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The massive genomic data from The Cancer Genome Atlas (TCGA), including proteomics data from Clinical Proteomic Tumor Analysis Consortium (CPTAC), provides a unique opportunity to study cancer systematically. While most observations are made from a single type of genomics data, we apply big data analytics and systems biology approaches by simultaneously analyzing DNA amplification, mRNA and protein abundance. Using multiple genomic profiles, we have discovered widespread dosage compensation for the extensive aneuploidy observed in TCGA breast cancer samples. We do identify 11 genes that show strong correlation across all features (DNA/mRNA/protein) analogous to that of the well-known oncogene HER2 (ERBB2). These genes are generally less well-characterized regarding their role in cancer and we advocate their further study. We also discover that shRNA knockdown of these genes has an impact on cancer cell growth, suggesting a vulnerability that could be used for cancer therapy. Our study shows the advantages of systematic big data methodologies and also provides future research directions.
This article was published in the following journal.
Name: PloS one
Pathway enrichment analysis helps researchers gain mechanistic insight into gene lists generated from genome-scale (omics) experiments. This method identifies biological pathways that are enriched in ...
Integrative analysis of multi-omics data from different high-throughput experimental platforms provides valuable insight into regulatory mechanisms associated with complex diseases, and gains statisti...
Sequencing the first genome took 15 yr and $3 billion to complete. Currently, a genome can be sequenced in a day for a few thousand dollars. Comparing the relative abundance of nearly every mRNA trans...
Co-inertia analysis (CIA) is a multivariate statistical analysis method that can assess relationships and trends in two sets of data. Recently CIA has been used for an integrative analysis of multiple...
Compartmentalized translation allows rapid synthesis of proteins in targeted cellular locations. Microarray and RNA sequencing combined with physical subcellular separation methods have enabled extens...
This study aims to analyze the multi-omics results between eutopic endometrium, adenomyosis and endometriosis of patients diagnosed of adenomyosis with and without endometriosis. The multi...
This study aims to analyze the multi-omics results between epithelial ovarian cancer (EOC) patient with different FIGO stages and pathological subtypes. The multi-omics profiles include wh...
This study aims to analyze the multi-omics results between uterine cervical adenocarcinoma patients with and without human papillomavirus (HPV) infections. The multi-omics profiles include...
The purpose of this study is to assess the validity and usefulness of omics signatures for improved identification and risk stratification of patients with endocrine hypertension and strat...
This project aims to create a digital platform for personal, clinical, diagnostic and environmental data collection, management and analysis of patients with cardiovascular and neurologica...
The number of copies of a given gene present in the cell of an organism. An increase in gene dosage (by GENE DUPLICATION for example) can result in higher levels of gene product formation. GENE DOSAGE COMPENSATION mechanisms result in adjustments to the level GENE EXPRESSION when there are changes or differences in gene dosage.
Genetic mechanisms that allow GENES to be expressed at a similar level irrespective of their GENE DOSAGE. This term is usually used in discussing genes that lie on the SEX CHROMOSOMES. Because the sex chromosomes are only partially homologous, there is a different copy number, i.e., dosage, of these genes in males vs. females. In DROSOPHILA, dosage compensation is accomplished by hypertranscription of genes located on the X CHROMOSOME. In mammals, dosage compensation of X chromosome genes is accomplished by random X CHROMOSOME INACTIVATION of one of the two X chromosomes in the female.
The molecular designing of drugs for specific purposes (such as DNA-binding, enzyme inhibition, anti-cancer efficacy, etc.) based on knowledge of molecular properties such as activity of functional groups, molecular geometry, and electronic structure, and also on information cataloged on analogous molecules. Drug design is generally computer-assisted molecular modeling and does not include pharmacokinetics, dosage analysis, or drug administration analysis.
Work consisting of the designation of an article or book as retracted in whole or in part by an author or authors or an authorized representative. It identifies a citation previously published and now retracted through a formal issuance from the author, publisher, or other authorized agent, and is distinguished from RETRACTION OF PUBLICATION, which identifies the citation retracting the original published item.
A concept, developed in 1983 under the aegis of and supported by the National Library of Medicine under the name of Integrated Academic Information Management Systems, to provide professionals in academic health sciences centers and health sciences institutions with convenient access to an integrated and comprehensive network of knowledge. It addresses a wide cross-section of users from administrators and faculty to students and clinicians and has applications to planning, clinical and managerial decision-making, teaching, and research. It provides access to various types of clinical, management, educational, etc., databases, as well as to research and bibliographic databases. In August 1992 the name was changed from Integrated Academic Information Management Systems to Integrated Advanced Information Management Systems to reflect use beyond the academic milieu.
Cancer is not just one disease but many diseases. There are more than 100 different types of cancer. Most cancers are named for the organ or type of cell in which they start - for example, cancer that begins in the colon is called colon cancer; cancer th...