Emerging evidence suggests that the tumor microenvironment plays a critical role in regulating cancer
stem cells (CSCs) and tumor progression through both autocrine and paracrine signaling. Elevated
production of bone morphogenetic proteins (BMPs) from human ovarian cancer cells and stroma has
been shown to increase CSC proliferation and tumor growth....
Nearly all freshwaters and coastal zones of the US are degraded from inputs of excess reactive nitrogen (Nr), sources of which are runoff, atmospheric N deposition, and imported food and feed. Some major adverse effects include harmful algal blooms, hypoxia of fresh and coastal waters, ocean acidification, long-term harm to...
BACKGROUND: The impact of cell-composition effects in analysis of DNA methylation data is now widely appreciated.
With the availability of a reference data set consisting of DNA methylation measurements on isolated cell types, it is
possible to impute cell proportions and adjust for them, but there is increasing interest in...
Full Text:
Methylation Array Data: a Mathematical Perspective
Supplementary Material
E. Andres Houseman, Kelsey T
BACKGROUND: The impact of cell-composition effects in analysis of DNA methylation data is now widely appreciated.
With the availability of a reference data set consisting of DNA methylation measurements on isolated cell types, it is
possible to impute cell proportions and adjust for them, but there is increasing interest in...
Full Text:
methylation array data:
a mathematical perspective
Houseman, E. A., Kelsey, K. T., Wiencke, J. K., & Marsit
BACKGROUND: Cell lineage-specific DNA methylation patterns distinguish normal human leukocyte subsets and can
be used to detect and quantify these subsets in peripheral blood. We have developed an approach that uses DNA
methylation to simultaneously quantify multiple leukocyte subsets, enabling investigation of immune modulations
in virtually any blood sample including...
BACKGROUND: Cell lineage-specific DNA methylation patterns distinguish normal human leukocyte subsets and can
be used to detect and quantify these subsets in peripheral blood. We have developed an approach that uses DNA
methylation to simultaneously quantify multiple leukocyte subsets, enabling investigation of immune modulations
in virtually any blood sample including...
Full Text:
, Kruschewski M, Mustea A, Turbachova I,
Baron U, Olek S: Epigenetic quantification of tumor-infiltrating T
BACKGROUND: The impact of cell-composition effects in analysis of DNA methylation data is now widely appreciated. With the availability of a reference data set consisting of DNA methylation measurements on isolated cell types, it is possible to impute cell proportions and adjust for them, but there is increasing interest in...
BACKGROUND: Cell lineage-specific DNA methylation patterns distinguish normal human leukocyte subsets and can be used to detect and quantify these subsets in peripheral blood. We have developed an approach that uses DNA methylation to simultaneously quantify multiple leukocyte subsets, enabling investigation of immune modulations in virtually any blood sample including...
DNA methylation is a well-recognized epigenetic mechanism that has been the subject of a growing
body of literature typically focused on the identification and study of profiles of DNA methylation and their
association with human diseases and exposures. In recent years, a number of unsupervised clustering algorithms,
both parametric and...
Background: Recent interest in reference-free deconvolution of DNA methylation data has led to several supervised methods, but these methods do not easily permit the interpretation of underlying cell types.
Results: We propose a simple method for reference-free deconvolution that provides both proportions of putative cell types defined by their underlying...
