MitoGenesisDB:
  Mitochondrial Spatio-Temporal
    Expression Database
Biological Background
Definitions
References


HOW TO USE

MitoGenesisDB is composed of three parts:

To search the database information, three different accesses are available (see below for a complete description):

Note that complete datasets can be also downloaded using the following link (Excel spreadsheets): Download Data.


Access 1: Search by Feature List

Enter the list of gene names you want to query (1). Either systematic or standard names are allowed, they have to be separated by: line feed, comma, semicolon, point or space (otherwise, problems in the query can be encountered). Default gene list correspond to the known components involved in the cytochrome c oxidase (COX) assembly.

Using the check boxes (3, 4, 5), chose the information to be displayed on the result page.


Access 2: Search by Mitochondrial Functions

In MitoGenesisDB, Genes identified in Saint-Georges et al. (2008) as involved in mitochondrial biogenesis were manually clustered into eleven functional groups: Amino Acid Synthesis; Assembly Factors; Fe-S Clusters; Metabolism; Morphology; Protein Import; Respiratory Chain Complexes; TCA Cycle; Transport; Translation Machinery and Translation Regulation. If a particular function is chosen (2), the database is queried with all the genes that belong to this function.

For accesses 1 and 2, the search procedure is finally run by clicking the "Submit" button (6).


Access 3: Search by Keywords

Interrogation of the database can be performed by entering one or several keywords. Genes for which at least one keyword is found in their description are listed. Note that different keywords are underlined with different colors (1) and a text file can be downloaded for further investigations (2).


Image Gallery

To easily extract important information from the identified gene list, several graphical representations are dynamically generated. For instance, a representation of the mitochondrial cycle is generated, together with YMC expression profiles, MLR distributions or barplots for functional categories. More information concerning the interpretation of the mitochondrial cycle graph is provided here. All the graphs are summarized in an image gallery, where (1) a large version of a selected picture is presented and (2) miniature versions of all the pictures are shown.



Result Table

Below the Image Gallery, a table combining all the information extracted from the database is presented. Each column can be sorted by clicking on the arrows (1) and text files to be downloaded can be obtained by clicking on the "data" and "graph" links (2). Finally for each gene, a summary page can be accessed (3).

Note that the result table can be downloaded in a text format for further examinations with others tools (4).


Access 4: Search by Orthologue Conversion

To allow the analysis of genes from other model species than yeast, a module for orthologue conversion is available. The main idea is to convert gene names of other organisms into their orthologous counterpart in S. cerevisiae. For that we use orthologous relationships available in the InParanoid database. To perform the orthologue conversion, select first the species you want to analyse (1), and enter a list of genes for this species (2). Then, run the procedure for orthologue conversion using the button "Get Orthologues" (3).

Orthologous genes found in S. cerevisiae can be directly submit to MitoGenesis Access 1 (4) and InParanoid results are summarized in a table (5). Note that only orthologues with an InParanoid Score = 1 are provided.