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Ontological knowledge

Jian Ma, Zhi Zheng, Jiri Stiller, Xiu-Jin Lan, Yaxi Liu, Mei Deng, Penghao Wang, Zhien Pu, Guangdeng Chen, Qian-Tao Jiang, Yuming Wei, You-Liang Zheng
Gene loss during the formation of hexaploid bread wheat has been repeatedly reported. However, our knowledge on genome-wide analysis of the genes present on a single subgenome (SSG) in bread wheat is still limited. In this study, by analysing the 'Chinese Spring' chromosome arm shotgun sequences together with high-confidence gene models, we detected 433 genes on a SSG. Greater gene loss was observed in A and D subgenomes compared with B subgenome. More than 79% of the orthologs for these SSG genes were detected in diploid and tetraploid relatives of hexaploid wheat...
November 1, 2016: Genome Génome / Conseil National de Recherches Canada
Rohini Chopra-Dewasthaly, Melanie Korb, René Brunthaler, Reinhard Ertl
Mycoplasma agalactiae is a worldwide serious pathogen of small ruminants that usually spreads through the mammary route causing acute to subacute mastitis progressing to chronic persistent disease that is hard to eradicate. Knowledge of mechanisms of its pathogenesis and persistence in the mammary gland are still insufficient, especially the host-pathogen interplay that enables it to reside in a chronic subclinical state. This study reports transcriptome profiling of mammary tissue from udders of sheep experimentally infected with M...
2017: PloS One
Hasti Ziaimatin, Tudor Groza, Tania Tudorache, Jane Hunter
Collaboration platforms provide a dynamic environment where the content is subject to ongoing evolution through expert contributions. The knowledge embedded in such platforms is not static as it evolves through incremental refinements - or micro-contributions. Such refinements provide vast resources of tacit knowledge and experience. In our previous work, we proposed and evaluated a Semantic and Time-dependent Expertise Profiling (STEP) approach for capturing expertise from micro-contributions. In this paper we extend our investigation to structured micro-contributions that emerge from an ontology engineering environment, such as the one built for developing the International Classification of Diseases (ICD) revision 11...
December 2016: Journal of Intelligent Information Systems
Ze Peng, Fengxia Liu, Liping Wang, Hai Zhou, Dev Paudel, Lubin Tan, James Maku, Maria Gallo, Jianping Wang
The molecular mechanisms of symbiosis in cultivated peanut with a 'crack entry' infection process are largely understudied. In this study, we investigated the root transcriptional profiles of two pairs of non-nodulating (nod-) and nodulating (nod+) sister inbred peanut lines, E4/E5 and E7/E6, and their nod+ parents, F487A and PI262090 during rhizobial infection and nodule initiation by using RNA-seq technology. A total of 143, 101, 123, 215, 182, and 289 differentially expressed genes (DEGs) were identified in nod- E4, E7 and nod+ E5, E6, F487A, and PI262090 after inoculation with Bradyrhizobium sp...
January 6, 2017: Scientific Reports
Wei Gao, Abdul Qudair Baig, Haidar Ali, Wasim Sajjad, Mohammad Reza Farahani
In biology field, the ontology application relates to a large amount of genetic information and chemical information of molecular structure, which makes knowledge of ontology concepts convey much information. Therefore, in mathematical notation, the dimension of vector which corresponds to the ontology concept is often very large, and thus improves the higher requirements of ontology algorithm. Under this background, we consider the designing of ontology sparse vector algorithm and application in biology. In this paper, using knowledge of marginal likelihood and marginal distribution, the optimized strategy of marginal based ontology sparse vector learning algorithm is presented...
January 2017: Saudi Journal of Biological Sciences
Soo Young Cho, Minhye Choi, Hyo-Jeong Ban, Chang Hyeon Lee, Soojun Park, HanKyeom Kim, Young-Sik Kim, Young Seek Lee, Ji-Yun Lee
Cervical small cell neuroendocrine tumors (CSCNETs) are rare, aggressive neuroendocrine tumors (NETs). Reliable diagnostic and prognostic CSCNET markers are lacking, making diagnosis and prognosis prediction difficult, and treatment strategies limited. Here we provide mutation profiles for five tumor-normal paired CSCNETs using whole exome sequencing (WES). We expanded our assessment of frequently mutated genes to include publicly available data from 55 small intestine neuroendocrine tumors, 10 pancreatic neuroendocrine tumors, 42 small cell lung cancers, six NET cell lines, and 188 cervical cancers, along with our five CSCNETs...
December 22, 2016: Oncotarget
Jun Wang, James T Lamer, Sarah Gaughan, Michael Wachholtz, Chenghui Wang, Guoqing Lu
Bighead carp (Hypophthalmichthys nobilis) and silver carp (Hypophthalmichthys molitrix), collectively called bigheaded carps, are invasive species in the Mississippi River Basin (MRB). Interspecific hybridization between bigheaded carps has been considered rare within their native rivers in China; however, it is prevalent in the MRB. We conducted de novo transcriptome analysis of pure and hybrid bigheaded carps and obtained 40,759 to 51,706 transcripts for pure, F1 hybrid, and backcross bigheaded carps. The search against protein databases resulted in 20,336-28,133 annotated transcripts (over 50% of the transcriptome) with over 13,000 transcripts mapped to 23 Gene Ontology biological processes and 127 KEGG metabolic pathways...
December 2016: Ecology and Evolution
Nirin Udomsom, Amit Rai, Hideyuki Suzuki, Jun Okuyama, Ryosuke Imai, Tetsuya Mori, Ryo Nakabayashi, Kazuki Saito, Mami Yamazaki
The hairy roots (HR) of Ophiorrhiza pumila produce camptothecin (CPT), a monoterpenoid indole alkaloid used as a precursor in the synthesis of chemotherapeutic drugs. O. pumila HR culture is considered as a promising alternative source of CPT, however, the knowledge about the biosynthetic pathway and regulatory mechanism is still limited. In this study, five genes that encode AP2/ERF transcription factors, namely OpERF1-OpERF5, were isolated from HR of O. pumila. Phylogenetic analysis of AP2/ERF protein sequences suggested the close evolutionary relationship of OpERF1 with stress-responsive ERF factors in Arabidopsis and of OpERF2 with ERF factors reported to regulate alkaloid production, such as ORCA3 in Catharanthus roseus, NIC2 locus ERF in tobacco, and JRE4 in tomato...
2016: Frontiers in Plant Science
Sebastian John, Rashmi Mishra
Background: Galectins, a family of non-classically secreted, β-galactoside binding proteins is involved in several brain disorders; however, no systematic knowledge on the normal neuroanatomical distribution and functions of galectins exits. Hence, the major purpose of this study was to understand spatial distribution and predict functions of galectins in brain and also compare the degree of conservation vs. divergence between mouse and human species. The latter objective was required to determine the relevance and appropriateness of studying galectins in mouse brain which may ultimately enable us to extrapolate the findings to human brain physiology and pathologies...
2016: Frontiers in Molecular Neuroscience
Amy F Savage, Nikolay G Kolev, Joseph B Franklin, Aurelien Vigneron, Serap Aksoy, Christian Tschudi
African trypanosomes, the causative agents of sleeping sickness in humans and nagana in animals, have a complex digenetic life cycle between a mammalian host and an insect vector, the blood-feeding tsetse fly. Although the importance of the insect vector to transmit the disease was first realized over a century ago, many aspects of trypanosome development in tsetse have not progressed beyond a morphological analysis, mainly due to considerable challenges to obtain sufficient material for molecular studies. Here, we used high-throughput RNA-Sequencing (RNA-Seq) to profile Trypanosoma brucei transcript levels in three distinct tissues of the tsetse fly, namely the midgut, proventriculus and salivary glands...
2016: PloS One
Tanja Waldmann, Marianna Grinberg, André König, Eugen Rempel, Stefan Schildknecht, Margit Henry, Anna-Katharina Holzer, Nadine Dreser, Vaibhav Shinde, Agapios Sachinidis, Jörg Rahnenführer, Jan G Hengstler, Marcel Leist
Analysis of transcriptome changes has become an established method to characterize the reaction of cells to toxicants. Such experiments are mostly performed at compound concentrations close to the cytotoxicity threshold. At present, little information is available on concentration-dependent features of transcriptome changes, in particular, at the transition from noncytotoxic concentrations to conditions that are associated with cell death. Thus, it is unclear in how far cell death confounds the results of transcriptome studies...
December 21, 2016: Chemical Research in Toxicology
Hang Zhou, Yang Yang, Hong-Bin Shen
MOTIVATION: Protein subcellular localization prediction has been an important research topic in computational biology over the last decade. Various automatic methods have been proposed to predict locations for large scale protein datasets, where statistical machine learning algorithms are widely used for model construction. A key step in these predictors is encoding the amino acid sequences into feature vectors. Many studies have shown that features extracted from biological domains, such as gene ontology and functional domains, can be very useful for improving the prediction accuracy...
December 19, 2016: Bioinformatics
Efejiro Ashano, Itunuoluwa Isewon, Jelili Oyelade, Ezekiel Adebiyi
In this study, we interpreted RNA-seq time-course data of three developmental stages of Plasmodium species by clustering genes based on similarities in their expression profile without prior knowledge of the gene function. Functional enrichment of clusters of upregulated genes at specific time-points reveals potential targetable biological processes with information on their timings. We identified common consensus sequences that these clusters shared as potential points of coordinated transcriptional control...
2016: F1000Research
Riqiang Liu, Tianhua Liu, Wei Wei, Kun Guo, Ning Yang, Siqi Tian, Jia Zhu, Yinkun Liu, Wenting Zhou, Huawei Yang
Ribosomal S6 protein kinase 4 (RSK4) is an important novel tumor suppressor that inhibits breast cancer cell growth and induces senescence. However, RSK4m, which is a variant of RSK4 resulting from alternative splicing, may play distinct roles in some aspects. Knowledge about the mechanisms of RSK4 or RSK4m activity has been lacking. Analysis of the RSK4 and RSK4m interactome could provide insight into their specific functions and integrative mechanisms. Using tandem affinity purification, we obtained protein complexes that interacted with RSK4 or RSK4m...
December 13, 2016: International Journal of Biological Macromolecules
Yan Li, Manoj Thomas, Kweku-Muata Osei-Bryson, Jason Levy
With the growing popularity of data analytics and data science in the field of environmental risk management, a formalized Knowledge Discovery via Data Analytics (KDDA) process that incorporates all applicable analytical techniques for a specific environmental risk management problem is essential. In this emerging field, there is limited research dealing with the use of decision support to elicit environmental risk management (ERM) objectives and identify analytical goals from ERM decision makers. In this paper, we address problem formulation in the ERM understanding phase of the KDDA process...
December 15, 2016: International Journal of Environmental Research and Public Health
Boris Kotchoubey, Felix Tretter, Hans A Braun, Thomas Buchheim, Andreas Draguhn, Thomas Fuchs, Felix Hasler, Heiner Hastedt, Thilo Hinterberger, Georg Northoff, Ingo Rentschler, Stephan Schleim, Stephan Sellmaier, Ludger Tebartz Van Elst, Wolfgang Tschacher
Neuroscience is a multidisciplinary effort to understand the structures and functions of the brain and brain-mind relations. This effort results in an increasing amount of data, generated by sophisticated technologies. However, these data enhance our descriptive knowledge, rather than improve our understanding of brain functions. This is caused by methodological gaps both within and between subdisciplines constituting neuroscience, and the atomistic approach that limits the study of macro- and mesoscopic issues...
2016: Frontiers in Integrative Neuroscience
Hai Fang, Bogdan Knezevic, Katie L Burnham, Julian C Knight
BACKGROUND: Biological interpretation of genomic summary data such as those resulting from genome-wide association studies (GWAS) and expression quantitative trait loci (eQTL) studies is one of the major bottlenecks in medical genomics research, calling for efficient and integrative tools to resolve this problem. RESULTS: We introduce eXploring Genomic Relations (XGR), an open source tool designed for enhanced interpretation of genomic summary data enabling downstream knowledge discovery...
December 13, 2016: Genome Medicine
Yunli Wang, Rene Richard, Youlian Pan
BACKGROUND: Expression quantitative trait loci (eQTL) mapping is often used to identify genetic loci and candidate genes correlated with traits. Although usually a group of genes affect complex traits, genes in most eQTL mapping methods are considered as independent. Recently, some eQTL mapping methods have accounted for correlated genes, used biological prior knowledge and applied these in model species such as yeast or mouse. However, biological prior knowledge might be very limited for most species...
December 13, 2016: BMC Bioinformatics
Jie Mei, Ming-Qing Li, Da-Jin Li, Hai-Xiang Sun
The chemokine stromal cell-derived factor-1 (C-X-C motif chemokine ligand 12; CXCL12) is important in the recruitment of leukocytes to the peritoneal cavity and the regulation of endometriotic tissue growth in endometriosis patients. However, the alterations in microRNA (miRNA) expression induced by CXCL12 remain to be fully elucidated. The present study evaluated key miRNAs in CXCL12‑stimulated endometrial stromal cells (ESCs), and investigated the underlying cellular regulatory mechanisms of CXCL12 in endometriosis by building networks between miRNAs, genes and gene ontologies (GOs)...
January 2017: Molecular Medicine Reports
Karin Verspoor, Anika Oellrich, Nigel Collier, Tudor Groza, Philippe Rocca-Serra, Larisa Soldatova, Michel Dumontier, Nigam Shah
This special issue covers selected papers from the 18th Bio-Ontologies Special Interest Group meeting and Phenotype Day, which took place at the Intelligent Systems for Molecular Biology (ISMB) conference in Dublin in 2015. The papers presented in this collection range from descriptions of software tools supporting ontology development and annotation of objects with ontology terms, to applications of text mining for structured relation extraction involving diseases and phenotypes, to detailed proposals for new ontologies and mapping of existing ontologies...
December 12, 2016: Journal of Biomedical Semantics
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