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Help

Help and explanation
This page is intended to get you started with the HEK293-comparison tool.
The web-tool can be divided into three major blocks:
  1. The Header
  2. The Genome-view
  3. The Exone-view
    4. And additionally we will look at the sequence-blocks in closer detail
  4. The Sequence

Header - the constant on the page

The header is composed out of 5 elements:

  1. Home
    2. Click the complete header banner to go to the Homepage
  2. Search
    3. Click the Search-button to go to the Search-page and find variations with certain characteristics
  3. IGV
    4. Click the IGV-button to go to the IGV-page and find more information about the integration of this tool with IGV
  4. About
    5. Click the About-button to go to the About-page
  5. Help
    6. Click the Help-button to go to the Help-page
  6. Contact
    7. Click the Contact-button to go to the Contact-page
  7. Cite
    8. Click the Cite-button to go to the Cite-page

Genome - the complete view

Drag / Zoom - Complete view - Variation indication type
Switch between Drag and Zoom
When the drag option is set, it's possible to drag a box along the sequence representation to obtain the sequence view of the location in the drag box, the position where the box is dropped will be displayed in the sequence frame.
When the zoom option is set, it is possible to draw a square on the sequence representation. When the left mouse button is released the tool will zoom in to the location wrapped by the selection. Before the zoom is executed, a confirm-popup will appear. It's possible to alter the zoom-location in this popup
Before the zoom is executed, a confirm-popup will appear. It's possible to alter the zoom-location in this popup
Return to Complete View
When the view is zoomed in, it's possible to return to the complete view by clicking this button
Change type of Variation Indication
The gene-representation is a block representing the sequence. On this block the different variations between the genomes and refseq are indicated. How this indication is visualized can be altered with this drop down.
There are 3 possibilities:
Variation Density
This is the type that can handle the largest amount of data. The chosen genome location can be many thousands of nucleotides long and can hold many variations. To handle this many variations it's impossible to show them all separately. This view will create a bar on. The relative location on the gene-representation. The height of the bar corresponds with the number of variations on that relative location. Note: relative location --> when a sequnece of 10000nt is condensed into a representation of 1000px, 10nt correspond with 1px. So multiple variations can be called an the same relative position.
Variation Types
This type can handle the second most data. In this case the variations are visualized by variation type, for example a simple snp will be displayed in blue and a deletion in red. The color intensity corresponds with the number of genomes that have this variation
Variation Types
per Genome
This visualization type shows the most information but is the heaviest for the browser to render. Each individual snp is visualized as a arrow. The color of the arrow corresponds with a certain genome (e.g.: black = HEK293A) where the line-colors correspond with the variation type (e.g.: orange = substitution).


Annotation
The position of a certain gene is indicated on the region visualization by a (gene)block. The positions of the blocks correspond with the actual location on the genome. Clicking one of these blocks will insert this gene as a new query in the tool
Expand
Sometimes it is informative to check which genomic alterations occur in the surrounding area of the region of interest. To answer this need, the possibility exists to expand the current frame 500, 1000 or 2000 nucleotides in either direction. The expansion will be indicated in this expansion-frame and also at the query-field on top of the page. Clicking on the x inside the circle, in the middle of the expand-bar will reset the current expansion.

Browse Sequence - Visualization options
Go Lower/Higher
By clicking one of these arrows, you can move the frame to left are to the right. The size of the jump can be set in the visualization parameters (1, 5, 10 or 100 nucleotides per jump).
Frame to IGV
If the region in the frame has to be examined in closer detail, the IGV-button can be clicked. This will launch IGV and visualize the current frame position.
Reduce/Enlarge nucleotide size
Clicking the minus-button will decrease the font-size meaning more nucleotides will fit in the frame.
The dot-button will reset the font-size to the default value.
The plus-button will enlarge the font-size.
Visualization parameters
Clicking the visualization parameters button will release a drop down with all the parameters.
Here we will go over all the options and it function.
No visualization parameter is changed: default setting
When the parameter Show Genome Color is enabled, the background of the sequence will be colored according to the color assigned to the genome-name on top of the page
When the parameter Show Copynumber is enabled, a little square on top of each nucleotide will indicate the copy-number at that particular position. Each copy-number is assigned a color to nicely visualize the blocks with the same copy-number.
Hover over the little copy-number-blocks to get the exact copy-number linked to that color and position
When the parameter Show Genome Names is enabled, the sequence starts with the name of the genome. When no name is given, the sequence is the RefSeq
When the parameter Show Exons is enabled, it is not the sequence that changes appearance but the region representation. Instead of a full colored bar, the bar is split up in chunks according to the exon-locations in the visualized region.
When the parameter Show Exons is enabled, it is not the sequence that changes appearance but the region representation. Instead of a full colored bar, the bar is split up in chunks according to the exon-locations in the visualized region.
When the parameter Show Insertions is enabled, all insertion (whenever the RefSeq needs to spaced out by "-") will be collapsed. An indicator will be inserted instead. Clicking The arrowhead of the indicator will fold open this particular insertion. Open folded insertions can be closed by clicking the indicator-head again.
The last functionality in this drop down menu is the possibility to set the number of nucleotides that a jump spans. Check the ‘Go Lower/Higher’ paragraph for more information on these jumps.

Exon - the limited, zoomed view

Browse Exons

This view is only composed of exon regions. When a search-term is entered and a transcript is chosen, the tool will grep all the exon-regions and calculate and display the variations. The exon is completely visualized and it is possible to scroll through the sequence and view the variations in this exon-region.
Because the tools only needs the exons, no location can be entered in this visualization-type, because exons have to be defined...

Head
The head of the page is more or less the same as in the genome-view, with the important difference that the exon-view will not accept locations, only gene/transcript-identifiers.
Exon Head
At the start of every exon-block, a header is displayed. This header contains some information about the exon.
  • Exon number
  • The exact position of the exon
  • The nucleotide-length of the exon
  • The number of variations present in this exon

    When there are variations present in the exon, an extra bar is created inside the exon-block. Otherwise the bare sequence is visualized.

    Exon Variation Bar: variation buttons
    Each variation that is present in the exon is represented by a button on top of the exon-block.
    The text-color, the color of the exon-number, corresponds with the type of variation (e.g.: red = deletion, blue = SNP,...)
    The squares at the bottom of the button indicate which of the genomes has this particular variation.
    Clicking the variation will scroll the frame to the variation location in the exon-block. This position will be indicated by a triangle at the bottom of the exon-block
    Exon Variation Bar: next/previous
    To easily navigate through all of the variations in a given exon, the navigation-buttons can be used. Clicked them will move the frame, and indicator, to the next/previous variation.

    Sequence - the essence

    Sequence

    Each line of the sequence block corresponds with a certain genome. The first row is the RefSeq-sequence, the other rows correspond with the chosen genomes. The order of the rows is equal to the order of the genome-names on top of the page. The distinguish which genome is which, the genome-color-background and/or the genome-names can be displayed.

    The sequence itself is constructed so all nucleotides are visualized. If an insertion occurs, the refSeq (and all genomes without the variation), will be spaced out by '-'.

    Each variation also has his own color:

    • Red: deletion
    • Orange: substitution (can also insert a part)
    • Green: insertion
    • Blue: SNP
    As shown in the picture, there are two types of deletions.
    When the RefSeq is striked through it means one allele has the deletion called and the other not.
    When there is no Refseq visualized, on both alleles the deletion is called
    The difference between the two alleles can be explained by the polyploidy of the genomes and the detection grade of the algorithms.

    The grey areas are "No Call"-regions. This means the SNP-calling and/or sequence assembly in this region is unclear. So the presented sequence inside this regions should be considered unreliable.

    Pop-Ups

    When a variation is clicked a popup will be displayed with extra information about this particular variation. The lower right corner can be dragged around to re-size the popup-window to obtain the ideal width to display the information.
    The popup has two major displays: The global overview (summary) and the specific annovar data (details).

    Summary
    This popup gives an overview of the variation:
    • Type: Indicates the variation-type
    • Ref: Shows the reference sequence
    • Alt: this field contains the actual sequence of the two alleles
    • Coverage: The number of reads overlapping this area
    • Impact The consequences of the variation predicted by two algorithms
    Clicking the the Additional Annovar Information will reveal the second (more detailed) view.
    Clicking IGV will open the current variation in IGV (see tab IGV for more information).
    Clicking the X will close the current variation-popup
    Details
    This popup gives an overview of the variation specifics
    • Region: Tells in which genomic region the variation is located
    • Location: Tells where the variation is located in relation to the closest genes
    • Impact: The consequences of the variation predicted by two algorithms
    • Change: The exact variation information, what nucleotide changed in to which and how did this change the proteins
    • LJB_LRT:
    • LJB_mutationTaster:
    • LJB_phyloP:
    • polyPhen2:
    • SIFT: Ranges from 0 to 1. The amino acid substitution is predicted damaging is the score is <= 0.05, and tolerated if the score is > 0.05.
    Clicking the the Additional Annovar Information will hide this view