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Objective: To observe the changes of gene expression in breast cancer stroma and peripheral blood mononuclear cells(PBMCs) of breast cancer patients. To investigate similarities and differences between them. Method: Datasets of gene expression profilings were downloaded from the Gene Expression Omnibus (GEO) database, including profilings of breast cancer vs. normal stroma and breast cancer patients'...
Purpose To discover, elucidate the structure-activity relationship (SAR), and explore the mechanism of action of excipients able to drastically lower the viscosities of concentrated aqueous solutions of humanized monoclonal antibodies (MAbs). Methods Salts prepared from hydrophobic cations and anions were dissolved into humanized MAbs solutions. Viscosities of the resulting solutions were measured...
The causation of cancer often involves the joint deregulation of multiple biological processes. Thus, it is interesting to extract multi-function features of cancer genes and study their functional coordination involved in tumorigenesis. Here, based on Gene Ontology, we proposed a heuristics strategy to extract multi-function features which are significantly overrepresented with cancer genes. We showed...
Since diseases might be related with each other, systematically assessing their relationships could provide us novel insight into their mechanisms. One of the most important methods to study diseases' relationships is to calculate their phenotype similarity scores based on the text and clinical synopsis parts of their records in the OMIM database. However, as demonstrated in this paper, the similarity...
Though the functional relationship analysis for gene products is useful, a convenient and user- friendly tool to measure the functional similarity for genome-wide gene products in multiple species is still not available. We computed the functional similarity of gene products in genome wide in human, mouse and rat based on our algorithm. Database and web services were built based on the precomputed...
The functional knowledge of cancer proteins and cancer pathways is currently limited and not detailed enough, remaining as a major hurdle to cancer studies. Particularly, many cancer proteins are only annotated to high-level general GO categories. Here, we apply an efficient algorithm, by constructing function-specific protein-protein interaction sub-networks, to find finer functions of the cancer...
Aging is a complex process associated with a number of molecular events at multidimensional levels. Understanding the characteristics of aging is important for elaborating the molecular mechanism of many diseases such as Alzheimer. In this paper, we systematically analyzed topological features of proteins encoded by human aging genes versus those encoded by non-aging genes in protein-protein interaction...
Selecting differentially expressed genes (DEGs) is one of the most important tasks in microarray applications. However, the sample sizes typically used in current cancer studies may only partially reflect the widely altered gene expressions in cancers. By analyzing three large cancer datasets, we show that, in each cancer, a wide range of functional modules are altered and have high disease classification...
Based on high-throughput data, numerous algorithms have been designed for finding functions of novel proteins. However, the effectiveness of such algorithms is currently limited by some fundamental factors including the low a-priori probability of novel proteins participating in a detailed function and the lack of detailed functional knowledge for training algorithms. For such partially characterized...
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