Platform for Drug Discovery


Basic operation of Genome Explorer


Table of contents


About data for the explanation


  • Prior to the description of basic operation of Genome Explorer, we introduce a summary of a data for this explanation and the public version of the browser system which can be used without registration.
  • The following demo data were published by the ENCODE project, obtained from the short read archive DDBJ and processed by our analysis system Maser.
  • The three data are paired-end directional RNA-seq data generated by Illumina GAII.
  • Because each sample are from different human cell line, many genes show sample specific expression pattern.
  • Sample #SRX_IDSample description
    Sample1SRX084666 MCF-7_cell_longPolyA
    Sample2SRX082565 GM12878_cell_longPolyA
    Sample3SRX084683 K562_cell_longPolyA
  • You can show these demo data with public version Genome Explorer from the following link.
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    • This screen shows a typical order of tracks of the Genome Explorer.
    • The first two tracks are known gene annotation tracks commonly displayed in Genome Explorer.
    • The first is the forward orientation and the second is the reverse orientation.
    • You can recognize strandness from the "(+)" sign in the track title "(+)Gene". "(+)" means forward and "(-)" means reverse.
    • Third and fourth tracks (labeled green) are the common RefSeq annotation in which isoforms are displayed.
    • The fifth and the sixth (labeled black) are the gene annotation track which is uploaded by a user.
    • The remaining tracks are tracks of raw mapping results of RNA-seq reads of each sample.
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    • This is a typical entire screen of Genome Explorer.

How to move


  • The followings are operations to move the location in Genome Explorer.
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    1. Push the 'Left' button or the 'Right' button on the header menu to move horizontally.
    2. Push an arrow button on the right of each track to move vertically.
    3. You can move to drag an empty area with your mouse to move horizontally and vertically.
    4. You can jump to a specific site in which a gene or a landmark exists.
      • You can specify the landmark from the 'Search' tab on the left side of the screen.
    5. You can jump to a specific site, of which coordinate and chromosome are specified by user.
    6. You can jump to a specific chromosomal location when you click the image of a chromosome on the top of the screen.
      • Note that the pink bars on the chromosomal image represent the gene density. It is not the read density of your data.
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    • This is some search examples.
    1. You can search genes with a keyword in the gene description.
    2. You can search a cytoband specifier in chromosomes when you select 'Cytoband' as the search category.
    3. You can search a gene ID when you select 'Gene ID' or 'All fields' as the search category.
    4. You can search a gene name when you select 'Gene Name' or 'All fields' as the search category.
    5. You can search a gene symbol when you select 'Gene Symbol' or 'All fields' as the search category.
    6. You can search a RefSeq ID when you select 'RefSeq ID' or 'All fields' as the search category.
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    • When you jump to a specific location you specified 'By location', the red vertical line in the center of the screen become the position you specified.

How to zoom


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    • You can horizontally zoom in or zoom out with 'Zoom In' button or 'Zoom Out' button on the header menu.
    • You also zoom with zoom button on the right of each track.

Plot style of tracks


Default plot type 'Auto'

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    • At the default plot type 'Auto', the display format of the data is automatically selected in the following rule.
    • #Range of scaleDisplay formatDescription
      1Over 16 base/pxBand chart modeDepth of coverage is displayed.
      21 - 8 base/pxConnected box modeAll reads are independently displayed.
      Aligned region like an exon are indicated by thick boxes.
      Gaps between paired reads and introns are indicated by thin lines.
      3detailDetail modeAlignment region of each read is displayed on a single base resolution.
      When the sequence is not available, blank box are displayed.

How to change the plot type

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  • While the default plot type is 'Auto' described above, the plot type can be switched in the following operations.
    1. Push the 'option' button on the right side of header menu.
    2. Select 'Plot Style' tab of the displayed sub window.
    3. Click target tracks of which you want to change the style.
      • When you want to activate multiple tracks, click tracks while holding down the 'SHIFT' or 'Ctrl' key on your keyboard.
    4. Select 'Plot type' from the select box.
    5. Push 'OK' button.

Comparison of plot styles

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  • #Plot styleDescription
    1AutoAutomatically change the style.
    1-8 base/px:Connected Box.
    Over 16 base/px:Band Chart(AVG.)
    The detail is described above.
    2Band Chart(SUM)Depth of coverage is displayed.
    The meaning of '(SUM)' is described below.
    3Connected BoxAll reads are independently displayed.
    Aligned region like a exon are indicated by thick boxes.
    Gaps between paired reads and introns are indicated by thin lines.
    4Band Chart(SUM) + SNPs PlotMismatches and InDels are displayed on the Band Chart(SUM).
    5Connected Box + SNPs PlotMismatches and InDels are displayed on the Connected Box.

Difference of '(AVG)', '(PEAK)' and 'SUM' of the plot style Band Chart.

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    • To display depth of coverage, the three different manners are selectable.
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  • '4 base/px' means that one vertical var represents the depth of 4 bases reference region.
  • In order to represent single value for the values of four bases, an aggregate method is required.
  • #SignDescription
    1AVGThe average of the depth of coverage in the region is displayed.
    2PEAKThe max of the depth of coverage in the region is displayed.
    3SUMThe sum of the depth of coverage in the region is displayed.
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  • In the 'AVG.' or 'PEAK' style, the displayed height does not change by zoom.
  • In the 'Band Chart(SUM)' style, the displayed height becomes about 2 times in the case of 2base/px and the displayed height becomes about 4 times in the case of 4base/px.
  • In the 'SNPs Plot' style, if multiple SNVs are included in a region, display color of the SNVs becomes orange, which means mixed color.

Change of scale height


  • When the depth of coverage is high, it is often that the distribution of the depth exceeds the displayed area.
  • In such a case, you can change the scale of the height.
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How to change the height scale

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  • You can change the height scale by the following steps.
    1. Push the 'option' button on the right side of header menu.
    2. Select 'Plot Style' tab of the displayed sub window.
    3. Click target tracks of which you want to change the scale.
      • When you want to activate multiple tracks, click tracks while holding down the 'SHIFT' or 'Ctrl' key on your keyboard.
    4. Slide the slider of the 'Plot Height'.
      • When you check the 'Auto Adjustment', the scale will automatically adjust so that the height around the displayed area is within the display range of the height.
      • When the automatic adjustment is turned on, it is difficult to distinguish the expression level or depth of coverage. Therefore we turn of the auto adjustment at the default.
    5. Push 'OK' button.