Genomes and Genes
Summary: Sets of structured vocabularies used for describing and categorizing genes, and gene products by their molecular function, involvement in biological processes, and cellular location. These vocabularies and their associations to genes and gene products (Gene Ontology annotations) are generated and curated by the Gene Ontology Consortium.
Publications109 found, 100 shown here
- Guo B, Defaveri J, Sotelo G, Nair A, Merilä J. Population genomic evidence for adaptive differentiation in Baltic Sea three-spined sticklebacks. BMC Biol. 2015;13:19 pubmed publisher..Taken together, our results provide strong evidence for heterogenic genomic divergence driven by local adaptation in the face of gene flow along an environmental gradient in the post-glacially formed Baltic Sea. ..
- Kiseleva Y, Ptitsyn K, Tikhonova O, Radko S, Kurbatov L, Vakhrushev I, et al. [PCR analysis of the absolute number of copies of human chromosome 18 transcripts in liver and HepG2 cells]. Biomed Khim. 2017;63:147-153 pubmed publisher..Razlichiia transkriptomnykh profile? dolzhny uchityvat'sia pri ispol'zovanii kletok linii HepG2 v kachestve modeli gepatotsitov pecheni. ..
- Reinhold D, Morrow J, Jacobson S, Hu J, Ringel B, Seibold M, et al. Meta-analysis of peripheral blood gene expression modules for COPD phenotypes. PLoS ONE. 2017;12:e0185682 pubmed publisher..06); some associations were stronger in the case-control cohorts, and others in the cases-only subcohorts. Gene Ontology terms that were overrepresented included "immune response" and "defense response...
- Wu X, Ruan L, Yang Y, Mei Q. Analysis of gene expression changes associated with human carcinoma-associated fibroblasts in non-small cell lung carcinoma. Biol Res. 2017;50:6 pubmed publisher..Then we performed gene ontology (GO) and pathway enrichment analysis and protein-protein interaction (PPI) network construction using the ..
- Zhu Y, Li B, Wu T, Ye L, Zeng Y, Zhang Y. Cell cycle and histone modification genes were decreased in placenta tissue from unexplained early miscarriage. Gene. 2017;636:17-22 pubmed publisher..05). After Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, we found that almost down-regulation ..
- Lavallée Adam M, Cloutier P, Coulombe B, Blanchette M. Functional 5' UTR motif discovery with LESMoN: Local Enrichment of Sequence Motifs in biological Networks. Nucleic Acids Res. 2017;45:10415-10427 pubmed publisher..these motifs are evolutionary conserved and the genes containing them are significantly enriched for various gene ontology terms suggesting new associations between 5' UTR motifs and a number of biological processes...
- Xu K, Niu Q, Zhao H, Du Y, Jiang Y. Transcriptomic analysis to uncover genes affecting cold resistance in the Chinese honey bee (Apis cerana cerana). PLoS ONE. 2017;12:e0179922 pubmed publisher..Across the temperature treatments, 501 DEGs were identified. A gene ontology analysis showed that DEGs were enriched in pathways related to sugar and amino acid biosynthesis and ..
- Cheng X, Xiao X, Chou K. pLoc-mVirus: Predict subcellular localization of multi-location virus proteins via incorporating the optimal GO information into general PseAAC. Gene. 2017;628:315-321 pubmed publisher..Using the multi-label theory, we present a new predictor called "pLoc-mVirus" by extracting the optimal GO (Gene Ontology) information into the general PseAAC (Pseudo Amino Acid Composition)...
- Brown L, Williams J, Taylor L, Thomson R, Nolan P, Foster R, et al. Meta-analysis of transcriptomic datasets identifies genes enriched in the mammalian circadian pacemaker. Nucleic Acids Res. 2017;45:9860-9873 pubmed publisher..SCN-enriched transcripts identified in this study provide novel insights into SCN function, including identifying genes which may play key roles in SCN physiology or provide SCN-specific drivers...
- Yip B, Steeples V, Repapi E, Armstrong R, Llorian M, Roy S, et al. The U2AF1S34F mutation induces lineage-specific splicing alterations in myelodysplastic syndromes. J Clin Invest. 2017;127:2206-2221 pubmed publisher..These data have critical implications for understanding MDS phenotypic heterogeneity and support the development of therapies targeting splicing abnormalities. ..
- Lv Y. Proteome-wide profiling of protein lysine acetylation in Aspergillus flavus. PLoS ONE. 2017;12:e0178603 pubmed publisher..Our findings illustrating abundant lysine acetylation in A. flavus expand our understanding of the fungal acetylome and provided insight into the regulatory roles of acetylation in secondary metabolism. ..
- Lv Y, Wang Y, Sun J, Gong C, Chen Y, Su G, et al. MicroRNA profiles of fibroblasts derived from in vivo fertilized and fat-1 transgenic cattle. Gene. 2017;636:70-77 pubmed publisher..Together, these results suggest that miRNAs potentially play a role in expression of lipogenic and lipolytic genes as well as in synthesis of ?-3 fatty acids facilitated by fat-1. ..
- Pokorn T, Radisek S, Javornik B, Stajner N, Jakse J. Development of hop transcriptome to support research into host-viroid interactions. PLoS ONE. 2017;12:e0184528 pubmed publisher..These results provide a deep transcriptome of hop and the first insights into complex viroid-hop plant interactions. ..
- Rhee C, Lee B, Beck S, LeBlanc L, Tucker H, Kim J. Mechanisms of transcription factor-mediated direct reprogramming of mouse embryonic stem cells to trophoblast stem-like cells. Nucleic Acids Res. 2017;45:10103-10114 pubmed publisher..Therefore, we reveal that CAG factors function as both decommission and pioneer factors during ES to TS-like cell fate conversion. ..
- Shi L, Zhang N, Xie X, Chen Y, Wang R, Shen L, et al. Transcriptome profile of rat genes in injured spinal cord at different stages by RNA-sequencing. BMC Genomics. 2017;18:173 pubmed publisher..05 by DESeq. Gene ontology (GO) enrichment analysis showed that differentially expressed genes were most enriched in immune response, MHC ..
- Liew Y, Li Y, Baumgarten S, Voolstra C, Aranda M. Condition-specific RNA editing in the coral symbiont Symbiodinium microadriaticum. PLoS Genet. 2017;13:e1006619 pubmed publisher..This in turn may provide further acclimatization capacity to these organisms, and by extension, their coral hosts. ..
- Song J, Hu Y, Li J, Zheng H, Wang J, Guo L, et al. Different microRNA profiles reveal the diverse outcomes induced by EV71 and CA16 infection in human umbilical vein endothelial cells using high-throughput sequencing. PLoS ONE. 2017;12:e0177657 pubmed publisher..b>Gene ontology (GO) and pathway analysis of the predicted targets showed the enrichment of 14 biological processes, 9 ..
- Martina F, Beccuti M, Balbo G, Cordero F. Peculiar Genes Selection: A new features selection method to improve classification performances in imbalanced data sets. PLoS ONE. 2017;12:e0177475 pubmed publisher..Finally, the Gene Ontology enrichments performed on the signatures selected with the proposed pipeline, confirm the biological relevance ..
- Muller M, Seifert S, Lübbe T, Leuschner C, Finkeldey R. De novo transcriptome assembly and analysis of differential gene expression in response to drought in European beech. PLoS ONE. 2017;12:e0184167 pubmed publisher..This study gives first insights into the genomic drought stress response of European beech, and provides new genetic resources for adaptation research in this species. ..
- Li X, Ye Y, Ng M, Wu Q. MultiFacTV: module detection from higher-order time series biological data. BMC Genomics. 2013;14 Suppl 4:S2 pubmed publisher..indeed identifies some interesting modules in these datasets, which have been validated and explained by Gene Ontology analysis with DAVID or other analysis...
- Luo S, Cao N, Tang Y, Gu W. Identification of key microRNAs and genes in preeclampsia by bioinformatics analysis. PLoS ONE. 2017;12:e0178549 pubmed publisher..The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses of the DEGs were performed ..
- Schmidt A, Forne I, Imhof A. Bioinformatic analysis of proteomics data. BMC Syst Biol. 2014;8 Suppl 2:S3 pubmed publisher..Here we discuss current strategies on how to gather, filter and analyze proteomic data sates using available software packages. ..
- Ma C, Wang Y, Gu D, Nan J, Chen S, Li H. Overexpression of S-Adenosyl-l-Methionine Synthetase 2 from Sugar Beet M14 Increased Arabidopsis Tolerance to Salt and Oxidative Stress. Int J Mol Sci. 2017;18: pubmed publisher..To our knowledge, the function of the sugar beet SAMS has not been reported before. Our results have provided new insights into SAMS functions in sugar beet. ..
- Wang X, Li W, Zhang Y, Feng Y, Zhao X, He Y, et al. Chronic obstructive pulmonary disease candidate gene prioritization based on metabolic networks and functional information. PLoS ONE. 2017;12:e0184299 pubmed publisher..Top 100 genes might be potential markers for diagnostic and effective therapies. ..
- Chen L, Zhang Y, Wang S, Zhang Y, Huang T, Cai Y. Prediction and analysis of essential genes using the enrichments of gene ontology and KEGG pathways. PLoS ONE. 2017;12:e0184129 pubmed publisher..this study, we investigated the essential and non-essential genes reported in a previous study and extracted gene ontology (GO) terms and biological pathways that are important for the determination of essential genes...
- Li T, Qi X, Zeng Q, Xiang Z, He N. MorusDB: a resource for mulberry genomics and genome biology. Database (Oxford). 2014;2014: pubmed publisher..predicted genes and functional annotations, expressed sequence tags (ESTs), transposable elements (TEs), Gene Ontology (GO) terms, horizontal gene transfers between mulberry and silkworm and ortholog and paralog groups...
- Mao Y, Van Auken K, Li D, Arighi C, McQuilton P, Hayman G, et al. Overview of the gene ontology task at BioCreative IV. Database (Oxford). 2014;2014: pubmed publisherb>Gene ontology (GO) annotation is a common task among model organism databases (MODs) for capturing gene function data from journal articles...
- Wan Z, Song F, Sun Z, Chen Y, Zhang W, Samartzis D, et al. Aberrantly expressed long noncoding RNAs in human intervertebral disc degeneration: a microarray related study. Arthritis Res Ther. 2014;16:465 pubmed publisher..Our study noted that up-regulated RP11-296A18.3 highly likely induced the over-expression of FAF1, which eventually promoted the aberrant apoptosis of disc cells. Such findings further broaden the understanding of the etiology of IDD. ..
- Meinken J, Walker G, Cooper C, Min X. MetazSecKB: the human and animal secretome and subcellular proteome knowledgebase. Database (Oxford). 2015;2015: pubmed publisher..We also compared the protein families in secretomes of different primates. The Gene Ontology and protein family domain analysis of human secreted proteins revealed that these proteins play important ..
- Xiao Q, Wang Y, Du J, Li H, Wei B, WANG Y, et al. ZmMYB14 is an important transcription factor involved in the regulation of the activity of the ZmBT1 promoter in starch biosynthesis in maize. FEBS J. 2017;284:3079-3099 pubmed publisher..Our results provide crucial information related to the regulation of starch biosynthesis in maize and would be helpful in devising strategies for modulating starch production in maize endosperm. ..
- Lin Y, Zhu J, Wang Y, Li Q, Lin S. Identification of differentially expressed genes through RNA sequencing in goats (Capra hircus) at different postnatal stages. PLoS ONE. 2017;12:e0182602 pubmed publisher..Functional classification by Gene Ontology (GO) analysis was used for selecting the genes showing highest expression related to lipid metabolism...
- Ibn Salem J, Kohler S, Love M, Chung H, Huang N, Hurles M, et al. Deletions of chromosomal regulatory boundaries are associated with congenital disease. Genome Biol. 2014;15:423 pubmed publisher..Our results suggest that enhancer adoption caused by deletions of regulatory boundaries may contribute to a substantial minority of copy-number variation phenotypes and should thus be taken into account in their medical interpretation. ..
- Gabriele M, Vulto van Silfhout A, Germain P, Vitriolo A, Kumar R, Douglas E, et al. YY1 Haploinsufficiency Causes an Intellectual Disability Syndrome Featuring Transcriptional and Chromatin Dysfunction. Am J Hum Genet. 2017;100:907-925 pubmed publisher..Collectively, these results define a clinical syndrome caused by haploinsufficiency of YY1 through dysregulation of key transcriptional regulators. ..
- Espitia C, Saldarriaga O, Travi B, Osorio E, Hernandez A, Band M, et al. Transcriptional profiling of the spleen in progressive visceral leishmaniasis reveals mixed expression of type 1 and type 2 cytokine-responsive genes. BMC Immunol. 2014;15:38 pubmed publisher..Further dissection of mechanisms that lead to polarization of macrophages toward a permissive state is needed to fully understand the pathogenesis of visceral leishmaniasis. ..
- Sui W, Shi Z, Xue W, Ou M, Zhu Y, Chen J, et al. Circular RNA and gene expression profiles in gastric cancer based on microarray chip technology. Oncol Rep. 2017;37:1804-1814 pubmed publisher..Among them, 2,390 differentially expressed genes were upregulated and 3,070 genes were downregulated. Gene Ontology (GO) analysis of the differentially expressed genes revealed these genes involved in biological process ..
- Gao R, Li J. Correspondence of D. melanogaster and C. elegans developmental stages revealed by alternative splicing characteristics of conserved exons. BMC Genomics. 2017;18:234 pubmed publisher..b>Gene ontology and KEGG enrichment analyses provide a detailed functional annotation of the identified stage-associated exons,..
- Wang X, Wen X, Zhou J, Qi Y, Wu R, Wang Y, et al. MicroRNA-223 and microRNA-21 in peripheral blood B cells associated with progression of primary biliary cholangitis patients. PLoS ONE. 2017;12:e0184292 pubmed publisher..Taken together, our study offers novel perspectives on the role of miRNAs in PBC pathogenesis. ..
- Wang D, Li L, Wu G, Vasseur L, Yang G, Huang P. De novo transcriptome sequencing of Isaria cateniannulata and comparative analysis of gene expression in response to heat and cold stresses. PLoS ONE. 2017;12:e0186040 pubmed publisher..These results enhance our understanding of the molecular mechanisms of I. cateniannulata in response to temperature stresses and provide a valuable resource for the future investigations...
- Xiang Z, Qin T, Qin Z, He Y. A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks. BMC Syst Biol. 2013;7 Suppl 3:S9 pubmed publisher..The GenoMesh algorithm and web program provide the first genome-wide, MeSH-based literature mining system that effectively predicts implicit gene-gene interaction relationships and networks in a genome-wide scope. ..
- Khan I, Chen Y, Dong T, Hong X, Takeuchi R, Mori H, et al. Genome-scale identification and characterization of moonlighting proteins. Biol Direct. 2014;9:30 pubmed publisher..First, we analyzed Gene Ontology (GO) annotations of known moonlighting proteins...
- Kim H, Shim J, Shin J, Lee I. EcoliNet: a database of cofunctional gene network for Escherichia coli. Database (Oxford). 2015;2015: pubmed publisher..All integrated cofunctional associations can be downloaded, enabling orthology-based reconstruction of gene networks for other bacterial species as well. Database URL: http://www.inetbio.org/ecolinet. ..
- Moni M, Lio P. Genetic Profiling and Comorbidities of Zika Infection. J Infect Dis. 2017;216:703-712 pubmed publisher..The difficulty in distinguishing infection by Zika virus (ZIKV) from other flaviviruses is a global health concern, particularly given the high risk of neurologic complications (including Guillain-Barré syndrome [GBS]) with ZIKV infection...
- Naour S, Espinoza B, Aedo J, Zuloaga R, Maldonado J, Bastias Molina M, et al. Transcriptomic analysis of the hepatic response to stress in the red cusk-eel (Genypterus chilensis): Insights into lipid metabolism, oxidative stress and liver steatosis. PLoS ONE. 2017;12:e0176447 pubmed publisher..This study offers an integrative molecular and biochemical analysis of the hepatic response to handling-stress, and reveals unknown aspects of lipid metabolism in a non-model teleost. ..
- CUTLER A, Dammer E, Doung D, Seyfried N, Corbett A, Pavlath G. Biochemical isolation of myonuclei employed to define changes to the myonuclear proteome that occur with aging. Aging Cell. 2017;16:738-749 pubmed publisher..Our technique will enable future studies into a heretofore underrepresented compartment of skeletal muscle...
- Fast I, Hewel C, Wester L, Schumacher J, Gebert D, Zischler H, et al. Temperature-responsive miRNAs in Drosophila orchestrate adaptation to different ambient temperatures. RNA. 2017;23:1352-1364 pubmed publisher..Together, our results show that small RNAs are an important part of epigenetic regulatory mechanisms that ensure homeostasis and adaptation under fluctuating environmental conditions. ..
- Chen T, van Steensel B. Comprehensive analysis of nucleocytoplasmic dynamics of mRNA in Drosophila cells. PLoS Genet. 2017;13:e1006929 pubmed publisher..Our approach provides insights into the genome-wide nucleocytoplasmic kinetics of mRNA and should be generally applicable to other cell systems. ..
- Fu C, Zeng Q, Li F, Wang H, Sun J, Wang H. Comparative Transcriptome Analysis Reveals Related Regulatory Mechanisms of Androgenic Gland in Eriocheir sinensis. Biomed Res Int. 2017;2017:4956216 pubmed publisher..A total of 72,000 unigenes and 4,027 differentially expressed genes were obtained. Gene ontology enrichment analysis indicated that biological processes and metabolic pathways related to protein synthesis ..
- Liu W, Laulederkind S, Hayman G, Wang S, Nigam R, Smith J, et al. OntoMate: a text-mining tool aiding curation at the Rat Genome Database. Database (Oxford). 2015;2015: pubmed publisher..With the use of bioNLP tools, RGD has added more automation to its curation workflow. Database URL: http://rgd.mcw.edu. ..
- He L, Zhang A, Chu P, Li Y, Huang R, Liao L, et al. Deep Illumina sequencing reveals conserved and novel microRNAs in grass carp in response to grass carp reovirus infection. BMC Genomics. 2017;18:195 pubmed publisher..The present study provides a new insight into understanding the mechanism underlying GCRV pathogenesis and hemorrhagic symptoms. ..
- Fan W, Zhong Y, Qin M, Lin B, Chen F, Yan H, et al. Differentially expressed microRNAs in diapausing versus HCl-treated Bombyx embryos. PLoS ONE. 2017;12:e0180085 pubmed publisher..The potential target genes of differentially expressed miRNAs were predicted by miRanda. Gene Ontology and KEGG pathway enrichment analysis of these potential target genes revealed that they were mainly located ..
- Belair D, Wolf C, Wood C, Ren H, Grindstaff R, Padgett W, et al. Engineering human cell spheroids to model embryonic tissue fusion in vitro. PLoS ONE. 2017;12:e0184155 pubmed publisher..The method described here may broadly apply to the generation of three-dimensional epithelial-mesenchymal co-cultures to study developmental fusion events in a format that is amenable to predictive toxicology applications. ..
- Hubstenberger A, Courel M, Bénard M, Souquere S, Ernoult Lange M, Chouaib R, et al. P-Body Purification Reveals the Condensation of Repressed mRNA Regulons. Mol Cell. 2017;68:144-157.e5 pubmed publisher..Thus, we uncovered how P-bodies, by condensing and segregating repressed mRNAs, provide a physical substrate for the coordinated regulation of posttranscriptional mRNA regulons...
- Zhou H, Rezaei J, Hugo W, Gao S, Jin J, Fan M, et al. Stringent DDI-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions. BMC Syst Biol. 2013;7 Suppl 6:S6 pubmed publisher..DDI-based approach for predicting PPIs based on gold standard intra-species PPIs and coherent informative Gene Ontology terms assessment...
- Wu M, Kwoh C, Li X, Zheng J. Finding trans-regulatory genes and protein complexes modulating meiotic recombination hotspots of human, mouse and yeast. BMC Syst Biol. 2014;8:107 pubmed publisher..Moreover, the experimental data and results are available on our web site http://www.ntu.edu.sg/home/zhengjie/data/RecombinationHotspot/NetPipe/. ..
- Engchuan W, Dhindsa K, Lionel A, Scherer S, Chan J, Merico D. Performance of case-control rare copy number variation annotation in classification of autism. BMC Med Genomics. 2015;8 Suppl 1:S7 pubmed publisher..annotations (brain expression, synaptic components and neurodevelopmental phenotypes) outperform Gene Ontology and pathway-based annotations...
- Wei H, Li K, Zhang S, Cao Y, Yin J. Identification of candidate chemosensory genes by transcriptome analysis in Loxostege sticticalis Linnaeus. PLoS ONE. 2017;12:e0174036 pubmed publisher..sticticalis. Our findings will provide the basic knowledge for further studies on the molecular mechanisms of the olfactory system of L. sticticalis and potential novel targets for pest control strategies. ..
- Zhang H, Yin L, Wang H, Wang G, Ma X, Li M, et al. Genome-wide identification of Hami melon miRNAs with putative roles during fruit development. PLoS ONE. 2017;12:e0180600 pubmed publisher..Specific miRNAs could be selected for further research and applications in breeding practices. ..
- Delacher M, Imbusch C, Weichenhan D, Breiling A, Hotz Wagenblatt A, Träger U, et al. Genome-wide DNA-methylation landscape defines specialization of regulatory T cells in tissues. Nat Immunol. 2017;18:1160-1172 pubmed publisher..Thus, tissue Treg cells integrate multiple waves of epigenetic reprogramming that define their tissue-restricted specialization. ..
- Kooi I, Mol B, Moll A, van der Valk P, de Jong M, de Graaf P, et al. Loss of photoreceptorness and gain of genomic alterations in retinoblastoma reveal tumor progression. EBioMedicine. 2015;2:660-70 pubmed publisher..Therefore, retinoblastomas should not be categorized in distinct subtypes, but be described according to their stage of progression. ..
- . Expansion of the Gene Ontology knowledgebase and resources. Nucleic Acids Res. 2017;45:D331-D338 pubmed publisherThe Gene Ontology (GO) is a comprehensive resource of computable knowledge regarding the functions of genes and gene products...
- Su S, Chen S, Lu I, Chiang Y, Wang Y, Chen P, et al. TEA: the epigenome platform for Arabidopsis methylome study. BMC Genomics. 2016;17:1027 pubmed publisher..It provides several ways to help users exploit WGBS data. TEA is freely accessible for academic users at: http://tea.iis.sinica.edu.tw . ..
- Wei Q, Khan I, Ding Z, Yerneni S, Kihara D. NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology. BMC Bioinformatics. 2017;18:177 pubmed publisher..With the well-defined structure and manual curation, Gene Ontology (GO) is the most frequently used vocabulary for representing gene functions...
- Hajrah N, Obaid A, Atef A, Ramadan A, Arasappan D, Nelson C, et al. Transcriptomic analysis of salt stress responsive genes in Rhazya stricta. PLoS ONE. 2017;12:e0177589 pubmed publisher..Although the results of PPR gene family indicated regulation of a large number of transcripts under salt stress, PPR actions were independent of the salt stress because their RNA editing patterns were unchanged. ..
- Singh A, Sharma A, Singh N, Sharma T. PpTFDB: A pigeonpea transcription factor database for exploring functional genomics in legumes. PLoS ONE. 2017;12:e0179736 pubmed publisher..sequence repeats (SSRs) with primers derived from their motifs, orthology with related legume crops, and gene ontology (GO) assignment to respective TFs. (PpTFDB: http://22.214.171.124/PpTFDB/Home...
- Jin X, Xu Z, Cao J, Shao P, Zhou M, Qin Z, et al. Proteomics analysis of human placenta reveals glutathione metabolism dysfunction as the underlying pathogenesis for preeclampsia. Biochim Biophys Acta. 2017;1865:1207-1214 pubmed publisher..Results of this study revealed that glutathione metabolism disorder of placenta tissues may contribute to the occurrence of PE disease. ..
- Deng M, Dong Y, Zhao Z, Li Y, Fan G. Dissecting the proteome dynamics of the salt stress induced changes in the leaf of diploid and autotetraploid Paulownia fortunei. PLoS ONE. 2017;12:e0181937 pubmed publisher..This study offers a better understanding of the mechanisms of salt tolerance in P. fortunei and provides a list of potential target genes that could be engineered for salt acclimation in plants, especially trees. ..
- Wang Y, Qian X. Joint clustering of protein interaction networks through Markov random walk. BMC Syst Biol. 2014;8 Suppl 1:S9 pubmed publisher..Experimental results demonstrate that ASModel outperforms the existing single network clustering algorithms as well as another recent joint clustering algorithm in terms of complex prediction and Gene Ontology (GO) enrichment analysis.
- Chen B, Sirota M, Fan Minogue H, Hadley D, Butte A. Relating hepatocellular carcinoma tumor samples and cell lines using gene expression data in translational research. BMC Med Genomics. 2015;8 Suppl 2:S5 pubmed publisher..Our study will be used to guide the selection of HCC cell lines and pinpoint the specific genes that are differentially expressed in either tumors or cell lines. ..
- Yu F, Yang Z, Hu X, Sun Y, Lin H, Wang J. Protein complex detection in PPI networks based on data integration and supervised learning method. BMC Bioinformatics. 2015;16 Suppl 12:S3 pubmed publisher..In addition, our protein complexes detection method can achieve better performance than ClusterONE. ..
- Li H, Hu T, Amombo E, Fu J. Transcriptome profilings of two tall fescue (Festuca arundinacea) cultivars in response to lead (Pb) stress. BMC Genomics. 2017;18:145 pubmed publisher..b>Gene ontology (GO) and pathway enrichment analysis demonstrated that the DEGs were mainly implicated in energy metabolism, ..
- Yang M, You W, Wu S, Fan Z, Xu B, Zhu M, et al. Global transcriptome analysis of Huperzia serrata and identification of critical genes involved in the biosynthesis of huperzine A. BMC Genomics. 2017;18:245 pubmed publisher..The transcriptome data from this work not only could provide an important resource for further investigating on metabolic pathways in H. serrata, but also shed light on synthetic biology study of HupA. ..
- Liu X, Yang Z, Lin H, Simmons M, Lu Z. DIGNiFI: Discovering causative genes for orphan diseases using protein-protein interaction networks. BMC Syst Biol. 2017;11:23 pubmed publisher..since genes with similar phenotypes tend to be functionally related, we have integrated PPI data with gene ontology (GO) annotations and protein complex data to further improve the performance of this approach...
- Sutphin G, Backer G, Sheehan S, Bean S, Corban C, Liu T, et al. Caenorhabditis elegans orthologs of human genes differentially expressed with age are enriched for determinants of longevity. Aging Cell. 2017;16:672-682 pubmed publisher..elegans as a comparative tool for prioritizing human candidate aging genes, confirm age-associated gene expression data as valuable source of novel longevity determinants, and prioritize select genes for mechanistic follow-up...
- Chen Z, Guo X, Chen Z, Chen W, Wang J. Identification and positional distribution analysis of transcription factor binding sites for genes from the wheat fl-cDNA sequences. Biosci Biotechnol Biochem. 2017;81:1125-1135 pubmed publisher..Moreover, the positional distribution of TFBSs indicates that some types of wheat TFBS have different positional distribution preferences in the upstream regions of genes. ..
- Xu E, Mager E, Grosell M, Stieglitz J, Hazard E, Hardiman G, et al. Developmental transcriptomic analyses for mechanistic insights into critical pathways involved in embryogenesis of pelagic mahi-mahi (Coryphaena hippurus). PLoS ONE. 2017;12:e0180454 pubmed publisher..analysis by multiple bioinformatic tools, a larger number of significantly altered genes and more diverse gene ontology terms were observed during transition 2 than transition 1...
- Xiao J, Jin R, Yu X, Shen M, Wagner J, Pai A, et al. Cis and trans determinants of epigenetic silencing by Polycomb repressive complex 2 in Arabidopsis. Nat Genet. 2017;49:1546-1552 pubmed publisher..Thus PRC2 recruitment in Arabidopsis relies in large part on binding of trans-acting factors to cis-localized DNA sequence motifs. ..
- Taha K. GRtoGR: a system for mapping GO relations to gene relations. IEEE Trans Nanobioscience. 2013;12:289-97 pubmed..We evaluated GRtoGR experimentally and compared it with nine other methods. Results showed marked improvement. ..
- Atreya R, Sun J, Zhao Z. Exploring drug-target interaction networks of illicit drugs. BMC Genomics. 2013;14 Suppl 4:S1 pubmed publisher..The observation of illicit-related drugs, with partial verification from previous studies, demonstrated that the network-assisted approach is promising for the identification of drug repositioning. ..
- Tan F, Tu H, Liang W, Long J, Wu X, Zhang H, et al. Comparative metabolic and transcriptional analysis of a doubled diploid and its diploid citrus rootstock (C. junos cv. Ziyang xiangcheng) suggests its potential value for stress resistance improvement. BMC Plant Biol. 2015;15:89 pubmed publisher..Compared to diploid, higher expression level of stress related genes and higher content of stress related metabolites in doubled diploid could be beneficial for its stress tolerance. ..
- Kumagai Y, Vandenbon A, Teraguchi S, Akira S, Suzuki Y. Genome-wide map of RNA degradation kinetics patterns in dendritic cells after LPS stimulation facilitates identification of primary sequence and secondary structure motifs in mRNAs. BMC Genomics. 2016;17:1032 pubmed publisher..Identification of novel motif candidates implied post-transcriptional controls different from that by known pairs of RNA-binding protein and RNA motif. ..
- Laurent B, Moinard M, Spataro C, Ponts N, Barreau C, Foulongne Oriol M. Landscape of genomic diversity and host adaptation in Fusarium graminearum. BMC Genomics. 2017;18:203 pubmed publisher..The annotated genetic variants discovered for this major pathogen are valuable resources for further genetic and genomic studies. ..
- Wang X, Xu Y, Zhang S, Cao L, Huang Y, Cheng J, et al. Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction. Nat Genet. 2017;49:765-772 pubmed publisher..This study provides new insights into citrus apomixis and constitutes a promising resource for the mining of agriculturally important genes. ..
- Baruah I, Panda D, M V J, Das D, Acharjee S, Sen P, et al. Bruchid egg induced transcript dynamics in developing seeds of black gram (Vigna mungo). PLoS ONE. 2017;12:e0176337 pubmed publisher..This library would be useful to clone defense related gene(s) such as defensin as represented in our library for crop improvement. ..
- Ezura K, Ji Seong K, Mori K, Suzuki Y, Kuhara S, Ariizumi T, et al. Genome-wide identification of pistil-specific genes expressed during fruit set initiation in tomato (Solanum lycopersicum). PLoS ONE. 2017;12:e0180003 pubmed publisher..This study provides important information about pistil-specific genes, which may play specific roles in regulating pistil development in relation to fruit set. ..