The GENCODE human gene set by Searle, S., Frankish, A., Bignell, A., Aken, B., Derrien, Thomas, Diekhans, M., Harte, R., Howald, C., Kokocinski, F., Lin, M., Tress, M., Van Baren, M., Barnes, I., Hunt, T., Carvalho-Silva, D., Davidson, C., Donaldson, S., Gilbert, J., Kay, M., Lloyd, D., Loveland, J., Mudge, J., Snow, C., Vamathevan, J., Wilming, L., Brent, M., Gerstein, Mark B., Guigo, Roderic, Kellis, Manolis, Reymond, A., Zadissa, A., Valencia, A., Harrow, J., Hubbard, T.

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Quantitative model of R-loop forming structures reveals a novel level of RNA–DNA interactome complexity by Wongsurawat, Thidathip, Jenjaroenpun, Piroon, Kwoh, Chee Keong, Kuznetsov, Vladimir

“…We created R-loopDB (http://rloop.bii.a-star.edu.sg/), the database that collects all RLFS identified within over half of the human genes and links to the UCSC Genome Browser for information integration and visualisation across a variety of bioinformatics sources. …”
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Galbase: a comprehensive repository for integrating chicken multi-omics data by Weiwei Fu, Rui Wang, Naiyi Xu, Jinxin Wang, Ran Li, Hojjat Asadollahpour Nanaei, Qinghua Nie, Xin Zhao, Jianlin Han, Ning Yang, Yu Jiang

“…Additionally, a series of convenient tools, including the UCSC Genome Browser, WashU Epigenome Browser, BLAT, BLAST, and LiftOver, were also integrated to facilitate search, visualization, and analysis of sequence features. …”
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BGVD: An Integrated Database for Bovine Sequencing Variations and Selective Signatures by Ningbo Chen, Weiwei Fu, Jianbang Zhao, Jiafei Shen, Qiuming Chen, Zhuqing Zheng, Hong Chen, Tad S. Sonstegard, Chuzhao Lei, Yu Jiang

“…To further investigate and visualize the relationships between variants and signatures of selection, the Genome Browser integrates all variations, selection data, and resources, from NCBI, the UCSC Genome Browser, and Animal QTLdb. Collectively, all these features make the BGVD a useful archive for in-depth data mining and analyses of cattle biology and cattle breeding on a global scale. …”
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Differential expression profile of circRNAs in oral leukoplakia by XU Siming, SONG Yuhan, SHAO Yanxiong, TAO Lan, ZHOU Haiwen

“…CircHLA-C was visualized using the UCSC genome browser (genome.ucsc.edu). The function of differentially expressed circRNAs was analyzed by GO and KEGG enrichment analyses. …”
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Classification and monomer-by-monomer annotation dataset of suprachromosomal family 1 alpha satellite higher-order repeats in hg38 human genome assembly by L.I. Uralsky, V.A. Shepelev, A.A. Alexandrov, Y.B. Yurov, E.I. Rogaev, I.A. Alexandrov

“…The annotation can be viewed as UCSC Genome Browser custom track (the HOR-track) and used together with our previous annotation of AS suprachromosomal families (SFs) in the same assembly, where each AS monomer can be viewed in its genomic context together with its classification into one of the 5 major SFs (the SF-track). …”
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Methylation of <i>TET2</i> Promoter Is Associated with Global Hypomethylation and Hypohydroxymethylation in Peripheral Blood Mononuclear Cells of Systemic Lupus Erythematosus Patie... by Wan-Yu Sung, Yuan-Zhao Lin, Daw-Yang Hwang, Chia-Hui Lin, Ruei-Nian Li, Chia-Chun Tseng, Cheng-Chin Wu, Tsan-Teng Ou, Jeng-Hsien Yen

“…Putative transcription factors were investigated using the UCSC Genome Browser on the Human Dec. 2013 (GRCh38/hg38) Assembly. (3) Results: 5-mC and 5-hmC were both decreased in SLE. …”
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A novel mutation in PRPF31, causative of autosomal dominant retinitis pigmentosa, using the BGISEQ-500 sequencer by Yu Zheng, Hai-Lin Wang, Jian-Kang Li, Li Xu, Laurent Tellier, Xiao-Lin Li, Xiao-Yan Huang, Wei Li, Tong-Tong Niu, Huan-Ming Yang, Jian-Guo Zhang, Dong-Ning Liu

“…Data were aligned to UCSC Genome Browser build hg19, using the Burroughs Wheeler Aligner MEM algorithm. …”
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Genomic analysis of the chromosome 15q11-q13 Prader-Willi syndrome region and characterization of transcripts for GOLGA8E and WHCD1L1 from the proximal breakpoint region by Kashork Catherine D, Pan Yanzhen, Bressler Jan, Liu Qian, Wauki Kekio, Jiang Yong-hui, Shaffer Lisa G, Beaudet Arthur L

“…</p> <p>Results</p> <p>We have characterized transcripts for the first time for two UCSC Genome Browser predicted protein-coding genes, <it>GOLGA8E </it>(golgin subfamily a, 8E) and <it>WHDC1L1 </it>(WAS protein homology region containing 1-like 1) and have further characterized two previously reported genes, <it>CYF1P1 </it>and <it>NIPA2</it>; all four genes are in the region close to the proximal/centromeric deletion breakpoint (BP1). …”
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HOXD9/miR-451a/PSMB8 axis is implicated in the regulation of cell proliferation and metastasis via PI3K/AKT signaling pathway in human anaplastic thyroid carcinoma by Yong Zhong, Fan Yu, Ling Yang, Yu Wang, Lin Liu, Chengyou Jia, Haidong Cai, Jianshe Yang, Shiyang Sheng, Zhongwei Lv, Li Weng, Bo Wu, Xiaoping Zhang

“…Knockdown of HOXD9 inhibited cell proliferation, migration, invasion, and EMT but increased apoptosis in ATC cells. The UCSC Genome Browser and JASPAR database identified HOXD9 as an upstream regulator of miR-451a. …”
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Genetic variants in Hippo pathway genes are associated with house dust mite‐induced allergic rhinitis in a Chinese population by Min Chen, Rui Zheng, Fei Li, Jun‐Yi Xin, Si‐Lu Chen, Xin‐Jie Zhu, Xiang Gu, Meng‐Di Dai, Yi‐Fan Yang, Hai‐Yan Chu, Zheng‐Dong Zhang, Mei‐Ping Lu, Lei Cheng

“…Histone modification and transcription factor binding sites were visualized by UCSC genome browser. Moreover, expression qualitative trait loci (eQTL) analysis was obtained from Genotype‐Tissue Expression (GTEx) database. …”
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Exome Sequencing Diagnoses X-Linked Moesin-Associated Immunodeficiency in a Primary Immunodeficiency Case by Gabrielle Bradshaw, Robbie R. Lualhati, Cassie L. Albury, Neven Maksemous, Deidre Roos-Araujo, Robert A. Smith, Miles C. Benton, David A. Eccles, Rod A. Lea, Heidi G. Sutherland, Larisa M. Haupt, Lyn R. Griffiths

“…WES trio analysis, data filtering and in silico prediction identified a novel, damaging (SIFT: 0; Polyphen 1; Grantham score: 101) and disease-causing (MutationTaster) single base mutation in the X chromosome (c.511C &gt; T p.Arg171Trp) MSN gene not identified in the UCSC Genome Browser database. The mutation was validated by Sanger sequencing, confirming the proband was hemizygous X-linked recessive (–/T) at this locus and inherited the affected T allele from his non-symptomatic carrier mother (C/T), with other family members (father, sister) confirmed to be wild type (C/C). …”
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The value of primary transcripts to the clinical and non‐clinical genomics community: Survey results and roadmap for improvements by Joannella Morales, Aoife C. McMahon, Jane Loveland, Emily Perry, Adam Frankish, Sarah Hunt, Irina M. Armean, Paul Flicek, Fiona Cunningham

“…This was publicised on the Ensembl and UCSC genome browsers, by email and on social media. Results The survey had 788 responses from 32 different countries, the results of which we report here. …”
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GENCODE reference annotation for the human and mouse genomes

“…GENCODE gene annotations are accessible via the Ensembl and UCSC Genome Browsers, the Ensembl FTP site, Ensembl Biomart, Ensembl Perl and REST APIs as well as https://www.gencodegenes.org.…”
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GENCODE reference annotation for the human and mouse genomes by Frankish, Adam, Diekhans, Mark, Ferreira, Anne-Maud, Johnson, Rory, Jungreis, Irwin, Loveland, Jane, Mudge, Jonathan M, Sisu, Cristina, Wright, James, Armstrong, Joel, Barnes, If, Berry, Andrew, Bignell, Alexandra, Carbonell Sala, Silvia, Chrast, Jacqueline, Cunningham, Fiona, Di Domenico, Tomás, Donaldson, Sarah, Fiddes, Ian T, García Girón, Carlos, Gonzalez, Jose Manuel, Grego, Tiago, Hardy, Matthew, Hourlier, Thibaut, Hunt, Toby, Izuogu, Osagie G, Lagarde, Julien, Martin, Fergal J, Martínez, Laura, Mohanan, Shamika, Muir, Paul, Navarro, Fabio C P, Parker, Anne, Pei, Baikang, Pozo, Fernando, Ruffier, Magali, Schmitt, Bianca M, Stapleton, Eloise, Suner, Marie-Marthe, Sycheva, Irina, Uszczynska-Ratajczak, Barbara, Xu, Jinuri, Yates, Andrew, Zerbino, Daniel, Zhang, Yan, Aken, Bronwen, Choudhary, Jyoti S, Gerstein, Mark, Guigó, Roderic, Hubbard, Tim J P, Kellis, Manolis, Paten, Benedict, Reymond, Alexandre, Tress, Michael L, Flicek, Paul

“…GENCODE gene annotations are accessible via the Ensembl and UCSC Genome Browsers, the Ensembl FTP site, Ensembl Biomart, Ensembl Perl and REST APIs as well as https://www.gencodegenes.org.…”
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The Consensus Coding Sequence (Ccds) Project: Identifying a Common Protein-Coding Gene Set for the Human and Mouse Genomes by Kellis, Manolis, Lin, Michael F.

“…The collaborative consensus coding sequence (CCDS) project tracks identical protein annotations on the reference mouse and human genomes with a stable identifier (CCDS ID), and ensures that they are consistently represented on the NCBI, Ensembl, and UCSC Genome Browsers. Importantly, the project coordinates on manually reviewing inconsistent protein annotations between sites, as well as annotations for which new evidence suggests a revision is needed, to progressively converge on a complete protein-coding set for the human and mouse reference genomes, while maintaining a high standard of reliability and biological accuracy. …”
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GENCODE: The reference human genome annotation for The ENCODE Project by Lin, Michael F., Kellis, Manolis

“…GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers.…”
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