a Property Report. The MeSH description of each disease is accessible from the Property Report.
Preventative
Indicates a preventative relationship between the protein and the disease and can be either confirmed or hypothetical. A tabular breakdown of the data supporting the linkage with each disease (including cited references) is accessible by clicking on [details], which opens a Property Report. The MeSH description of each disease is accessible from the Property Report.
Negative
Indicates a negative relationship between the protein and the disease, including negative relationships from all categories listed above. A tabular breakdown of the data supporting the linkage with each disease (including cited references) is accessible by clicking on [details], which opens a Property Report. The MeSH description of each disease is accessible from the Property Report.
Indication
Categories listed here describe what the protein/disease association might indicate about the utility of the biomarker.
Disease Mechanism
Indicates that this protein has been reported to provide information on the mechanism behind the disease. A tabular breakdown of the data supporting the linkage with each disease (including cited references) is accessible by clicking on [details], which opens a Property Report.
Prognosis
Indicates that this protein has been reported to provide information on the progression or severity of a disease. A tabular breakdown of the data supporting the linkage with each disease (including cited references) is accessible by clicking on [details], which opens a Property Report.
Therapeutic Target
Indicates that reports on this protein suggest a use as a target for treatment of this disease. A tabular breakdown of the data supporting the linkage with each disease (including cited references) is accessible by clicking on [details], which opens a Property Report.

Clinical Trials Displays a tabular summary of clinical trials for which the disease is under investigation. All data is taken from ClinicalTrials.gov, then mapped to BKL disease and drug entities using text-based strategies. For an entry to appear in the BKL, the text within the ClinicalTrials.gov Condition field must match a name or synonym of a BKL disease and the text within the Intervention field must be of type "Drug" and must match a name or synonym of a BKL drug. The first five entries are shown, additional entries can be viewed by clicking the [more �] link. Entries may be sorted by clicking on the column headers.  
Drug
Lists the BKL drug entity that has been mapped to the ClinicalTrials.gov Intervention field. The corresponding BKL Drug Report is accessed by clicking the entry.
Phase
Lists the phase of the clinical trial.
Study Title
Lists the title of the clinical trial. Mousing over the information icon displays an overview of the trial. Click the link provided to view the full entry for the trial at the clinicaltrials.gov site.
Status
Lists the status of the clinical trial.
Start Date
Lists the start date of the clinical trial.
End Date
Lists the end date of the clinical trial.

Association Characteristics  
Subtypes or forms of the disease
Identifies symptoms or additional disease states associated with the disease of the page. Annotations describing the relationship between each characteristic and the individual protein(s) involved are accessible by clicking on [details], which opens a Property Report.
Biological processes affected by the disease
Identifies alterations in the biological process associated with the disease of the page. Terms are derived from the Gene Ontology, a hierarchical classification system used to describe protein attributes. Annotations describing the relationships between each characteristic and the individual protein(s) involved are accessible by clicking on [details], which opens a Property Report.
Cell types or tissues affected by the disease
Provides a list of cell and tissue types in which expression of a protein, or its underlying transcript, is altered (or not altered) when diseased cell and tissue types are compared to non-diseased cell and tissue types. Annotations describing the particulars of each alteration, or lack of alteration, in expression pattern, and the protein(s) involved, are accessible by clicking on [details], which opens a Property Report.
Diseases associated with the disease
Lists additional diseases for which the disease of the page may be associated with. Annotations describing the relationship between each characteristic and the individual protein(s) involved are accessible by clicking on [details], which opens a Property Report.

Disease Similarity Inferred disease-disease relationships on the basis of shared causal biomarker genes. A disease vicinity network visualizes clusters of diseases with apparent biomedical relevance. A link to a heatmap illustrates connections between causal biomarker genes and clustered diseases. The table displays the strongest associations first, ranked by the lowest false discovery rate (More details...). The first five entries are shown by default, additional entries can be viewed by clicking the [more ...] link. Entries may be sorted by clicking on the column headers.  
Disease
The name of the associated disease. The corresponding BKL Disease Report is accessed by clicking the entry.
MeSH ID
Identifier of MeSH ontology heading.
MeSH relationship
Description whether a disease is also parent or child within the MeSH hierarchy
Overlap (common biomarkers)
The number of shared causal biomarker genes.
False discovery rate (FDR)
Adjusted p-value indicating the false discovery rate.

Biomarker Search Tool Allows user to retrieve a list of biomarkers for Export or Pathfinder viewing. Clicking the Search button will retrieve the full list of proteins associated with the disease of the page. The user can focus this list of biomarkers based on causality, molecule type, or expression in secreted substances by clicking the check box next to the desired criteria and choosing the desired term from the drop-down menu, then clicking on the Search button The search output will allow the user to export the biomarker list, load the biomarkers onto the pathfinder, or perform additional searches within the list.  

Mouse Models  
Mouse genes that provide a model for the disease when knocked out
Provides a list of mouse proteins for which a knockout mutation of the corresponding gene produces an experimental model for the disease. A summary of findings associated with the disease model are accessible by clicking on [details], which opens a Property Report.

Identifiers Displays BIOBASE accession numbers and MeSH IDs  
BIOBASE accession
Displays the BIOBASE accession number.
MeSH
Displays the MeSH ID.

References  
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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