Understand the main concepts of Manteia.
This 12 minutes video gives you an overview of the tools and concepts developped for Manteia.
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Gene search.
How to search for a gene in one or several species and access its annotation in Manteia.
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Refine.
Refine is a tool accessible from every result page of the system. It allows to use the genes listed as a result from a previous query as a search space for the next query. Hence, all the tools of the system can be linked in a sequential manner, the final gene list corresponding to the intersection of all the steps of the analysis.
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This tutorial shows how to search for the mouse transcription factors having an homeobox domain and get their orthologs in the chicken using Manteia "Refine" tool.
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Query builder.
Query builder is a tool that allows to combine a mixture of data from the system using a variety of logical operators.
This tool can be used in two different ways:
Users can write their own queries assisted or not by the interface. E.g. [ GO("GO:0003700") and KEGG("Wnt signaling pathway") and SPECIES("Mus musculus") ] not IP("IPR013629") will return all the genes from the mouse dataset that are annotated as Transcription factors in Gene Onthology (GO:0003700), involved in the Wnt pathway according to KEGG, with no Zinc finger domain detected by Interpro (IPR013629).
The second way to use this tool is to design several Boolean queries and have them all evaluated at the same time by the system. The list of genes returned have to correspond at least to one of theses conditions, and are ordered by the number of conditions they meet. Each query can be assigned a weight to reflect its importance in the analysis. This powerful approach permits to evaluate several conditions without discarding the genes that do not meet them all. Instead, a score is given reflecting the pertinence of a gene as a candidate to meet different parameters.
Query builder can be used in combination with Refine providing unlimited ways to merge the information contained in Manteia.
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This tutorial examplifies how to search for genes related to somitogenesis or leading to an axial skeleton phenotype using Manteia query builder.
It also illustrates how to perform several queries at the same time and sort the resulting genes according to the number of criteria they meet.
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How to analyze statistically a set of genes.
When large lists of molecules from high throughput experiments are being studied together, it is interesting to analyze the annotation of this group to understand its characteristics and specificities.
For this, we designed statistic tools able to list every annotation of a group of genes and tell the user if a given category is enriched or depleted compared to a reference like a genome, a microarray, or a custom designed list.
Statistic tools are available for several type of data: Gene Ontology, Interpro, phenotype and chromosome distribution.
The significance of each result is given with a P-value computed with a hypergeometric test and corrected for multiple testing using the Bonferroni and the Benjamini-Hochberg false data rate.
The resulting table allows to retrieve the genes associated to each annotation, making it possible to select them specifically for further analysis using Refine or Querybuilder.
Additional features allow to dynamically filter the results and highlight annotation categories that are related together which greatly ease the analysis of the results.
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This tutorial examplifies how to analyze the Gene Ontology annotation from a list of genes.
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