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Articles 1 - 11 of 11
Full-Text Articles in Genetics and Genomics
Tbx5 Is Required For Avian And Mammalian Epicardial Formation And Coronary Vasculogenesis., Nata Y Diman, Gabriel Brooks, Boudewijn P Kruithof, Olivier Elemento, Jonathan G Seidman, Christine Seidman, Craig T Basson, Cathy J. Hatcher
Tbx5 Is Required For Avian And Mammalian Epicardial Formation And Coronary Vasculogenesis., Nata Y Diman, Gabriel Brooks, Boudewijn P Kruithof, Olivier Elemento, Jonathan G Seidman, Christine Seidman, Craig T Basson, Cathy J. Hatcher
PCOM Scholarly Papers
Rationale: Holt-Oram syndrome (HOS) is an autosomal dominant heart-hand syndrome caused by mutations in the TBX5 gene. Overexpression of Tbx5 in the chick proepicardial organ (PEO) impaired coronary blood vessel formation. However, the potential activity of Tbx5 in the epicardium itself, and Tbx5's role in mammalian coronary vasculogenesis, remains largely unknown. Objective: To evaluate the consequences of altered Tbx5 gene dosage during PEO and epicardial development in the embryonic chick and mouse. Methods and Results: Retroviral-mediated knockdown or upregulation of Tbx5 expression in the embryonic chick PEO as well as proepicardial-specific deletion of Tbx5 in the embryonic mouse (Tbx5(epi-/-)) impaired …
Egonet: Identification Of Human Disease Ego-Network Modules, Rendong Yang, Yun Bai, Zhaohui Qin, Tianwei Yu
Egonet: Identification Of Human Disease Ego-Network Modules, Rendong Yang, Yun Bai, Zhaohui Qin, Tianwei Yu
PCOM Scholarly Papers
Background: Mining novel biomarkers from gene expression profiles for accurate disease classification is challenging due to small sample size and high noise in gene expression measurements. Several studies have proposed integrated analyses of microarray data and protein-protein interaction (PPI) networks to find diagnostic subnetwork markers. However, the neighborhood relationship among network member genes has not been fully considered by those methods, leaving many potential gene markers unidentified. The main idea of this study is to take full advantage of the biological observation that genes associated with the same or similar diseases commonly reside in the same neighborhood of molecular networks.Results: …
Genome-Wide Sequencing Of Small Rnas Reveals A Tissue-Specific Loss Of Conserved Microrna Families In Echinococcus Granulosus, Yun Bai, Zhuangzhi Zhang, Lei Jin, Hui Kang, Yongquiang Zhu, Lu Zhang, Xia Li, Fengshou Ma, Li Zhao, Et Al.
Genome-Wide Sequencing Of Small Rnas Reveals A Tissue-Specific Loss Of Conserved Microrna Families In Echinococcus Granulosus, Yun Bai, Zhuangzhi Zhang, Lei Jin, Hui Kang, Yongquiang Zhu, Lu Zhang, Xia Li, Fengshou Ma, Li Zhao, Et Al.
PCOM Scholarly Papers
Background: MicroRNAs (miRNAs) are important post-transcriptional regulators which control growth and development in eukaryotes. The cestode Echinococcus granulosus has a complex life-cycle involving different development stages but the mechanisms underpinning this development, including the involvement of miRNAs, remain unknown. Results: Using Illumina next generation sequencing technology, we sequenced at the genome-wide level three small RNA populations from the adult, protoscolex and cyst membrane of E. granulosus. A total of 94 pre-miRNA candidates (coding 91 mature miRNAs and 39 miRNA stars) were in silico predicted. Through comparison of expression profiles, we found 42 mature miRNAs and 23 miRNA stars expressed with …
Genome-Wide Expression Analysis In Down Syndrome: Insight Into Immunodeficiency, Chong Li, Lei Jin, Yun Bai, Qimin Chen, Lijun Fu, Minjun Yang, Huasheng Xiao, Guoping Zhao, Shengyue Wang
Genome-Wide Expression Analysis In Down Syndrome: Insight Into Immunodeficiency, Chong Li, Lei Jin, Yun Bai, Qimin Chen, Lijun Fu, Minjun Yang, Huasheng Xiao, Guoping Zhao, Shengyue Wang
PCOM Scholarly Papers
Down syndrome (DS) is caused by triplication of Human chromosome 21 (Hsa21) and associated with an array of deleterious phenotypes, including mental retardation, heart defects and immunodeficiency. Genome-wide expression patterns of uncultured peripheral blood cells are useful to understanding of DS-associated immune dysfunction. We used a Human Exon microarray to characterize gene expression in uncultured peripheral blood cells derived from DS individuals and age-matched controls from two age groups: neonate (N) and child (C). A total of 174 transcript clusters (gene-level) with eight located on Hsa21 in N group and 383 transcript clusters including 56 on Hsa21 in C group …
Capturing Changes In Gene Expression Dynamics By Gene Set Differential Coordination Analysis, Tianwei Yu, Yun Bai
Capturing Changes In Gene Expression Dynamics By Gene Set Differential Coordination Analysis, Tianwei Yu, Yun Bai
PCOM Scholarly Papers
Analyzing gene expression data at the gene set level greatly improves feature extraction and data interpretation. Currently most efforts in gene set analysis are focused on differential expression analysis - finding gene sets whose genes show first-order relationship with the clinical outcome. However the regulation of the biological system is complex, and much of the change in gene expression dynamics do not manifest in the form of differential expression. At the gene set level, capturing the change in expression dynamics is difficult due to the complexity and heterogeneity of the gene sets. Here we report a systematic approach to detect …
Improving Gene Expression Data Interpretation By Finding Latent Factors That Co-Regulate Gene Modules With Clinical Factors, Tianwei Yu, Yun Bai
Improving Gene Expression Data Interpretation By Finding Latent Factors That Co-Regulate Gene Modules With Clinical Factors, Tianwei Yu, Yun Bai
PCOM Scholarly Papers
Background: In the analysis of high-throughput data with a clinical outcome, researchers mostly focus on genes/proteins that show first-order relations with the clinical outcome. While this approach yields biomarkers and biological mechanisms that are easily interpretable, it may miss information that is important to the understanding of disease mechanism and/or treatment response. Here we test the hypothesis that unobserved factors can be mobilized by the living system to coordinate the response to the clinical factors.Results: We developed a computational method named Guided Latent Factor Discovery (GLFD) to identify hidden factors that act in combination with the observed clinical factors to …
Help3 Directly Modulates The Expression Of Hsp70 Gene In Hela Cells Via Hat Activity, Fen Li, Jixian Ma, Yu Ma, Yanyan Hu, Shuhuan Tian, Richard E. White, Guichun Han
Help3 Directly Modulates The Expression Of Hsp70 Gene In Hela Cells Via Hat Activity, Fen Li, Jixian Ma, Yu Ma, Yanyan Hu, Shuhuan Tian, Richard E. White, Guichun Han
PCOM Scholarly Papers
Human Elongator complex, which plays a key role in transcript elongation in vitro assay, is incredibly similar in either components or function to its yeast counterpart. However, there are only a few studies focusing on its target gene characterization in vivo. We studied the effect of down-regulation of the human elongation protein 3 (hELP3) on the expression of HSP70 through antisense strategy. Transfecting antisense plasmid p1107 into HeLa cells highly suppressed hELP3 expression, and substantially reduced expression of HSP70 mRNA and protein. Furthermore, chromatin immunoprecipitation assay (ChIP Assay) revealed that hElp3 participates in the transcription elongation of HSPA1A in HeLa …
Taking A Bite Out Of Hypertrophic Cardiomyopathy: Soy Diet And Disease, Cathy J. Hatcher, Craig T. Basson
Taking A Bite Out Of Hypertrophic Cardiomyopathy: Soy Diet And Disease, Cathy J. Hatcher, Craig T. Basson
PCOM Scholarly Papers
Some forms of hypertrophic cardiomyopathy (HCM) are caused by mutations in cardiac sarcomeric genes, but environmental factors are believed to influence the hypertrophic response. A highly variable but potentially significant environmental factor is diet. Since soy-rich diets have been speculated to confer protection against cardiovascular disease, Stauffer et al. have explored the influence of a soy diet on cardiac growth and function in a transgenic mouse model of HCM (see the related article beginning on page 209). They report that mice fed a soy diet exhibited significantly worse HCM than mice fed a soy-free (milk protein) diet. This study provides …
Jmjd2a Is A Novel N-Cor-Interacting Protein And Is Involved In Repression Of The Human Transcription Factor Achaete Scute-Like Homologue 2 (Ascl2/Hash2), Dianzheng Zhang, Hoguen Yoon, Jiemin Wong
Jmjd2a Is A Novel N-Cor-Interacting Protein And Is Involved In Repression Of The Human Transcription Factor Achaete Scute-Like Homologue 2 (Ascl2/Hash2), Dianzheng Zhang, Hoguen Yoon, Jiemin Wong
PCOM Scholarly Papers
Corepressor N-CoR (nuclear receptor corepressor) and the highly related protein SMRT (silencing mediator of retinoid and thyroid hormone receptor) play important roles in different biological processes including proliferation, differentiation, and development. Understanding the biological function of these corepressors requires identification and characterization of their interacting proteins. Here we report the characterization of a novel N-CoR-interacting protein, JMJD2A (previously known as KIAA0677). JMJD2A is an evolutionarily conserved nuclear protein containing many functionally unknown domains. JMJD2A directly interacts with the N-terminal region of N-CoR through a small NID (N-CoR interaction domain) both in vitro and in vivo. Despite its copurification with N-CoR, …
A Digital Atlas To Characterize The Mouse Brain Transcriptome, James P. Carson, Tao Ju, Hui-Chen Lu, Christina Thaller, Mei Xu, Sarah Pallas, Michael C. Crair, Joe Warren, Wah Chiu, Gregor Eichele
A Digital Atlas To Characterize The Mouse Brain Transcriptome, James P. Carson, Tao Ju, Hui-Chen Lu, Christina Thaller, Mei Xu, Sarah Pallas, Michael C. Crair, Joe Warren, Wah Chiu, Gregor Eichele
PCOM Scholarly Papers
Massive amounts of data are being generated in an effort to represent for the brain the expression of all genes at cellular resolution. Critical to exploiting this effort is the ability to place these data into a common frame of reference. Here we have developed a computational method for annotating gene expression patterns in the context of a digital atlas to facilitate custom user queries and comparisons of this type of data. This procedure has been applied to 200 genes in the postnatal mouse brain. As an illustration of utility, we identify candidate genes that may be related to Parkinson …
A Role For Tbx5 In Proepicardial Cell Migration During Cardiogenesis, Cathy J. Hatcher, Nata Diman, Minsu Kim, David Pennisi, Yan Song, Marsha M. Goldstien, Takashi Mikawa, Craig T. Basson
A Role For Tbx5 In Proepicardial Cell Migration During Cardiogenesis, Cathy J. Hatcher, Nata Diman, Minsu Kim, David Pennisi, Yan Song, Marsha M. Goldstien, Takashi Mikawa, Craig T. Basson
PCOM Scholarly Papers
Transcriptional regulatory cascades during epicardial and coronary vascular development from proepicardial progenitor cells remain to be defined. We have used immunohistochemistry of human embryonic tissues to demonstrate that the TBX5 transcription factor is expressed not only in the myocardium, but also throughout the embryonic epicardium and coronary vasculature. TBX5 is not expressed in other human fetal vascular beds. Furthermore, immunohistochemical analyses of human embryonic tissues reveals that unlike their epicardial counterparts, delaminating epicardial-derived cells do not express TBX5 as they migrate through the subepicardium before undergoing epithelial-mesenchymal transformation required for coronary vasculogenesis. In the chick, Tbx5 is expressed in the …