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Many characteristics of functional synthetic siRNAs have been identified. Our three-phase algorithm was developed to design siRNA on a whole-genome scale based on these characteristics. When this algorithm was applied to design shRNAs, the validated success rate was over 70%, which was almost double the rate reported for TRC library. This indicates that the designs of siRNA and shRNA may share the...
Dilated Cardiomyopathy is one of leading courses of heart failure. Recent advances in microarray technology have promised significant advantages in understanding the molecular mechanisms underlying dilated cardiomyopathy and heart failure. Several microarray studies have successfully yielded a set of signature genes associated with heart failure. However, it has been found that the overlap of these...
Most of the proposed clustering approaches are heuristic in nature. As a result, it is difficult to interpret the obtained clustering outcomes from a statistical standpoint. Mixture model-based clustering has received much attention from the gene expression community due to its sound statistical background and its flexibility in data modeling. However, current clustering algorithms following the model-based...
Sex steroid hormones receptors bind to regions of the DNA called hormone response elements (HREs), in order to facilitate the regulation of gene expression. While the biological, functional and molecular basis of this interaction between the response elements and their corresponding transcription factor is not fully understood, the sequences of these HREs are known to be conserved for certain nucleotides...
This paper describes an interactive data exploration system for molecular and clinical data in the field of personalized medicine. It addresses the essential but to date unsolved problem of how to identify connections between genetic variants and their corresponding diseases or the response to certain drugs and treatments, respectively. It is therefore necessary to connect genetic with clinical data...
Cluster analysis is widely applied to discover the function of previously unannotated genes. This paper presents a novel stratified beta-Gaussian mixture model, sBGMM, for clustering genes based on gene expression data, protein-DNA binding data and data that can provide information for constructing priors such as protein-protein interaction (PPI) data. An expectation maximization (EM) type of algorithm...
It is well-known that the Fourier spectrum of a DNA protein-coding region exhibits an f = 1/3 peak. This is due to an unbalanced nucleotide distribution and open reading frame (ORF) positional bias that introduces a 3-base periodicity into the sequence. Until now, the f = 1/3 property has mainly been used to detect protein-coding regions, but in our paper, we use the f = 1/3 spectral height to detect...
Several studies demonstrate that the codon context is an important characteristic in gene primary structure that modulates the translation of mRNA. To better understand these features we developed a software package that uses sequences of open reading frames (ORFs) available in public databases and applies several statistic and visualization methodologies to unveil codon-context patterns, codon usage...
RNA interference has been widely used to identify genes involved in the production of particular biological phenotypes. This type of gene silencing technology has been used in plants, invertebrates and mammalian systems [1]. The availability of the sequences of large numbers of genes has allowed large libraries of siRNAs to be produced. To effectively use these libraries in screens, high-throughput...
We characterize three small gene signatures derived consequently from the original 232-gene breast cancer aggressiveness signature which could improve biological classification and clinical assignment of ~50% of breast cancer patients having histologic grade 2 tumors . Here, we develop a novel approach to identify small gene signatures providing statistically reliable, biological important and clinical...
Both correct and harmonic expression of genes became an important factor of health care development. Genes expression changes are consider to be a reason of many diseases. Early detection of mentioned above changes allow for application of common treatment procedures before the first symptom are observed. Statistical methods applied for those purposes allow relatively simple selection of patients...
To explore how to calculate the effect of solanine on the Michaelis constant and the maximum reaction rate of NAT, high performance liquid chromatography (HPLC) was used, with 2-AF as substrate, and the rate at which 2-AF is acetylated into 2-AAF in intact HepG2 cells or in the cytoplasm of HepG2 cells as the reaction rate. The double reciprocal plot was made, with 1/S (reciprocal of the concentration...
We present an algorithm for automatic detection of solid- phase (polony) Polymerase Chain Reaction (PCR) objects. The goal is to detect the location and size of each polony present in an image. Using a statistical model for an image of a polony, we are able to weigh different hypothesis, including arrangements of multiple overlapping objects. The algorithm uses a coarse-to-fine approach. A coarse...
We examine approaches to the incorporation of anatomic structural information into the inverse problem of fluorescence molecular tomography (FMT). Using an appropriate relationship between anatomic and reconstruction image resolution, we build an inverse problem parameterized along the anatomical segmentation. These values serve as the basis for two new regularization techniques. The first regularizes...
This paper defines a new correlation coefficient SMBS which using both quantity and tendency in gene expression changing to measure the similarity among genes. The SMBS applies to K-means clustering algorithm and the result shows more co-regulated genes are found comparing with the CLUSTER3.0.
HER-2/neu (HER2) has been shown to be a valuable biomarker for breast cancer. However, inter-observer variability has been reported in the evaluation of HER2 with immunohistochemistry. It has been suggested that automated computer-based evaluation can provide a consistent and objective measure of HER2 expression. In this manuscript, we present an automated method for the quantitative assessment of...
The fast development of array technology has raised the density of oligonucleotide SNP arrays from 10 K and 50 K to 100 K and 500 K. However, methods for SNP genotyping have not been developed as fast. Most methods are based on sample-dependent multi-array training and may not be suitable for cross-laboratory studies and small sample studies, few use full information of array technology efficiently...
Differential in-gel electrophoresis (DIGE) technique has been used for differential protein analysis to improve the reproducibility of comparative 2D gel experiments. Because the sample size in 2D DIGE experiments is usually very small, the traditional statistical methods such as student t-test could not provide an accurate and reliable detection/identification of differentially expressed protein...
The allelic frequencies distribution of 15 tetrameric short tandem repeats (STR) loci [D8S1179, D21S11, D7s820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, FGA] were obtained from 1530 unrelated individuals of three tribal populations [Han, Yao, Miao] inhibiting in South China. Statistic methods based on cluster and least significant difference (LSD) analysis...
This paper describes the research to reduce high false positive discovery rates when discovering possible molecular diagnostic patterns. This effort combines information from the gene ontology with multiple sets of discriminating patterns discovered in a publicly available gene expression dataset on breast cancer. Using a second validation dataset, we identify candidate patterns with good and poor...
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