Proteogenomics of the human hippocampus: The road ahead

Kang, Myoung-Goo; Byun, Kyunghee; Kim, Jae Ho; Park, Nam Hyun; Heinsen, Helmut; Ravid, Rivka; Steinbusch, Harry W.; Lee, Bong-Hee; Park, Young Mok

doi:10.1016/j.bbapap.2015.02.010

Cited by 25 publications

(24 citation statements)

References 99 publications

(24 reference statements)

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“…The hippocampus generally consists of several subregions forming the so-called hippocampal formation, including the dentate gyrus, the subiculum, and the cornu ammonis regions with the CA1-CA4 fields (25,28,29). The dentate gyrus is thereby particularly involved in the process of generating new neurons in the hippocampus throughout life, a process called neurogenesis (30,31).…”

Section: Introduction Rationalementioning

confidence: 99%

Hippocampus—Related Cognitive and Affective Impairments in Patients With Breast Cancer—A Systematic Review

et al. 2020

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Background: Although improvements in medical treatment lead to a steadily rising survival rate of breast cancer patients (BCP), it is associated with a decrease in cognitive and affective function. The hippocampus, a brain region with a high influence on both cognitive and affective function, is increasingly becoming the focus of current research because of its high vulnerability to adverse direct (chemotherapeutic agents, endocrine therapeutic agents, and radiation) or indirect (stress and other psycho-social factors) treatment-related effects. Methods: This systematic review analyses current data from literature combining hippocampus-related brain changes due to breast cancer treatment with associated cancer-related cognitive and affective impairments (CRCI/CRAI). The seven studies that met the inclusion criteria consisted of six cross-sectional studies and one longitudinal study. Results: The study results indicate hippocampal differences across all types of treatment. Those differences include volume loss, deformation, and changes in functional connectivity. They are associated with CRCI, revealing executive function as well as working memory, episodic memory, and prospective memory as the most affected domains. Although an interaction between hippocampus-related brain changes, CRCI, and CRAI can be hypothesized, CRAI are less reflected in current research. Discussion: More research including longitudinal assessments with better overall methodology is needed to fully understand the interaction between hippocampal alterations and both CRCI and CRAI due to breast cancer treatment.

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Section: Introduction Rationalementioning

confidence: 99%

Hippocampus—Related Cognitive and Affective Impairments in Patients With Breast Cancer—A Systematic Review

et al. 2020

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“…(Note: annotations may use identifiers for genes as proxies for their products, and we use "genes" for simplicity in the remainder of this report.) The GO annotation corpus is widely used for a variety of genome-scale analyses, including broad characterization of whole genomes, interpretation of highthroughput transcriptomic and proteomic experiments, network analysis, and more [10,11,12,13,14]. In many cases, functional studies use subsets of the ontology (sometimes known as "GO Slims"), that exclude highly specific terms and take advantage of the fact that annotations are propagated over transitive relations (e.g., is a, part of ) in the ontology.…”

Section: Introductionmentioning

confidence: 99%

Term Matrix: A novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns

Wood

Carbon

Harris

et al. 2020

Preprint

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Biological processes are accomplished by the coordinated action of gene products. Gene products often participate in multiple processes, and can therefore be annotated to multiple Gene Ontology (GO) terms. Nevertheless, processes that are functionally, temporally, and/or spatially distant may have few gene products in common, and co-annotation to unrelated processes likely reflects errors in literature curation, ontology structure, or automated annotation pipelines. We have developed an annotation quality control workflow that uses rules based on mutually exclusive processes to detect annotation errors, based on and validated by case studies including the three we present here: fission yeast protein-coding gene annotations over time; annotations for cohesin complex subunits in human and model species; and annotations using a selected set of GO biological process terms in human and five model species. For each case study, we reviewed available GO annotations, identified pairs of biological processes which are unlikely to be correctly co-annotated to the same gene products (e.g., amino acid metabolism and cytokinesis), and traced erroneous annotations to their sources. To date we have generated 107 quality control rules, and corrected 289 manual annotations in eukaryotes and over 2.5 million automatically propagated annotations across all taxa.

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“…Several genes associated with monogenic Alzheimer' s disease (AD) have been identified (1); however, the disease can also be caused by polygenic and environmental risk factors (1,2). To understand the cellular processes and risk factors associated with AD, numerous transcriptomic, proteomic, and genome-wide association (GWA) studies have been conducted (3)(4)(5). Researchers are now turning to pathway-based GWA analysis and Next Generation Sequencing (NGS) to identify the genes contributing to the "missing heritability" (6,7).…”

Section: Introductionmentioning

confidence: 99%

Gene Ontology: A Resource for Analysis and Interpretation of Alzheimer’s Disease Data

Kramarz

Lovering

2019

Alzheimer’s Disease

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Gene Ontology (GO) is a universal resource for analyses and interpretation of high-throughput biological datasets. GO is developed and curated by several different groups, based at scientific institutions around the world, working together under the auspices of the GO Consortium. GO annotations capture biological functional knowledge by associating gene products with GO terms. GO term and gene product records all have computer-readable accession numbers; therefore, these annotations can be easily used for analyses of large datasets while retaining human-readable labels. The UCL Functional Gene Annotation group focuses on GO annotation of human gene products. Our group has led initiatives to systematically annotate proteins and microRNAs across specific biomedical fields, and our current biocuration effort, funded by the Alzheimer' s Research UK foundation, is focused on dementia and Alzheimer' s disease. Our group has also contributed to the development and revision of the ontology describing neurological domains of biology. Here we present an overview of GO and explain how our work, as well as the work of other members of the GO Consortium, is improving the neurological domains of the GO resource. These biocuration efforts will benefit the dementia and Alzheimer' s research community by rendering GO more suitable for analyses of neurological datasets.

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Proteogenomics of the human hippocampus: The road ahead

Cited by 25 publications

References 99 publications

Hippocampus—Related Cognitive and Affective Impairments in Patients With Breast Cancer—A Systematic Review

Hippocampus—Related Cognitive and Affective Impairments in Patients With Breast Cancer—A Systematic Review

Term Matrix: A novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns

Gene Ontology: A Resource for Analysis and Interpretation of Alzheimer’s Disease Data

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