MANGO is a database of genes mapped to cell types and processes that have been curated from the literature concerning adult neurogenesis. In its present state, the database is restricted to neurogenesis in the hippocampus. Although the literature contains data from several species, for the sake of uniformity, all genes in the database are reported as the mouse homologue.
Each entry corresponds to a discrete effect of a gene as reported in a single study. Thus a study may report multiple effects for one gene, and several studies may report data for the same gene.
The ‘annotations’ view
In this view mode, each individual entry in the database is visible. The columns are headed by text boxes or pull-down menus allowing you to refine the visible list of entries. These filters are combinatorial, so that complex queries can be constructed. Clicking on the ‘x’ icons in the text boxes or selecting the empty option at the beginning of the pull-down menu will remove the filter for that column. Clicking on ‘Annotations’ in the menu bar will reset all fields ready for a new search.
Searching by gene
Type in the name of a gene, and a selector lists possible genes matching your search term. Choose one to see all entries reporting this gene. Clicking on any one of the gene names in the table will open a new window with more information about that gene including links to the relevant pages from MGI and the NCBI Gene database.
Searching by process/outcome
A pull-down menu allows you to search for all entries associated with each of the process or outcome categories. ‘Neuritogenesis’ is simply the union of ‘Dendritogenesis’, ‘Axonogenesis’ and ‘Maturation’.
Searching by ontology term
A pull-down menu allows you to search for all entries associated with each of the ontology terms, cell types or key markers. Searching for a higher-level ontology term will also return data for all child terms. Thus, a search for ‘New neuron’ also includes results for ‘Immature neuron’, ‘Early immature neuron’, ‘Late immature neuron’ and ‘Mature neuron’.
Searching by effect code
Each process or outcome has been annotated as being increased (+), unchanged (±) or decreased (−) by the activity of the gene in question. For the outcome ‘expression’, these codes can be interpreted as present (+), present in a subset of the cell type (±), or absent (−).
Searching by evidence code
The experimental approach used in each study has been noted in three broad categories; the authors looked only at expression of a gene or its product (*), the authors manipulated the effect of a gene or its product via extrinsic means, such as pharmacological stimulation or blocking (**), the expression of the gene itself was modified, such as by overexpression or knockout technologies (***).
Searching by species
Results can also be limited by species in which the study was performed. Irrespective of species, the reported gene effects have been translated into Mus musculus GeneIDs for compatibility within the MANGO database.
Searching by experiment type
Some studies using cultures derived from adult hippocampal precursor cells have been included. Such studies are marked ‘in vitro’. A category ‘ex vivo’ has also been included to cover studies using slice culture systems.
Searching by reference
Type in the name of an author or the title of a reference, and a selector lists possible publications matching your search term. Select one to see all annotations extracted from this publication. Clicking on any one of the references in the table will open a new window with the NCBI PubMed record for that publication.
Limiting the results shown
A pull-down menu at the bottom of the table allows only the first 20, 50 or 100 entries to be shown, or to show all entries. Regardless of this setting, all results will be returned if the download option is used.
Filtering expression data
As MANGO grows, an increasing amount of expression data will be added to the database. This will include results of large-scale microarray and RNA sequencing projects. This large amount of information might not be relevant for a casual browser of the database, so an include expression data checkbox is provided to filter these data if required.
Filtering negative results
Negative results are important and, if these are present in a manuscript presented for annotation, we will include all relevant information into the database. Results classed here as ‘negative’ are where a gene has been shown not to be expressed (−) in a defined cell type, or where a gene results in no change (±) to any other process (see searching by effect code above). It may be useful, however, to just retrieve a list of genes with some real effect on adult neurogenesis. To enable control over whether negative results are returned, an include negative results checkbox is provided. Unchecking this filter will hide all negative results.
The ‘genes’ view
This view mode provides a list of all of the genes that have been annotated to MANGO together with some basic information. Each column can be sorted by clicking the column header. Clicking on any one of the gene names in the table will open a new window with the relevant page from the NCBI Gene database.
For any table, clicking on the ‘Download’ button allows you to download the data in the current results table as a tab-delimited text file.
Our aim is to cover all published literature on adult hippocampal neurogenesis. We have an ongoing effort to catch studies we have missed so far and to keep up with the flow of new research in this field. If you find any studies we have not yet annotated, you can help us improve the database by letting us know.
Please keep in mind the scope of this project: non-pathological neurogenesis in the adult hippocampus.
We are also interested in any other feedback, praise, comments, problems...