Apr 25, 2020

Efficient Representations of Tumor Diversity with Paired DNA-RNA Anomalies

BioRxiv : the Preprint Server for Biology
Q. KeDonald Geman

Abstract

Cancer cells display massive dysregulation of key regulatory pathways due to now well- catalogued mutations and other DNA-related aberrations. Moreover, enormous heterogeneity has been commonly observed in the identity, frequency, and location of these aberrations across individuals with the same cancer type or subtype, and this variation naturally propagates to the transcriptome, resulting in myriad types of dysregulated gene expression programs. Many have argued that a more integrative and quantitative analysis of heterogeneity of DNA and RNA molecular profiles may be necessary for designing more systematic explorations of alternative therapies and improving predictive accuracy. We introduce a representation of multi-omics profiles which is sufficiently rich to account for observed heterogeneity and support the construction of quantitative, integrated metrics of variation. Starting from the network of interactions existing in Reactome, we build a library of "paired DNA- RNA anomalies" that represent prototypical and recurrent patterns of dysregulation in cancer; each two-gene "motif" consists of a "source" regulatory gene and a "target" gene whose expression is "controlled" by the source gene. The pair motif is then "active" ...Continue Reading

  • References
  • Citations

References

  • We're still populating references for this paper, please check back later.
  • References
  • Citations

Citations

  • This paper may not have been cited yet.

Mentioned in this Paper

Meta Analysis (Statistical Procedure)
Genome
Nucleic Acid Sequencing
Sequencing
probe gene fragment
Fragments

Related Feeds

BioRxiv & MedRxiv Preprints

BioRxiv and MedRxiv are the preprint servers for biology and health sciences respectively, operated by Cold Spring Harbor Laboratory. Here are the latest preprint articles (which are not peer-reviewed) from BioRxiv and MedRxiv.

CZI Human Cell Atlas Seed Network

The aim of the Human Cell Atlas (HCA) is to build reference maps of all human cells in order to enhance our understanding of health and disease. The Seed Networks for the HCA project aims to bring together collaborators with different areas of expertise in order to facilitate the development of the HCA. Find the latest research from members of the HCA Seed Networks here.