Abstract：
:The development of convenient serum bioassays for cancer screening, diagnosis, prognosis, and monitoring of treatment is one of top priorities in cancer research community. Although numerous biomarker candidates have been generated by applying high-throughput technologies such as transcriptomics, proteomics, and metabolomics, few of them have been successfully validated in the clinic. Better strategies to mine omics data for successful biomarker discovery are needed. Using a data set of 22,794 tumor and normal samples across 23 tissues, we systematically analyzed current problems and challenges of serum biomarker discovery from gene expression data. We first performed tissue specificity analysis to identify genes that are both tissue-specific and up-regulated in tumors compared to controls, but identified few novel candidates. Then, we designed a novel computation method, the multiple normal tissues corrected differential analysis (MNTDA), to identify genes that are expected to be significantly up-regulated even after their expressions in other normal tissues are considered, and, in a simulation study, showed that the multiple normal tissues corrected differential analysis outperformed the single tissue differential analysis combined with tissue specificity analysis. By applying the multiple normal tissues corrected differential analysis, we identified some genes as novel biomarker candidates. However, the number of potential candidates was disappointingly small, exemplifying the difficulty of finding serum cancer biomarkers. We discussed a few important points that should be considered during biomarker discovery from omics data.
journal_name
J Biomed Informjournal_title
Journal of biomedical informaticsauthors
Jin H,Lee HC,Park SS,Jeong YS,Kim SYdoi
10.1016/j.jbi.2011.08.010subject
Has Abstractpub_date
2011-12-01 00:00:00pages
1076-85issue
6eissn
1532-0464issn
1532-0480pii
S1532-0464(11)00137-7journal_volume
44pub_type
杂志文章abstract：:We studied how lagged linear regression can be used to detect the physiologic effects of drugs from data in the electronic health record (EHR). We systematically examined the effect of methodological variations ((i) time series construction, (ii) temporal parameterization, (iii) intra-subject normalization, (iv) diffe...
journal_title：Journal of biomedical informatics
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journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2012.01.002
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journal_title：Journal of biomedical informatics
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journal_title：Journal of biomedical informatics
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journal_title：Journal of biomedical informatics
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journal_title：Journal of biomedical informatics
pub_type： 杂志文章
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journal_title：Journal of biomedical informatics
pub_type： 杂志文章
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journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2015.06.014
更新日期：2015-12-01 00:00:00
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journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2007.11.006
更新日期：2008-08-01 00:00:00
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journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2018.07.015
更新日期：2018-09-01 00:00:00
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journal_title：Journal of biomedical informatics
pub_type： 杂志文章,评审
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journal_title：Journal of biomedical informatics
pub_type： 杂志文章,评审
doi：10.1016/j.jbi.2019.103159
更新日期：2019-05-01 00:00:00
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journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2014.10.002
更新日期：2015-02-01 00:00:00
abstract：:The Foundational Model of Anatomy (FMA), initially developed as an enhancement of the anatomical content of UMLS, is a domain ontology of the concepts and relationships that pertain to the structural organization of the human body. It encompasses the material objects from the molecular to the macroscopic levels that c...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2003.11.007
更新日期：2003-12-01 00:00:00
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journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2020.103634
更新日期：2021-01-01 00:00:00
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journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2016.03.015
更新日期：2016-06-01 00:00:00
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journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2012.11.003
更新日期：2013-04-01 00:00:00
abstract：:Attention Deficit Hyperactive Disorder (ADHD) is one of the most common diseases in school aged children. In this paper, we consider using fMRI data with classification techniques to aid the diagnosis of ADHD and propose a bi-objective ADHD classification scheme based on L1-norm support vector machine (SVM). In our cl...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2018.07.011
更新日期：2018-08-01 00:00:00
abstract：:The 2014 i2b2/UTHealth natural language processing shared task featured a track focused on the de-identification of longitudinal medical records. For this track, we de-identified a set of 1304 longitudinal medical records describing 296 patients. This corpus was de-identified under a broad interpretation of the HIPAA ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2015.07.020
更新日期：2015-12-01 00:00:00
abstract：:Phylogeography is a field that focuses on the geographical lineages of species such as vertebrates or viruses. Here, geographical data, such as location of a species or viral host is as important as the sequence information extracted from the species. Together, this information can help illustrate the migration of the...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2011.06.005
更新日期：2011-12-01 00:00:00
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journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2016.05.007
更新日期：2016-08-01 00:00:00
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journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2017.07.017
更新日期：2017-09-01 00:00:00
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journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2013.01.005
更新日期：2013-06-01 00:00:00
abstract：:Multi-dimensional Bayesian network classifiers (MBCs) are probabilistic graphical models recently proposed to deal with multi-dimensional classification problems, where each instance in the data set has to be assigned to more than one class variable. In this paper, we propose a Markov blanket-based approach for learni...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2012.07.010
更新日期：2012-12-01 00:00:00
abstract：:The National Drug File - Reference Terminology (NDF-RT) is a large and complex drug terminology consisting of several classification hierarchies on top of an extensive collection of drug concepts. These hierarchies provide important information about clinical drugs, e.g., their chemical ingredients, mechanisms of acti...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2017.07.013
更新日期：2017-09-01 00:00:00
abstract：:The 2014 i2b2/UTHealth natural language processing shared task featured a track focused on identifying risk factors for heart disease (specifically, Cardiac Artery Disease) in clinical narratives. For this track, we used a "light" annotation paradigm to annotate a set of 1304 longitudinal medical records describing 29...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2015.05.009
更新日期：2015-12-01 00:00:00
abstract：:In this case study, we describe a method that has potential to provide systematic support for public health information management. Public health agencies depend on specialized information that travels throughout an organization via communication networks among employees. Interactions that occur within these networks ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2006.09.004
更新日期：2007-08-01 00:00:00
abstract：:Domain reference ontologies represent knowledge about a particular part of the world in a way that is independent from specific objectives, through a theory of the domain. An example of reference ontology in biomedical informatics is the Foundational Model of Anatomy (FMA), an ontology of anatomy that covers the entir...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2005.09.002
更新日期：2006-06-01 00:00:00
abstract：:This study developed a medicine query system based on Semantic Web and open data especially for self-medication users to search over-the-counter (OTC) medicines. Most existing medicine query systems are based on keyword searches. If users are uncertain about the exact search words, these query systems do not offer eff...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2020.103504
更新日期：2020-08-01 00:00:00
abstract：:Hypotheses of homology are the basis of phylogenetic analysis. All character data are considered to be equivalent regardless of the source of those characters. Putative homology statements are designated based on observations of similarity. Pairwise sequence alignment using the Needleman-Wunsch algorithm is the basis ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章,评审
doi：10.1016/j.jbi.2005.11.005
更新日期：2006-02-01 00:00:00
