Refine
Has Fulltext
- yes (2)
Document Type
- Conference Proceeding (1)
- Postprint (1)
Language
- English (2)
Is part of the Bibliography
- yes (2)
Keywords
- MOOC (1)
- differential gene expression (1)
- digital education (1)
- e-learning (1)
- experience (1)
- gene expression matrix (1)
- heterogeneous tissue (1)
- higher education (1)
- homogeneous cell population (1)
- microcredential (1)
Background: For heterogeneous tissues, such as blood, measurements of gene expression are confounded by relative proportions of cell types involved. Conclusions have to rely on estimation of gene expression signals for homogeneous cell populations, e.g. by applying micro-dissection, fluorescence activated cell sorting, or in-silico deconfounding. We studied feasibility and validity of a non-negative matrix decomposition algorithm using experimental gene expression data for blood and sorted cells from the same donor samples. Our objective was to optimize the algorithm regarding detection of differentially expressed genes and to enable its use for classification in the difficult scenario of reversely regulated genes. This would be of importance for the identification of candidate biomarkers in heterogeneous tissues.
Results: Experimental data and simulation studies involving noise parameters estimated from these data revealed that for valid detection of differential gene expression, quantile normalization and use of non-log data are optimal. We demonstrate the feasibility of predicting proportions of constituting cell types from gene expression data of single samples, as a prerequisite for a deconfounding-based classification approach. Classification cross-validation errors with and without using deconfounding results are reported as well as sample-size dependencies. Implementation of the algorithm, simulation and analysis scripts are available.
Conclusions: The deconfounding algorithm without decorrelation using quantile normalization on non-log data is proposed for biomarkers that are difficult to detect, and for cases where confounding by varying proportions of cell types is the suspected reason. In this case, a deconfounding ranking approach can be used as a powerful alternative to, or complement of, other statistical learning approaches to define candidate biomarkers for molecular diagnosis and prediction in biomedicine, in realistically noisy conditions and with moderate sample sizes.
EMOOCs 2021
(2021)
From June 22 to June 24, 2021, Hasso Plattner Institute, Potsdam, hosted the seventh European MOOC Stakeholder Summit (EMOOCs 2021) together with the eighth ACM Learning@Scale Conference.
Due to the COVID-19 situation, the conference was held fully online.
The boost in digital education worldwide as a result of the pandemic was also one of the main topics of this year’s EMOOCs. All institutions of learning have been forced to transform and redesign their educational methods, moving from traditional models to hybrid or completely online models at scale. The learnings, derived from practical experience and research, have been explored in EMOOCs 2021 in six tracks and additional workshops, covering various aspects of this field. In this publication, we present papers from the conference’s Experience Track, the Policy Track, the Business Track, the International Track, and the Workshops.