Straightforward validation of the models network is not tested in terms of their consistency or cross-valdiation within COPD high dimensional assays - where it should be possible to see evidence of enrichment for co-expression etc. Contextual nature of networks is mentioned and attempts are made to address contextual pathway structures, but the context is not tested.
We developed a three-dimensional assay prepared from primary breast cancer tissue and quantified tumor response to tamoxifen therapy.
The advent of high-dimensional assay technology and 'systems biology' along with a vaccinomics approach [1,2] is spawning a new era in the science of vaccine development.
To investigate the relationship between chromatin organization and tumor phenotype, we used an established three-dimensional assay in which normal and malignant human breast cells can be easily distinguished by the morphology of the structures they make (acinus-like versus tumor-like, respectively).
We observed similar results regarding the contribution of CD47 and COX-2 in intestinal cell migration in both a 2-dimensional assay on a collagen I coated surface and in a 3-dimensional assay that required migration through a collagen I containing gel.
Therefore, a one-dimensional assay protocol cannot be used alone to test all relevant parameters.
PDGF treatment stimulated HSC migration approximately two-fold and, as in the two-dimensional assay, the chemotactic activity of C5a and PDGF were not additive under these conditions.
Capicúa-knockdown also enhanced cell invasion in a two-dimensional assay, and how ETV1 and/or other downstream targets mediate the effects of capicúa on proliferation and migration is a critical question for future research.
Kenny, P. A. et al. The morphologies of breast cancer cell lines in three-dimensional assays correlate with their profiles of gene expression.
Statistical issues and design and analysis techniques for learning about such correlates of vaccine efficacy are discussed, including on the use of high-dimensional assays such as whole genome transcriptomic and mass cytometry assays.
A high content clonogenic survival drug screen has been developed recently [ 28], but including three-dimensional assays for drug screens could tremendously accelerate preclinical testing in the future.
