Triplex Target Analysis Examples

Triplex-target search on example of cyclin D1 in mice

Cyclin D1 belongs to the highly conserved cyclin family that shows very different protein abundance throughout the cell cycle.

To find sites for triplex-targeting Triplex-Inspector was executed on the complete ccnd1 gene locus considering the whole mouse genome when searching for off-targets (click here to see the ccnd1 locus on the UCSC genome browser).

The Triplex-Inspector search took about 15 minutes on a quad-core iMac with 16 GB of memory.

The resulting data can be accessed via:
  • inspector_report.html
    - allows navigating all through the rich data set
    - simultaneous filtering and sorting of all targets
    - clicking a target in the lower table links to a detailed view
  • inspector_circos.html
    - provides overview of the best sites per target region
    - links target sites to the detailed view

Triplex-target search on example of exons in human bcl-2

Bcl-2 (B-cell lymphoma 2) is a protein that regulates programmed cell death (apoptosis).

To find sites for triplex-targeting Triplex-Inspector was executed on the exon of human bcl2 including 100bp flanking region when searching for off-targets (click here to see the bcl2 locus on the UCSC genome browser).

The resulting data can be accessed via:
  • inspector_report.html
    - allows navigating all through the rich data set
    - simultaneous filtering and sorting of all targets
    - clicking a target in the lower table links to a detailed view

Triplex-target search on example of c-myc in human

The c-myc gene codes for a codes for a transcription factor that is often found misregulated in cancer.

To find sites for triplex-targeting Triplex-Inspector was executed on the complete locus of c-myc in human when searching for off-targets (click here to see the c-myc locus on the UCSC genome browser).

The resulting data can be accessed via:
  • inspector_report.html
    - allows navigating all through the rich data set
    - simultaneous filtering and sorting of all targets
    - clicking a target in the lower table links to a detailed view

Triplex-target search on example of ccr5 in human

The C-C chemokine receptor type 5 (CCR5) gene encodes a protein receptor for chemokines, which is found on the surface of white blood cells and that has been implcated as an entry point for viruses such as HIV.

To find sites for triplex-targeting Triplex-Inspector was executed on the complete locus of ccr5 in human when searching for off-targets (click here to see the ccr5 locus on the UCSC genome browser).

The resulting data can be accessed via:
  • inspector_report.html
    - allows navigating all through the rich data set
    - simultaneous filtering and sorting of all targets
    - clicking a target in the lower table links to a detailed view
See the video tutorial for additional information.