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ABSTRACT: Pleiotropy is a common phenomenon in the genetics of cancers, which is rarely systematically evaluated. A novel idea for identifying shared gene functional modules using biclustering was proposed in this paper to explore the common molecular mechanisms among cancers and the relationships between different types of cancers. Gene expression datasets for 20 cancers were obtained. And genes differentially expressing in at least two types of cancers were selected using both moderated t-statistic and fold change to construct a 10417 × 20 matrix (gene-cancer matrix). 22 gene clusters shared by cancers were found by using the biclustering method. Further, Gene Ontology (GO)-based enrichment analysis identified 17 gene functional modules (Bonferroni corrected P < 0.05). The involved biological processes primarily included regulation of chromatids separation during mitosis, cell differentiation, immune and inflammatory response, and collagen fibril organization. These modules undertook molecular functions of ATP binding and microtubule motor activity, MHC class II receptor activity, endopeptidase inhibitor activity and so on. And their activity sites were mostly located in cytoskeleton, chromosome, MHC protein complex, intermediate filament, fibrillar collagen and so on. The network constructed based on these modules indicates that gastric cancer, ovarian adenocarcinoma, cervical cancer and mesothelioma were highly relevant to each other. However, the molecular mechanisms of two hematologic malignancies (acute myeloid leukemia and multiple myeloma) seem very different from other cancers. It can be seen that gene functional modules shared by cancers are associated with many biological mechanisms, and similarities among cancers are probably attributed to cellular origin and shared carcinogenic mechanisms. The proposed method for analysis of pleiotropy in this paper will help understand the common molecular mechanisms for complex human diseases.
Hereditas (Beijing) 03/2013; 35(3):333-42.
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Bin-Sheng Gong,
Qing-Pu Zhang,
Guang-Mei Zhang,
Shao-Jun Zhang,
Wei Zhang,
Hong-Chao Lv, Fan Zhang,
Sa-Li Lv,
Chuan-Xing Li,
Shao-Qi Rao,
Xia Li
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ABSTRACT: Gene expression profiles and single-nucleotide polymorphism (SNP) profiles are modern data for genetic analysis. It is possible to use the two types of information to analyze the relationships among genes by some genetical genomics approaches. In this study, gene expression profiles were used as expression traits. And relationships among the genes, which were co-linked to a common SNP(s), were identified by integrating the two types of information. Further research on the co-expressions among the co-linked genes was carried out after the gene-SNP relationships were established using the Haseman-Elston sib-pair regression. The results showed that the co-expressions among the co-linked genes were significantly higher if the number of connections between the genes and a SNP(s) was more than six. Then, the genes were interconnected via one or more SNP co-linkers to construct a gene-SNP intermixed network. The genes sharing more SNPs tended to have a stronger correlation. Finally, a gene-gene network was constructed with their intensities of relationships (the number of SNP co-linkers shared) as the weights for the edges.
BMC proceedings 02/2007; 1 Suppl 1:S45.
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Shao-Qi Rao,
Liang-De Xu,
Guang-Mei Zhang,
Xia Li,
Lin Li,
Gong-Qing Shen,
Yang Jiang,
Yue-Ying Yang,
Bin-Sheng Gong,
Wei Jiang, Fan Zhang,
Yun Xiao,
Qing K Wang
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ABSTRACT: Traditional studies of familial aggregation are aimed at defining the genetic (and non-genetic) causes of a disease from physiological or clinical traits. However, there has been little attempt to use genome-wide gene expressions, the direct phenotypic measures of genes, as the traits to investigate several extended issues regarding the distributions of familially aggregated genes on chromosomes or in functions. In this study we conducted a genome-wide familial aggregation analysis by using the in vitro cell gene expressions of 3300 human autosome genes (Problem 1 data provided to Genetic Analysis Workshop 15) in order to answer three basic genetics questions. First, we investigated how gene expressions aggregate among different types (degrees) of relative pairs. Second, we conducted a bioinformatics analysis of highly familially aggregated genes to see how they are distributed on chromosomes. Third, we performed a gene ontology enrichment test of familially aggregated genes to find evidence to support their functional consensus. The results indicated that 1) gene expressions did aggregate in families, especially between sibs. Of 3300 human genes analyzed, there were a total of 1105 genes with one or more significant (empirical p < 0.05) familial correlation; 2) there were several genomic hot spots where highly familially aggregated genes (e.g., the chromosome 6 HLA genes cluster) were clustered; 3) as we expected, gene ontology enrichment tests revealed that the 1105 genes were aggregating not only in families but also in functional categories.
BMC proceedings 01/2007; 1 Suppl 1:S49.
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ABSTRACT: Laboratory studies were made to determine the capacity of Trichogramma dendrolimi to parasitize eggs of Ostrinia furnacalis, as affected by the rearing host species, substrate of host eggs, host age, original locality of host populations, and cold storage of host eggs. Wasps reared from eggs of Antheraea pernyi showed parasitic capacity on eggs of O. furnacalis on average twice as high as that of the wasps reared from eggs of Corcyra cephalonica. When the age of O. furnacalis eggs at 26 C increased from 0–6 h to 18–24 h, the proportion of wasps that successfully parasitized host eggs, the number of host eggs parasitized, and the rate of parasitization all decreased by >50%. The number of O. furnacalis eggs parasitized per female T. dendrolimi increased with the number of host eggs available, and reached 22.9 in a 24 h period. However, the parasitic capacity of female T. dendrolimi on eggs of O. furnacalis laid on plant leaves was similar to that of O. furnacalis eggs laid on wax paper. Levels of parasitism of O. furnacalis eggs from two widely separated localities, i.e. Changchun (43.50 N, 125.20 E) and Hangzhou (30.18 N, 120.07 E), were similar. Cold storage of O. furnacalis eggs at 4 C for 5 days did not affect parasitization. Results obtained in this study indicate that although O. furnacalis is a less preferred and less suitable host than many other hosts, such as Dendrolimus punctatus, Actias selene ningpoane, Philosamia cynthia, A. pernyi, C. cephalonica, within the host-species range of T. dendrolimi, the parasitoid has the potential to achieve 50–60% or even higher rates of parasitization of O. furnacalis eggs in corn fields under suitable conditions, and could be used in the biological control of the pest.
BioControl 08/1998; 43(3):273-287. · 1.93 Impact Factor
