Difference between revisions of "Part:BBa K3504011"

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We used multiple datasets which we filtered according to the more vicious traits of The tumor to know the most expressed genes in these samples ,and then according to logfc & t value by which we were able to minimize the data in them. Using 3 datasets we tried to find intersections between them using tools such as genevenn, in which by this we detected a list of 26 shared neoantigens to work on. Also this selection was done using literature mining techniques to find clinically used and tried neo-epitopes.
 
We used multiple datasets which we filtered according to the more vicious traits of The tumor to know the most expressed genes in these samples ,and then according to logfc & t value by which we were able to minimize the data in them. Using 3 datasets we tried to find intersections between them using tools such as genevenn, in which by this we detected a list of 26 shared neoantigens to work on. Also this selection was done using literature mining techniques to find clinically used and tried neo-epitopes.
  
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[[Image:Dataset_intersection.png|thumb|right|Figure 1. Hotspot identifcation of neoantigens.]]
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[[Image:Dataset_Intersection.png|thumb|right|Figure 1. Hotspot identifcation of neoantigens.]]
 
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<span class='h3bb'>Sequence and Features</span>
 
<span class='h3bb'>Sequence and Features</span>

Revision as of 18:58, 9 October 2020


Multi-Epitope TNBC Vaccine Version (1)

Part Description

A multi-epitope vaccine formed of highly expressed and specific TNBC neo-epitopes and specifically chosen according to egyptian population alleles which can work as a generalized vaccine and also personalized vaccine which would illicit an immune response specific to TNBC tumor cells

Usage

Characterization

Improvements

We used multiple datasets which we filtered according to the more vicious traits of The tumor to know the most expressed genes in these samples ,and then according to logfc & t value by which we were able to minimize the data in them. Using 3 datasets we tried to find intersections between them using tools such as genevenn, in which by this we detected a list of 26 shared neoantigens to work on. Also this selection was done using literature mining techniques to find clinically used and tried neo-epitopes.

Figure 1. Hotspot identifcation of neoantigens.

Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal PstI site found at 120
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal PstI site found at 120
    Illegal NotI site found at 44
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal PstI site found at 120
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal PstI site found at 120
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 584
    Illegal BsaI.rc site found at 935
    Illegal SapI.rc site found at 853