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Example 3 - Custom data upload by registered users




You will find here examples of data upload by registered users, for basic and advanced (generic and genetic) overlays.


Basic format

The file in basic format has two tab-separated columns Name and Value (see also Upload user-provided overlay data):

  • Name - names of elements to be colored
  • Value - a value from [-1, 1] range, to be transformed to blue-red coloring, with negative values colored blue, positive colored red; the saturation of the color will be defined by the absolute value.

Note: blue (for negative values) and red (for positive values) are configured in the admin panel (Overlays) and can differ between MINERVA instances.


Click here to download the basic overlay, containing a custom coloring for the example map.

To upload this dataset, do the following:

  1. Make sure you have the privileges to generate overlays in the example map
    1. Go to Projects tab and Edit the example map
    2. In the Users tab, check the box in the View project column
  2. Open the example map from the Projects tab by clicking on its name (map_example by default)
  3. Make sure that you are logged in by checking the Info tab in the left panel
  4. In Overlays > User-provided overlays section, choose Add overlay then press Choose File to select basic overlay file to upload
  5. In Overlays > User-provided Overlays tab, click View checkbox to examine generated view


Examine the generated coloring and the uploaded dataset. Please see image below and note that:

  • All SNCA elements are colored to the same color because of by-name matching
  • SNCA elements are blue-colored (the value in the file is -0.5)
  • PRKN is red (the value in the file is 0.75)

Basic format overlay


Advanced format - generic type

Advanced format foresees two parts of the uploaded dataset - header and body (see also Upload user-provided overlay data). The header lines start with #. It can contain the following elements:

  • # VERSION=xyz - a version of this custom layout

  • # NAME=xyz - a name that will be automatically assigned upon upload

  • # DESCRIPTION=xyz - a description that will be automatically assigned upon upload

The body is a table with a following set of columns:

  • Name, Value - same as in the basic layout

  • Compartment - name of a compartment in which coloring should take place
    Warning! Coloring of the elements in different compartments works ONLY for separate (not nested) compartments. Setting a color for elements in a compartment that encloses other compartments sets the color in the nested compartments as well.

  • ChEBI - ChEBI identifiers of elements to be colored

  • Entrez gene - Entrez identifiers of elements to be colored

  • Gene ontology - Gene Ontology identifiers of elements to be colored

  • Ensembl - Ensembl identifiers of elements to be colored

  • HGNC symbol - HGNC symbols of elements to be colored

  • UniProt - UniProt identifiers of elements to be colored

  • ReactionIdentifier - ID of interaction to be colored (interactions coloring only)

  • LineWidth - line width of the colored interaction (interactions coloring only)

  • Color - color of the colored element


By-identifier coloring

Click here to download the advanced overlay (generic), containing a custom coloring for the example map.

Upload this dataset as in basic format upload.

Examine the generated coloring and the uploaded dataset. Please see image below and note that:

  • elements are colored by their identifiers instead of their names

  • SNCA elements in the nucleus elements are colored blue, synapse elements are colored red due to by-compartment coloring

Warning! Coloring compartments works ONLY for separate (not nested) compartments. Setting the color for SNCA identifier in the cell compartment will color the contents of the nucleus and synapse as well. Setting different colors for the same SNCA identifier in the cell and in the nucleus will cause an error, as two different colors will be assigned to the same SNCA identifier in the nucleus inside the cell. Example warnings

  • removing compartment column will also cause the error described above

  • using SNCA coloring by-name overrides by-identifier coloring, the order of selection is as follows:

    • match by-name
    • match by-identifier
    • constrain by-compartment

Advanced format overlay


Custom colors and interaction coloring

User-defined colors can be assigned to both elements and interactions, using the hex code (e.g. #fffaaa).

Click here to download the interactions overlay, containing a custom coloring for the example map.

Upload this dataset as in basic format upload.

Examine the generated coloring and the uploaded dataset. Please see image below and note that:

  • color column replaces value for defining colors of interactions and elements; both parameters cannot be used simultaneously

  • reactionIdentifier is not affected by compartment constraint

Custom format overlay


Remarks

  • The uploaded dataset must be a text file

  • Column names work only if an element is annotated by one of the terms above.

  • Column Name refers to the full name in the annotation panel; e.g., HGNC gene name for genes/proteins; ChEBI name for simple molecules or GO name for a Gene Ontology term.

  • Identifiers of the elements in the dataset have to follow the MIRIAM standard; e.g., HGNC: 11138; Ensembl: ENSG00000184845; ChEBI: CHEBI:18243.

  • Most columns could be used simultaneously as long as the same element is not addressed in two different columns; e.g. LRRK2 by HGNC name (=LRRK2) and Entrez gene ID (=120892) or a reaction identifier and a PubMed target the same reaction.

  • Restrictions:

    • Either a value or a color columns is necessary in the uploaded dataset, but they mutually exclusive

    • Reactions to be colored should be identified only by reaction id or PubMed

    • If the compartment column is used, the field must be filled by a compartment name from the map, otherwise the element will not be displayed in the content.

Alternatively: you can always extract an area of interest as a CellDesigner file, open it in CellDesigner and color it there.


Advanced format - genetic variant

Genetic variant is an advanced overlay in a specific format. Click here to download the genetic variant overlay, for the example map.

Before upload, check if Organism type is defined for your project (see section Edit project). If it is missing, the genome browser will not be displayed. Upload the overlay as in basic format upload. Please note that field TYPE automatically switch onto GENETIC VARIANT after choosing the file, because of the header. Click View to display coloring on the map (see below).

Advanced genome overlay


In the map, SNCA and PRKN are colored, indicating that the overlay contains genetic variants for these elements. Clicking on the pin display popup window with the genome browser. To take a closer look at the sequence, you can zoom in/out using button +/-. In the bottom row, in our example named Genetic, we see the locus of the particular variant. There are four PRKN variants in the example. The height of the mark | corresponds to the allele frequency.