miRNA Report


Overview

The miRNA Report is a specialized form of the Locus Report the is provided in two views. The Locus Report view provides information about the gene, its encoded pre-miRNA, and its processed mature miRNA(s) while the Mature miRNA Report view provides information only about the specified mature miRNA. Each miRNA Report, presented as a web page, is similarly structured across all species.


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


miRNA Reports begin with a descriptive Title Line and comprise information about the gene and its encoded and processed products, curated as Properties that can be tabulated, and as free-text Annotations. Below the Title Line and list of curated Synonyms the various topics covered in the miRNA Report are listed. Specifically, each complete miRNA Report has eight Properties blocks: Biomarker Associations, Gene Ontology, Expression, Transcriptional Regulation, RNA Features, and mRNA Targets. Each of these Properties blocks contain links to Property Reports that display additional details about the curated information. For example, a subset of Gene Ontology (GO) terms appears in the Gene Ontology block. Clicking the [details] link opens a Property Report that provides the complete list of curated terms, with details about experimental evidence and links to cited references. In addition to the Properties blocks, 3 other sections are included in complete miRNA Reports: Identifiers, free-text Annotations, and References cited. Each section is described briefly below.

Gene and miRNA symbols mentioned in the Properties and Annotations are hyperlinked to their respective Locus Reports. When a Property or Annotation mentions something for which there exists a BKL Report, a hyperlink connects between Reports.

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


Anatomy of a miRNA Report

The structure of a miRNA Report is described below. Detailed documentation for the individual BKL components is accessed from links in the menu on the left, at the top of this page.

  • Access help by clicking the help menu  help  and clicking the Locus 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  .
  • Links providing an option to download content are indicated by a green bubble, such as the FASTA link shown here:  download content  .
  • Links providing an option to send data to another tool within the BKL are indicated by a gray bubble, such as the Pathfinder link shown here:  download content  .




Introduction Provides a description and synonyms for the gene, its pre-miRNA, and processed mature miRNAs. The Mature miRNA Report view provides a description and synonyms for the specific mature form.  
Description
The Locus Report view provides a concise, one-sentence description of the gene, its pre-miRNA, and processed mature miRNAs, including relevant aspects of their role or function in the cell. Title lines begin with a name phrase, followed by a description of the miRNA'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, family membership may be noted. The Mature miRNA Report view provides the same information specific to the mature form. Title lines that appear on miRNA Reports originate from the Proteome databases and are updated continually to reflect the current literature.
Synonyms
The Locus Report view lists synonyms for the the gene, its pre-miRNA, and processed mature miRNAs, including additional names and abbreviations, separated by semicolons. The Mature miRNA Report view lists only the synonyms for the specific mature form.
Encoded products / Encoded by
The Locus Report view lists the encoded pre-miRNA stem-loop and its processed mature miRNAs. The mature miRNA names are linked to their respective Mature miRNA Report view. A description is provided for each mature form listed. The Mature miRNA Report view lists the pre-miRNA or pre-miRNAs (stem-loop) that the mature miRNA is processed from and the gene or genes that encode the pre-miRNA(s). The pre-miRNA and gene names are linked to their respective Locus Report.

Biomarker Associations Displays a tabular summary of literature-derived relationships between human miRNAs and human disease processes. The first five entries are shown; click [more ...] to view all entries. Data may be alternately sorted by clicking on the column header. Click on the # associations link to view a tabular breakdown of the data supporting the disease-miRNA associations represented in each section. Click the disease entry listed in the Disease column to open the corresponding Disease View Report. In the Locus Report view, disease-miRNA associations are provided by default in a summary table with attribution to the specific mature form when possible. When not possible, based on the original publication not being specific about the mature form being studied, the attribution is assigned to mature form undetermined. Click one of the yellow, detailed view buttons below the summary table to display the detailed view for a specific form. In the Mature miRNA Report view the detailed view is provided by default. The detailed view is described below. In cases where the miRNA of the page shares the same or more specific disease association with at least one of its targets, two additional columns will be added to the summary table of the Locus Report view and an additional table will be added to the Mature miRNA report view. These columns/tables indicate the change in miRNA and relevant target(s) expression in the disease state compared to the normal state. A change in expression is only noted if a "may" qualifier is not part of the original curated statement.  
Type of Association
Categories listed here describe the types of relationship reported between the miRNA and a disease.
Causal
Indicates a causal relationship between the miRNA 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 miRNA 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 miRNA 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 miRNA 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 miRNA/disease association might indicate about the utility of the biomarker.
Disease Mechanism
Indicates that this miRNA 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 miRNA 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 miRNA 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.
Inherited Mutations
Provides a link to the Human Gene Mutation Database (HGMD) report for the gene with an overview of the mutation counts contained within. Note that access to HGMD requires a separate subscription.

Pharmacogenomic Variants This section lists the drugs that have been recorded in Drugbank as targeting the protein of interest, or are metabolized by the protein of the interest. Drugs are listed in alphabetical order.  
Drugs targeting the protein
Lists Drugbank drugs which target the protein, with links to the corresponding drug report.
Drugs metabolized by the protein
Lists Drugbank drugs which are metabolized by the protein, with links to the corresponding drug report.

Gene Ontology Gene Ontology (GO) is a hierarchical classification system used to describe miRNA attributes. More than one term indicates that the miRNA has multiple attributes not adequately described by a single term. In the Locus Report view a summary table is provided with attribution to the specific mature form when possible. When not possible, based on the original publication not being specific about the mature form being studied, the attribution is assigned to mature form undetermined. In the Mature miRNA Report view the assigned attributes are listed directly.  
Molecular function
Describes the biochemical activity of the miRNA. Additional information about function is accessible by clicking on [details], which opens a detailed Property Report.
Biological process
Describes the biological "objective" to which the miRNA contributes. Additional information about role is accessible by clicking on [details], which opens a detailed Property Report.
Cellular component
Identifies the place in a cell where the miRNA is active. Additional information about localization is accessible by clicking on [details], which opens a detailed Property Report.

Expression Spatial patterns of miRNA expression during the development and maintenance of a multicellular organism and regulation of that expression. In the Locus Report view a summary table is provided with attribution of the pattern to the specific mature form when possible. When not possible, based on the original publication not being specific about the mature form being studied, the pattern is assigned to mature form undetermined. In the Mature miRNA Report view the assigned patterns are listed directly.  
Tissue Expression
Organ/Tissue
Describes expression of human, mouse, or rat miRNA in organs and tissues. Additional details, including experimental methods, are accessible by clicking on [details], which opens a detailed Property Report.
Cell Type
Describes expression of human, mouse, or rat miRNA in specific cell types. Additional details, including experimental methods, are accessible by clicking on [details], which opens a detailed Property Report.
Tumor Type
Describes expression of human, mouse, or rat miRNA in specific tumor types. Additional details, including experimental methods, are accessible by clicking on [details], which opens a detailed Property Report.
Regulation of Gene Expression
Identifies proteins, complexes, or pathways that regulate the expression of the gene or genes that encode the pre-miRNAs which are processed into the mature miRNAs - either directly or indirectly.
Proteins, complexes, or pathways that influence expression
Identifies proteins, complexes, or pathways that regulate the expression of the gene, with hyperlinks to the corresponding Reports. Additional details, including the observed changes in expression and the cited references, are accessible by clicking on [details], which opens a detailed Property Report.

Transcriptional Regulation Describes features of the gene that contribute to its regulation, including the regulatory factors that regulate the gene. Clicking the icon loads the gene and its regulators into the BKL Pathfinder.  
Regulation of the gene's expression
Promoter
Displays hyperlinks to Promoter Reports that correspond to the gene. The provided Match link allows you to directly initiate a Match analysis for predicted transcription factor binding sites within the associated promoter(s). Clicking the Match link opens a dialog box where you are asked to specify whether you wish to analyze all promoters or only the best-supported promoter, the sequence window to be analyzed, and the profile to be used. Results are returned in a new window. For more information about Match or about promoters, please see the Match overview and Promoter Report overview respectively. For IP-only and installed customers, please note that access to the Match feature requires login. If you have not already done so before clicking the link you will be prompted to login before proceeding to the dialog box.
Regulatory Elements
Provides a graphical display of the location of transcription factor binding sites within the gene. Individual transcription factors are color coded for easy location within the Binding Sites and Composite Elements tables where more details are provided. Note that only transcription factors whose binding site coordinates are relative to the TSS (Transcription Start Site) are graphically displayed, while all binding sites are represented in the tabular display.
Transcription factor binding sites
A tabular display of the transcription factor binding sites within the gene, with hyperlinks to the corresponding Site Reports. Also provides the location of the binding site, the name(s) of the transcription factor(s) that bind the sites with hyperlinks to the corresponding Locus Reports, the associated DNA binding reaction, and a summary of the regulatory effect. The first five entries are shown, click [more ...] to view all entries.
Composite element binding sites
A tabular display of the composite elements sites within the gene, with hyperlinks to the corresponding Composite Element Reports. Also provides the location of the composite element, the factors that bind within the composite element with hyperlinks to the corresponding Locus Reports or Complex Reports, and a summary of the regulatory effect. The first five entries are shown, click [more ...] to view all entries.
Near by in vivo fragments
Identifies the regions bound in vivo, as determined by ChIP-Chip assays, with hyperlinks to the corresponding ChIP Fragment Reports. Also lists the names of transcription factors that bind the regions, with hyperlinks to the corresponding Locus Reports. The first five entries are shown, click [more ...] to view all entries.
Regions with characterized functionality
Describes the regions of a gene, for which functionality was shown under certain conditions, with hyperlinks to the corresponding Functional Region Reports. The first five entries are shown, click [more ...] to view all entries.

RNA Features Describes the nucleotide sequence of the mRNA, as well as the sequence information origin  
Locus Report View
Stem-loop:
Synonyms
Provides any synonyms for the pre-miRNA.
Nucleotide sequence
Provides the nucleotide sequence for the stem-loop pre-miRNA with, when relevant, the 5p mature miRNA sequence highlighted in yellow and the 3p mature miRNA sequence highlighted in pink. The seed sequence of each mature miRNA is underlined. Clicking the FASTA button allows for expore of the nucleotide sequence in fasta format. Clicking the miRBase identifier navigates to the corresponding report at miRBAse.
Genomic coordinates
Provides the chromosome, start position, end position and strand orientation of the gene relative to the hg19 reference genome. Clicking the View in UCSC genome browser button loads the coordinates into the UCSC genome browser.
Host gene
When relevant, identifies the protein coding or non-protein coding gene that the miRNA gene is located within.
miR cluster
When relevant, identifies other miRNAs that are located within 10,000 bp of each other and are potentially regulated in a coordinate manner.
miR family
When relevant, identifies the miRBase family that the pre-miRNA has been assigned to at miRBase. Clicking the Find all family members button performs a search for all entries assigned to the indicated family and displays the search results in a new window or tab.
Mature miRNA:
Synonyms
Provides any synonyms for the specified mature miRNA.
Nucleotide sequence
Provides the nucleotide sequence for the specified mature miRNA. The seed sequence is underlined. Clicking the FASTA button allows for expore of the nucleotide sequence in fasta format. Clicking the miRBase identifier navigates to the corresponding report at miRBAse.
TargetScan seed family
When relevant, identifies the TargetScan seed family that the specified mature miRNA has been assigned to at TargetScan. Clicking the Find all family members button performs a search for all entries assigned to the indicated family and displays the search results in a new window or tab.
Species conservation
Derived directly from the TargetScan seed family assignments, displays conserved mature miRNAs across human, mouse, rat, C. elegans, C. familiaris, C. griseus, D. rerio, M. mulatta, and M. nemestrina species.
 
Mature miRNA Report view
Encoding gene
Lists the gene that encodes the pre-miRNA from which the mature form is processed. If the mature form is processed from more than one pre-miRNA this section will be repeated.
Stem-loop
Lists the stem-loop pre-miRNA from which the mature form is processed. If the mature form is processed from more than one pre-miRNA this section will be repeated.
Host gene
When relevant, identifies the protein coding or non-protein coding gene that the miRNA gene is located within.
miR cluster
When relevant, identifies other miRNAs that are located within 10,000 bp of each other and are potentially regulated in a coordinate manner.
miR family
When relevant, identifies the miRBase family that the pre-miRNA has been assigned to at miRBase. Clicking the Find all family members button performs a search for all entries assigned to the indicated family and displays the search results in a new window or tab.
Nucleotide sequence
Provides the nucleotide sequence for the specified mature miRNA. The seed sequence is underlined. Clicking the FASTA button allows for expore of the nucleotide sequence in fasta format. Clicking the miRBase identifier navigates to the corresponding report at miRBAse.
TargetScan seed family
When relevant, identifies the TargetScan seed family that the specified mature miRNA has been assigned to at TargetScan. Clicking the Find all family members button performs a search for all entries assigned to the indicated family and displays the search results in a new window or tab.
Species conservation
Derived directly from the TargetScan seed family assignments, displays conserved mature miRNAs across human, mouse, rat, C. elegans, C. familiaris, C. griseus, D. rerio, M. mulatta, and M. nemestrina species.

mRNA Targets Describes the genes whose mRNAs are regulated by the miRNA.  
mRNA bound by the RNA
A tabular display of genes whose mRNA the miRNA binds, 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 mRNA, a graphical disply of the experimental methods used to determine binding, the effect of binding, as well as the quality score for the interaction. Additional experimental details can be viewed by navigating to the TRANSFAC Site Report for the binding site. The first five entries are shown, click [more ...] to view all entries.

The experimental evidence categories are organized as:

AL - predicted by algorithm
DM - DNA microarray
FA - functional analysis
MR - mRNA repression by miRNA/siRNA
NO - northern analysis
RT - RT-PCR
WE - western blot
OT - other

All experimental methods that do not fall into one of the other categories will be assigned to the OT (other) category.

Identifiers Displays internal and external identifiers associated with the gene or miRNA.  
BKL Accessions
Lists the primary and secondary identifiers for the gene and miRNA of the page.
External Identifiers
Displays hyperlinks to corresponding entries in external databases.

Annotations Displays free-text annotations manually curated from the scientific literature.  
Annotation Topics
  • Annotations compiled from the literature are presented in this view of the Locus Report for all species.
  • Each bulleted line is an free-text annotation extracted from the published, peer-reviewed scientific literature.
  • Annotations end with hyperlinked PubMed identifiers (in parentheses).
  • Reference numbers correspond to the numbered references in the References view of the Locus Report.
  • All Annotations are categorized and sorted by Annotation Topic, separated by a labeled gray bar as shown above.
  • See detailed documentation for the specific Proteome Database for information about the Annotation topics. Detailed documentation for each Proteome Database is accessible from the menu on the left, at the top of this page.
  • The first five entries are shown for each topic, click [more ...] to view all entries for the topic. Alternatively, click the 'Display all annotations' check box to view all entries for all annotation topics.

References Displays list of references cited in the Locus 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 Show abstract button which appears.

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