FlyBase:Metabolic Pathway Report
Last Updated: 30th November 2024
The ‘Metabolic Pathway Report’ is a sub-category of our Gene Group resource, which houses functional collections of genes such as complexes and gene families. ‘Metabolic Pathway Reports’ are compiled manually by FlyBase curators based on a review of representations at expert metabolic databases, Gene Ontology (GO) annotations and the research literature. Each report list genes that have been experimentally shown or predicted to act within a pathway, together with buttons to export these genes to: (i) our ‘Batch Download’ tool, if you wish to download associated data (phenotypes, expression data, protein interactions etc.); (ii) a standard FlyBase HitList, if you want to further refine or analyse the gene list; or (iii) our ortholog tool, to obtain a list of predicted orthologs. Two visual representations of the pathway are provided: a "text-book" representation (Pathway Thumbnail) manually drawn by FlyBase curators, and a GO-Causal Activity Model that is based directly on GO annotation data. In addition, there are links to pathway representations at external resources (typically FlyCyc, Reactome and KEGG) and source publications.
Below is a field-by-field guide to the information provided in the Pathway Report.
General Information
| Name | The FlyBase full name for the Pathway Group. |
| Symbol | The FlyBase symbol for the Pathway Group. |
| Date last reviewed | Date that the Pathway was created or last reviewed, in format 'YEAR-MONTH-DAY'. |
| Species | The species for which the Pathway has been compiled. (This is always D. melanogaster.) |
| FlyBase ID | The unique identifier for the FlyBase Pathway Group (FBgg number). |
| Number of members | The number of genes in the Pathway Group. |
Description
| Description | A short textual description of the pathway, written by FlyBase curators based on the given reference(s). References are hyperlinked to their respective Reference Report in FlyBase or to PubMed. This section also includes a Pathway Thumbnail, a “textbook” visual representation of the pathway, made by FlyBase through a review of the current literature and expert databases. The thumbnails are downloadable in an svg format, and the style is consistent across the different Metabolic Pathway Reports. Users may download these images and adapt them in graphics editor (e.g. Adobe Illustrator). |
| Notes on Group | Describes any ‘edge cases’ where the inclusion/exclusion of a specific gene is unclear or debated. This includes listings of uncharacterised paralogs. |
| Source Material | Mini-citations of the primary references, hyperlinked to their respective Reference Reports, used to compile the pathway. |
Key Gene Ontology (GO) terms
| Biological Process | Term(s) from the Biological Process branch of the Gene Ontology that are most relevant to the pathway, hyperlinked to the respective FlyBase 'Term Report'. This term, or a child of it, is used to annotate most/all member genes. |
| Cellular Component | Term(s) from the Cellular Component branch of the Gene Ontology that are most relevant to the pathway, hyperlinked to the respective FlyBase 'Term Report'. This term, or a child of it, is used to annotate most/all member genes. |
Related Gene Groups
| Parent group(s) | Any immediate parent pathways within FlyBase are shown here, hyperlinked to their respective Report. |
| Component group(s) | Any immediate child pathways within FlyBase are shown here, hyperlinked to their respective Report. |
| Other related group(s) | Any non-protein complex groups within FlyBase that are related to the current pathway but not through a parent-child relationship (e.g. immediate upstream/downstream pathways) are shown here, hyperlinked to their respective Report. |
| Protein Complex group(s) | Any protein complex groups within FlyBase that act in the featured pathway but not through a parent-child relationship are shown here, hyperlinked to their respective Report. |
GO Causal Activity Model (GO-CAM)
A manually constructed, interactive view of the pathway generated by manual connection of indiviudal GO annotations. See Introduction to GO-CAMs for more information.
Members
The Members table lists all member genes of the current Pathway and any sub-pathways - sub-pathways are partitioned into individual subsections, the title bar of which is hyperlinked to the Pathway Report for that subgroup. Member genes are listed alphabetically within each subsection.
For all members
| View Orthologs | Runs the list of genes through the QuickSearch Orthologs tool, and displays a list of orthologs from human and several different model organisms. |
| Export to HitList | Export all genes in the Members Table to a standard FlyBase HitList, which allows further refinement and analysis of the gene list. |
| Export to Batch Download | Export all genes in the Members Table to the FlyBase 'Batch Download' tool, which allows bulk download of any associated data fields. |
GO ribbon stack
Each row or 'ribbon' is a graphical summary of a gene product's properties and depth of characterization. The data used to populate ribbons are derived from the Gene Ontology (GO) terms associated with the gene, divided into aspects of molecular function, biological process and cellular component. The GO annotations are grouped under high-level summary categories and are presented as colored cells in the ribbon. The depth of color of each cell indicates how many unique terms are grouped in a particular category. The unique terms that group under a particular cell can be seen by mousing-over or clicking on the cell. Some terms may group under more than one cell because the GO allows multiple ancestry. By stacking the ribbons for each gene in the members table, an at-a-glance comparison of member genes is presented. For more details on how the ribbons are generated see Gene Report - Function.
Members Table
The table can be customised to order and display information of interest. Columns can be added or removed using the 'Show/Hide Columns' button and arranged horizontally by dragging columns. To sort vertically on the data in the column, mouse-over the column header and use the arrow button. The column header text box can be used to only display the genes that have matching text in the column field. By default, the first six columns listed below are shown. Click the 'Reset' button to the default column display.
| Gene Symbol | The FlyBase symbol for the gene, hyperlinked to the Gene Report for that gene. |
| Gene Name | The FlyBase full name for the gene. |
| Also Known As | A list of up to five commonly used symbol synonyms for the gene. (This list is made computationally, based on the frequency of alternative symbols that have been curated from the literature.) |
| Source Material for Membership | The reference(s) that state a specific gene is a member of this particular Gene Group, hyperlinked to the Reference Report for that reference. |
| Gene Groups | Gene Groups to which gene belongs. |
| Other pathways | Other FlyBase Signaling or Metabolic Pathway groups that the gene has been associated with. |
| # All Research Refs | Number of research publications that discuss the gene in any context. |
| Antibody | Indicates whether an antibody to the gene product has been curated by FlyBase. Links to Stocks and Reagents section of the Gene report which contains an Antibody Information subsection. |
| Classical/Insertion Alleles | Number of classical and insertion alleles for gene. Links to Alleles, Insertions and Transgenic Constructs section of the Gene report which contains a Classical and Insertion Alleles subsection. |
| Transgenic Constructs | Number of transgenic constructs for gene. Links to Alleles, Insertions and Transgenic Constructs section of the Gene report which contains a Transgenic Constructs subsection. |
| Disease Models (experimental) | List of diseases showing human disease(s) that are being modelled by a given mutant or transgenic allele. A more detailed table is available on the Disease Ontology (DO) Annotations section of the Gene report. |
| Potential Disease Models | List of diseases showing human disease(s) that are associated with the human ortholog of the given D. melanogaster gene (only when ortholog calls are supported by at least 3 algorithms). A more detailed table is available on the Disease Ontology (DO) Annotations section of the Gene report. |
| Human orthologs | Orthology calls between D. melanogaster and human, as provided by the DRSC Integrative Ortholog Prediction Tool (DIOPT). Only ortholog calls supported by at least 3 algorithms are shown. |
| Testis-Specificity Index | The testis-specificity index as calculated by Vedelek et al., 2018 from modENCODE tissue expression data. The scores indicate the degree of testis bias in expression and range from -2.52 (underrepresented) to 5.2 (very high testis bias). |
| Enzyme Name (EC) | The systematic name(s) for an enzyme together with its Enzyme Commission (EC) number(s). These data are derived from our Gene Ontology (GO) Molecular Function annotations by using the EC cross-references within the GO. Each EC number is linked to the corresponding page at the ExPASy ENZYME database. |
| GO Molecular Function (Experimental) | Any Molecular Function term or terms from the Gene Ontology (GO) that have been assigned to the gene based on experimental evidence (this may or may not relate the gene product's activity in the featured pathway). The exact term 'protein binding' (GO:0005515) has been excluded, as it has little meaning without display of the interacting partner. |
| GO Molecular Function (Non-Experimental) | Any Molecular Function term or terms from the Gene Ontology (GO) that have been assigned to the gene based on non-experimental evidence e.g. sequence similarity (this may or may not relate the gene product's activity in the featured pathway). The exact term 'protein binding' (GO:0005515) has been excluded, as it has little meaning without display of the interacting partner. |
| Cytogenic Map | A computed cytological location, based on the position on the genome to which the gene maps. See Computed cytological data for a detailed description of how this computed cytological location is calculated. |
External Data
| Other resource(s) | The name of other specialist websites (typically FlyCyc, Reactome and KEGG) that represent the equivalent Drosophila pathway, hyperlinked to that resource. Note that the Drosophila pathways shown at these resources are computed using different methods and may therefore differ from the manually curated and verified pathway shown above. |
Synonyms and Secondary IDs
| Synonyms(s) | Alternative commonly used symbols/names used in Drosophila literature and/or the wider field to refer the pathway. |
| Secondary FlyBase ID(s) | Any non-current FlyBase Gene Group ID(s) (FBgg numbers) that have been used previously to refer to the Pathway Gene Group but which have retired for some reason (e.g. a new FBgg number is assigned if two or more Gene Groups are merged, or if a single Gene Group is split into separate groups). |
References
The full citations of all references used to compile the pathway, organised by publication type, and hyperlinked to their respective Reference Reports.