Many large scale molecular biology experiments now use cDNA microarray technology for measuring expression levels of a large number of genes for a small tissue sample or cell. However, there are a number of projects underway to map spatial patterns of gene expression usingin situhybridization (ISH)...
Two-marker FDR remains below naive FDR until a p-value level of 0.01 and both increase slowly towards 1. FDR against the number of selected SNP plots are detailed by collection in Figure 5. As observed in other studies [13], the FDR is not monotonous with the p-value. The oscillations...
A gene's expression pattern can be defined as a series of differential accumulations of its products in subsets of cells as development progresses. Patterns of mRNA expression are studied by two principal methods - microarray analysis [1] andin situhybridization [2,3]. Microarray analysis provides...
where S is the number of gene sets and |A| is the cardinality of A. The bound is inflated because it assumes that none of S gene sets are associated with the phenotypic changes. When |A| = 0, i.e., none of the gene sets is identified, FDR is 0 by definition. Since in most ...
Since PBN is more suitable for GRN reconstruction from time series data and a Boolean network is just a special case of PBN and we only consider PBN for comparison. Boolean network We use the same definition as in [2, 18] for a Boolean network. A Boolean network G(V, F) is defined ...
The GO definition file released in April 2007 was downloaded from the GO website and used to construct a GO graph. We have developed a Python software package referred to as GOGrapher (manuscript in preparation), which contains a set of application programming interfaces for building a GO graph...
( max 2, 3 ). finally, the annotation information score is the sum of all self-similarities of terms in set 1 plus max 2, 3 . shalgi et al . utilized lord's definition for a subcellular clustering score based on the cellular component ontology. they calculate the similarity of two ...
The GO definition file released in April 2007 was downloaded from the GO website and used to construct a GO graph. We have developed a Python software package referred to as GOGrapher (manuscript in preparation), which contains a set of application programming interfaces for building a GO graph...
3. Shalgiet al. utilized Lord's definition for a subcellular clustering score based on the cellular component ontology. They calculate the similarity of two genes as the maximum similarity of GO terms annotated to one of the genes. Björklundet al. [24] developed a domain distance score for...
Systems biologic approaches such as Weighted Gene Co-expression Network Analysis (WGCNA) can effectively integrate gene expression and trait data to identify pathways and candidate biomarkers. Here we show that the additional inclusion of genetic marker