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1301por Zhang, Tiefeng, Gan, Yaxin, Bai, Yulan, Hao, Weijiang, Zeng, Ziqi, Wu, Feng, Li, Xianqi“…Differentially expressed genes were identified, and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were conducted. …”
Publicado 2023
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1302por Zhao, Siqi, Nan, Yanzi, Yao, Runyu, Wang, Langhong, Zeng, Xinan, Aadil, Rana Muhammad, Shabbir, Muhammad Asim“…Gene ontology (GO) enrichment analysis revealed that hesperetin inhibits Alicyclobacillus acidoterrestris by affecting the intracellular nitrogen metabolism and amino acid metabolism. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis explained that hesperetin was also able to prevent the growth of Alicyclobacillus acidoterrestris by affecting the processes of nutrient transport, energy metabolism, and flagella motility. …”
Publicado 2023
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1303por Shen, Mingjuan, Yang, Xi, Wang, Zhenxing, Sha, Xiaomei, Zhang, Xuechun, Sun, Jian“…Through gene ontology (GO) analysis, these proteins primarily affected the cellular and metabolic processes in the biological process category. Further Kyoto encyclopedia of genes and genomes (KEGG) analysis revealed that the “proteasome; protein processing in the endoplasmic reticulum (PPER)” pathway was the most significantly enriched signaling pathway during the oxidation process of arachin. …”
Publicado 2023
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1304por Rouka, Erasmia, Zarogiannis, Sotirios G., Hatzoglou, Chrissi, Gourgoulianis, Konstantinos I., Malli, Foteini“…Co-annotation analysis of the predicted interactors with respect to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and transcription factors (TFs) pointed to the complement and coagulation cascades as well as neutrophil extracellular trap formation. …”
Publicado 2023
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1305por Guo, Haijun, Zhi, Yunqing, Wang, Kaijing, Li, Na, Yu, Danlei, Ji, Zhonghua, Chen, Bo“…Next RNA-sequence analysis identified 4,675 dysregulated genes (DGs) in resistant cells, and most of the 12 randomly selected DGs were verified to be consistent with the sequence results. Kyoto Encyclopedia of Genes and Genomes analysis indicated that several DGs were involved in resistance- and phenotype-related pathways, of which the activations of PD-L1 and ERK1/2 were both verified in resistant cell lines. …”
Publicado 2023
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1306“…In this study, we aimed to explore the frequency and impact of these hotspots in 332 STAD patients and 1,043 cancer cells using data from the Cancer Genome Atlas (TCGA) and Cancer Cell Line Encyclopedia (CCLE). We studied the rates of DSB (Double-Strand Breaks) loci in STAD patients by employing the Non-Homogeneous Poisson Distribution (λ), based on which we identified 145 DSB-hotspots with genes affected. …”
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1307por de Langen, Pierre, Hammal, Fayrouz, Guéret, Elise, Mouren, Jean-Christophe, Spinelli, Lionel, Ballester, Benoit“…We developed a meta-clustering methodology to integrate our RNAPII atlas with active transcription across 28,797 RNA sequencing (RNA-seq) samples from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), and Encyclopedia of DNA Elements (ENCODE). This analysis revealed strong tissue- and disease-specific interconnections between RNAPII occupancy and transcriptional activity. …”
Publicado 2023
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1308por Dai, Jing, Dong, Xiang, Chen, Yuxin, Xue, Wanying, Wang, Qingqing, Shang, Feifei, Zhao, Yunxia, Li, Shujing, Gao, Yu, Wang, Yuanyuan“…The gene ontology analysis and Kyoto Encyclopedia of Genes and Genomes functional pathway analysis were used to further predict the function of DEGs after the overexpression of SPOP. …”
Publicado 2023
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1309“…METHODS: We reanalyzed differentially expressed genes in the gene expression dataset GSE114990 and predicted their target genes, followed by experimental Gene Ontology (GO) analysis and (Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. …”
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1310por Triantafyllidis, Charalampos P., Barberis, Alessandro, Hartley, Fiona, Cuervo, Ana Miar, Gjerga, Enio, Charlton, Philip, van Bijsterveldt, Linda, Rodriguez, Julio Saez, Buffa, Francesca M.“…Using data from established databases (Cancer Cell Line Encyclopedia, The Cancer Genome Atlas), machine learning could predict the mutation status, but not resolve different mutations. …”
Publicado 2023
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1311“…By identifying statistically significant enrichment of GO terms, Kyoto Encyclopedia of Genes and Genomes pathways, and TRANSFAC transcription factor binding sites, users can gain substantial insight into the physiological significance of sets of differentially expressed genes. …”
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1312por Caspi, Ron, Foerster, Hartmut, Fulcher, Carol A., Hopkinson, Rebecca, Ingraham, John, Kaipa, Pallavi, Krummenacker, Markus, Paley, Suzanne, Pick, John, Rhee, Seung Y., Tissier, Christophe, Zhang, Peifen, Karp, Peter D.“…Its goal is to serve as a metabolic encyclopedia, containing a collection of non-redundant pathways central to small molecule metabolism, which have been reported in the experimental literature. …”
Publicado 2006
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1313“…We describe metabolic MANET, a database that links information in the Structural Classification of Proteins (SCOP), the Kyoto Encyclopedia of Genes and Genomes (KEGG), and phylogenetic reconstructions depicting the evolution of protein fold architecture. …”
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1314“…Motivation: KEGG PATHWAY is a service of Kyoto Encyclopedia of Genes and Genomes (KEGG), constructing manually curated pathway maps that represent current knowledge on biological networks in graph models. …”
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1315por Huss, Jon W., Lindenbaum, Pierre, Martone, Michael, Roberts, Donabel, Pizarro, Angel, Valafar, Faramarz, Hogenesch, John B., Su, Andrew I.“…Directly integrated within the online encyclopedia, Wikipedia, the goal of this effort is to build a gene-specific review article for every gene in the human genome, where each article is collaboratively written, continuously updated and community reviewed. …”
Publicado 2010
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1316por Rosenbloom, Kate R., Dreszer, Timothy R., Pheasant, Michael, Barber, Galt P., Meyer, Laurence R., Pohl, Andy, Raney, Brian J., Wang, Ting, Hinrichs, Angie S., Zweig, Ann S., Fujita, Pauline A., Learned, Katrina, Rhead, Brooke, Smith, Kayla E., Kuhn, Robert M., Karolchik, Donna, Haussler, David, Kent, W. James“…The Encyclopedia of DNA Elements (ENCODE) project is an international consortium of investigators funded to analyze the human genome with the goal of producing a comprehensive catalog of functional elements. …”
Publicado 2010
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1317por Lapidus, Alla, Pukall, Rüdiger, LaButtii, Kurt, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Chen, Feng, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Rohde, Manfred, Göker, Markus, Pati, Amrita, Ivanova, Natalia, Mavrommatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, D'haeseleer, Patrik, Chain, Patrick, Bristow, Jim, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter“…This is the first complete genome sequence of a member of the actinobacterial family Dermabacteraceae, and the 3,614,992 bp long single replicon genome with its 3129 protein-coding and 69 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.…”
Publicado 2009
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1318por Copeland, Alex, Sikorski, Johannes, Lapidus, Alla, Nolan, Matt, Del Rio, Tijana Glavina, Lucas, Susan, Chen, Feng, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Pukall, Rüdiger, Chertkov, Olga, Brettin, Thomas, Han, Cliff, Detter, John C., Kuske, Cheryl, Bruce, David, Goodwin, Lynne, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Rohde, Manfred, Göker, Markus, Bristow, Jim, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter, Detter, John C.“…This is the first complete genome sequence of the genus Atopobium, and the 1,543,805 bp long single replicon genome with its 1369 protein-coding and 49 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.…”
Publicado 2009
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1319por Mavrommatis, Konstantinos, Pukall, Rüdiger, Rohde, Christine, Chen, Feng, Sims, David, Brettin, Thomas, Kuske, Cheryl, Detter, John C., Han, Cliff, Lapidus, Alla, Copeland, Alex, Glavina Del Rio, Tijana, Nolan, Matt, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ovchinnikova, Galina, Pati, Amrita, Ivanova, Natalia, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, D'haeseleer, Patrik, Göker, Markus, Bristow, Jim, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Rohde, Manfred, Klenk, Hans-Peter, Kyrpides, Nikos C.“…This is the first complete genome sequence of the actinobacterial family Coriobacteriaceae, and this 1,617,804 bp long single replicon genome with its 1364 protein-coding and 58 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.…”
Publicado 2009
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1320por Pukall, Rüdiger, Lapidus, Alla, Nolan, Matt, Copeland, Alex, Glavina Del Rio, Tijana, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Chertkov, Olga, Bruce, David, Goodwin, Lynne, Kuske, Cheryl, Brettin, Thomas, Detter, John C., Han, Cliff, Pitluck, Sam, Pati, Amrita, Mavrommatis, Konstantinos, Ivanova, Natalia, Ovchinnikova, Galina, Chen, Amy, Palaniappan, Krishna, Schneider, Susanne, Rohde, Manfred, Chain, Patrick, D'haeseleer, Patrik, Göker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Kyrpides, Nikos C., Klenk, Hans-Peter, Hugenholtz, Philip“…This is the first complete genome sequence of the genus Slackia, and the 3,165,038 bp long single replicon genome with its 2798 protein-coding and 60 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.…”
Publicado 2009
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