Filters








38 Hits in 3.4 sec

BodyMap incorporated PCR-based expression profiling data and a gene ranking system

J. Sese
<span title="2001-01-01">2001</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
BodyMap is a human and mouse gene expression database that is based on site-directed 3′-expressed sequence tags generated at Osaka University.  ...  In addition, a newly developed gene ranking system helps users obtain lists of genes that have desired expression patterns according to their significance.  ...  ACKNOWLEDGEMENTS This work was supported in part by a Grant-in-Aid for Scientific Research on Priority Areas, Genome Science, Medical Genome Science, and Genome Information Science  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/29.1.156">doi:10.1093/nar/29.1.156</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11125076">pmid:11125076</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC29776/">pmcid:PMC29776</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wdemc7twfrdn3giyfewvtessru">fatcat:wdemc7twfrdn3giyfewvtessru</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190224162812/http://pdfs.semanticscholar.org/5abd/5f2b581b151774628cc38386e4a5421620e5.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/5a/bd/5abd5f2b581b151774628cc38386e4a5421620e5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/29.1.156"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC29776" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Detect tissue heterogeneity in gene expression data with BioQC

Jitao David Zhang, Klas Hatje, Gregor Sturm, Clemens Broger, Martin Ebeling, Martine Burtin, Fabiola Terzi, Silvia Ines Pomposiello, Laura Badi
<span title="2017-04-04">2017</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
In a case study with whole-organ profiling data, BioQC predicted contamination events that are confirmed by quantitative RT-PCR.  ...  Gene expression data can be compromised by cells originating from other tissues than the target tissue of profiling.  ...  Acknowledgements We thank Guido Steiner, Gonzalo Durán Pacheco, and Marco Berrera for critically reading the manuscript and Laurent Essioux for discussions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12864-017-3661-2">doi:10.1186/s12864-017-3661-2</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28376718">pmid:28376718</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5379536/">pmcid:PMC5379536</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vtzv6uqgszclbasmxjqqfpxkvu">fatcat:vtzv6uqgszclbasmxjqqfpxkvu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190427151018/https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-017-3661-2" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/51/bd/51bdd24027ea7cda130f8161188f2419f633f1cf.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12864-017-3661-2"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5379536" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The GENCODE pseudogene resource

Baikang Pei, Cristina Sisu, Adam Frankish, Cédric Howald, Lukas Habegger, Xinmeng Mu, Rachel Harte, Suganthi Balasubramanian, Andrea Tanzer, Mark Diekhans, Alexandre Reymond, Tim J Hubbard (+2 others)
<span title="">2012</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rnpxl3dy6jexfas5kegb73tnbi" style="color: black;">Genome Biology</a> </i> &nbsp;
Based on their distribution, we develop simple statistical models for each type of activity, which we validate with largescale RT-PCR-Seq experiments.  ...  Results: As part of the GENCODE annotation of the human genome, we present the first genome-wide pseudogene assignment for protein-coding genes, based on both large-scale manual annotation and in silico  ...  Acknowledgements We thank the ENCODE Project Consortium and the Illumina Human Body Map project for making their data publicly available and members of the Lausanne Genomic Technologies Facility for technical  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2012-13-9-r51">doi:10.1186/gb-2012-13-9-r51</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22951037">pmid:22951037</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3491395/">pmcid:PMC3491395</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/teouzsasqbccreafugn4b6i4ou">fatcat:teouzsasqbccreafugn4b6i4ou</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170820021044/https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2012-13-9-r51?site=genomebiology.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/fa/54/fa546f05a405a35e91bb22c3ebed7ff39a4f94c2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2012-13-9-r51"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491395" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Whole-genome and transcriptome profiling of a metastatic thyroid-like follicular renal cell carcinoma

Jenny J. Ko, Jasleen K. Grewal, Tony Ng, Jean-Michel Lavoie, My Linh Thibodeau, Yaoqing Shen, Andrew J. Mungall, Greg Taylor, Kasmintan A. Schrader, Steven J.M. Jones, Christian Kollmannsberger, Janessa Laskin (+1 others)
<span title="2018-11-16">2018</span> <i title="Cold Spring Harbor Laboratory"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/vr52omacmbd27ilxbmtacnil3a" style="color: black;">Molecular Case Studies</a> </i> &nbsp;
Integrative genomic analysis with The Cancer Genome Atlas (TCGA) data set revealed the following outliers in gene expression profiles: CDK6 (81st percentile), MYC (99th percentile), AR (100th percentile  ...  Tumor somatic expression profiles were analyzed to detect aberrant expression.  ...  The results published here are in part based upon data generated by the following projects and obtained from dbGaP (http://www.ncbi.nlm.nih.gov/gap); The Cancer Genome Atlas managed by the NCI and NHGRI  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/mcs.a003137">doi:10.1101/mcs.a003137</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30446580">pmid:30446580</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6318773/">pmcid:PMC6318773</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fzxaxb2jybcrba3b5rjtgesau4">fatcat:fzxaxb2jybcrba3b5rjtgesau4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190430160144/http://molecularcasestudies.cshlp.org/content/4/6/a003137.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/61/2c/612c0aa1d2319e4c822579c559ccd0c896eea6a3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/mcs.a003137"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6318773" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Using RNA-Seq Data to Evaluate Reference Genes Suitable for Gene Expression Studies in Soybean

Aldrin Kay-Yuen Yim, Johanna Wing-Hang Wong, Yee-Shan Ku, Hao Qin, Ting-Fung Chan, Hon-Ming Lam, Sara Amancio
<span title="2015-09-08">2015</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
Differential gene expression profiles often provide important clues for gene functions.  ...  Using a probabilistic approach, we identified new and improved candidate reference genes.  ...  Qi, and S.-W. Tong for providing technical support and comments. Jee-Yan Chu copy-edited this manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0136343">doi:10.1371/journal.pone.0136343</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26348924">pmid:26348924</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4562714/">pmcid:PMC4562714</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xs7kuhmaqfad5onuow5qc4igou">fatcat:xs7kuhmaqfad5onuow5qc4igou</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171011035232/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0136343&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/fc/1b/fc1b13057f470570b543d3c8ea442f2ed5afc107.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0136343"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4562714" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Construction of a competitive endogenous RNA network and analysis of potential regulatory axis targets in glioblastoma

Kai Yu, Huan Yang, Qiao-li Lv, Li-chong Wang, Zi-long Tan, Zhe Zhang, Yu-long Ji, Qian-xia Lin, Jun-jun Chen, Wei He, Zhen Chen, Xiao-li Shen
<span title="2021-02-12">2021</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/24iikjdiwfezletlvdfiwv5xyy" style="color: black;">Cancer Cell International</a> </i> &nbsp;
Survival analysis using Gene Expression Profiling Interactive Analysis was based on the Kaplan–Meier curve method.  ...  Methods Transcriptome expression data from The Cancer Genome Atlas database and Gene Expression Omnibus were analyzed to identify differentially expressed genes between glioblastoma and normal tissues.  ...  Survival analysis of DEGs Gene Expression Profiling Interactive Analysis (GEPIA), a web server for cancer and normal gene expression profiling and interactive analysis, was used to perform survival analysis  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12935-021-01789-z">doi:10.1186/s12935-021-01789-z</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33579282">pmid:33579282</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/feq4semrybazvhoioqh2vbkdxu">fatcat:feq4semrybazvhoioqh2vbkdxu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210214035841/https://cancerci.biomedcentral.com/track/pdf/10.1186/s12935-021-01789-z.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/09/e7/09e73b30189e0d07133d2455669e630ba751022b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12935-021-01789-z"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a>

Co-expression analysis identifies long noncoding RNA SNHG1 as a novel predictor for event-free survival in neuroblastoma

Divya Sahu, Chia-Lang Hsu, Chen-Ching Lin, Tz-Wen Yang, Wen-Ming Hsu, Shinn-Ying Ho, Hsueh-Fen Juan, Hsuan-Cheng Huang
<span title="2016-08-09">2016</span> <i title="Impact Journals, LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/yubgl6cdcrekxpjzhshpw23l3i" style="color: black;">OncoTarget</a> </i> &nbsp;
Herein, we examined the expression profiles of lncRNAs and protein-coding genes between MYCN amplified and MYCN non-amplified NB from microarray (n = 47) and RNAseq datasets (n = 493).  ...  The co-expression analysis reveals lncRNA, SNHG1 and coding gene, TAF1D highly co-expressed in NB.  ...  We also thank Golam Haider, Girish Mokkapati and Dhani Ram Mahato for proofreading the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.18632/oncotarget.11158">doi:10.18632/oncotarget.11158</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27517149">pmid:27517149</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5295409/">pmcid:PMC5295409</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/d77n265w2vac3hvz547ym2cjny">fatcat:d77n265w2vac3hvz547ym2cjny</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180723235538/http://www.oncotarget.com/index.php?journal=oncotarget&amp;page=article&amp;op=download&amp;path%5B%5D=11158&amp;path%5B%5D=35338" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/de/c4/dec4bcca6916be28f81cb7bbde93e2721e0aa0ba.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.18632/oncotarget.11158"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5295409" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Regulation of CHD2 expression by the Chaserr long noncoding RNA gene is essential for viability

Aviv Rom, Liliya Melamed, Noa Gil, Micah Jonathan Goldrich, Rotem Kadir, Matan Golan, Inbal Biton, Rotem Ben-Tov Perry, Igor Ulitsky
<span title="2019-11-08">2019</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a4wan6l5o5dfzn767kyz7jqevi" style="color: black;">Nature Communications</a> </i> &nbsp;
genes.  ...  Here we show that Chaserr, a highly conserved long noncoding RNA transcribed from a region near the transcription start site of Chd2 and on the same strand, acts in concert with the CHD2 protein to maintain  ...  Data availability A reporting summary for this article is available as a Supplementary Information file.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41467-019-13075-8">doi:10.1038/s41467-019-13075-8</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31704914">pmid:31704914</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6841665/">pmcid:PMC6841665</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/g7qungojz5ffbjptznl354dh24">fatcat:g7qungojz5ffbjptznl354dh24</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200313002552/https://www.nature.com/articles/s41467-019-13075-8.pdf?error=cookies_not_supported&amp;code=705d047b-463e-4750-a62f-155cf3315855" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/66/8d/668dc6f537241a3c409340ec27cf2e29ebd22046.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41467-019-13075-8"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> nature.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6841665" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The human splicing code reveals new insights into the genetic determinants of disease

H. Y. Xiong, B. Alipanahi, L. J. Lee, H. Bretschneider, D. Merico, R. K. C. Yuen, Y. Hua, S. Gueroussov, H. S. Najafabadi, T. R. Hughes, Q. Morris, Y. Barash (+5 others)
<span title="2014-12-18">2014</span> <i title="American Association for the Advancement of Science (AAAS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qirzh7firjdsjhg4tutxtir6ey" style="color: black;">Science</a> </i> &nbsp;
We developed a computational technique that scores how strongly genetic variants alter RNA splicing, a critical step in gene expression whose disruption contributes to many diseases, including cancers  ...  Introduction-Advancing whole-genome precision medicine requires understanding how gene expression is altered by genetic variants, especially those that are outside of protein-coding regions.  ...  We thank the Center of Applied Genomics at the Toronto Hospital for Sick Children for providing HGMD annotations, Gary Schroth at Illumina for providing the BodyMap RNA-seq data, and Mike Brudno, Orion  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1126/science.1254806">doi:10.1126/science.1254806</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25525159">pmid:25525159</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4362528/">pmcid:PMC4362528</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/edozgs4f2fditd6iospuyytrge">fatcat:edozgs4f2fditd6iospuyytrge</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200502075507/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC4362528&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/4e/89/4e8935358f9dbe84d35e6222abf643fe1405c3c7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1126/science.1254806"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> sciencemag.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4362528" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Transcriptome reconstruction and annotation of cynomolgus and African green monkey

Albert Lee, Hossein Khiabanian, Jeffrey Kugelman, Oliver Elliott, Elyse Nagle, Guo-Yun Yu, Travis Warren, Gustavo Palacios, Raul Rabadan
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
We elucidate tissue-specific expression profiles and report 13 experimentally validated novel transcripts in these NHP animal models.  ...  RNA expression in NHPs provides specific signatures that are informative of disease mechanisms and therapeutic modes of action.  ...  Acknowledgements We thank Jiguang Wang for his invaluable help and comments on the manuscript. We also thank Pedro Rico and Carl Soffler for assisting with sample acquisition.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-15-846">doi:10.1186/1471-2164-15-846</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25277458">pmid:25277458</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4194418/">pmcid:PMC4194418</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rrkwbu3u4zd6dl23mjh4kbsmny">fatcat:rrkwbu3u4zd6dl23mjh4kbsmny</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20141226042128/http://www.biomedcentral.com:80/content/pdf/1471-2164-15-846.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d7/c5/d7c5107771b4caab8632d93bb6aa0ec1787e8099.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-15-846"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4194418" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A functional screen of translated pancreatic lncRNAs identifies a microprotein-independent role for LINC00261 in endocrine cell differentiation [article]

Bjoern Gaertner, Sebastiaan van Heesch, Valentin Schneider-Lunitz, Jana Felicitas Schulz, Franziska Witte, Susanne Blachut, Steven Nguyen, Regina Wong, Ileana Matta, Norbert Hubner, Maike Sander
<span title="2020-04-29">2020</span> <i title="Cold Spring Harbor Laboratory"> biorxiv/medrxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Our work highlights extensive translation of lncRNAs into recently evolved microproteins during human pancreas development and provides a blueprint for dissection of their coding and noncoding roles.  ...  Long noncoding RNAs (lncRNAs) are a heterogenous group of RNAs, which can encode small proteins.  ...  This work was supported by the National Institutes of Health (R01 DK068471 and R01 DK078803 to M.S.), an Alexander von Humboldt Foundation Research Award to M.S., and a postdoctoral fellowship from the  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.04.28.062679">doi:10.1101/2020.04.28.062679</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7nwsaapgozboxalfa2uxhuny64">fatcat:7nwsaapgozboxalfa2uxhuny64</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201104103304/http://edoc.mdc-berlin.de/18928/1/18928oa.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f0/5b/f05bdceab62ae533674c606af785040741e6484b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.04.28.062679"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Hypoxia-inducible C-to-U coding RNA editing downregulatesSDHBin monocytes

Bora E. Baysal, Kitty De Jong, Biao Liu, Jianmin Wang, Santosh K. Patnaik, Paul K. Wallace, Robert T. Taggart
<span title="2013-09-10">2013</span> <i title="PeerJ"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/eyfkjqp7sva5bbnwatk5zazi7q" style="color: black;">PeerJ</a> </i> &nbsp;
, immunologic cell separation, gene expression microarray, database analysis and high-throughput RNA sequencing.  ...  Microarray analysis showed expression changes in wound healing and immune response pathway genes as the editing rate increased in normoxic cultures.  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.7717/peerj.152">doi:10.7717/peerj.152</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24058882">pmid:24058882</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3775634/">pmcid:PMC3775634</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6zjn6v37dnhehpgkxj76jdjvlm">fatcat:6zjn6v37dnhehpgkxj76jdjvlm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170705094038/https://peerj.com/articles/152.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d4/1d/d41d1ca4edcb136cf6bd7aa92f24c70422cae894.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.7717/peerj.152"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3775634" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A coding and non-coding transcriptomic perspective on the genomics of human metabolic disease

James A Timmons, Philip J Atherton, Ola Larsson, Sanjana Sood, Ilya O Blokhin, Robert J Brogan, Claude-Henry Volmar, Andrea R Josse, Cris Slentz, Claes Wahlestedt, Stuart M Phillips, Bethan E Phillips (+2 others)
<span title="2018-07-09">2018</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
A network of ncRNA positively related to IS and interacted with RNA coding for viral response proteins (P < 1 × 10-48), while reduced amino acid catabolic gene expression occurred without a change in expression  ...  We illustrate that combining in-depth physiological phenotyping with robust RNA profiling methods, identifies molecular networks which are highly consistent with the genetics and biochemistry of human  ...  ACKNOWLEDGEMENTS We acknowledge the technical support at all clinical centers for data-production.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gky570">doi:10.1093/nar/gky570</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29986096">pmid:29986096</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6125682/">pmcid:PMC6125682</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/g2z5v4fg2ffhhp3ittqhg3jxfa">fatcat:g2z5v4fg2ffhhp3ittqhg3jxfa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210718000851/https://nottingham-repository.worktribe.com/1465637/1/gky570" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d6/33/d63300cdfe660da263e0a5bb93774985e59c7042.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gky570"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6125682" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Generation and network analysis of an RNA-seq transcriptional atlas for the rat

Kim M Summers, Stephen J Bush, Chunlei Wu, David A Hume
<span title="2022-01-13">2022</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dhm4lwu4tvbf5dklpg7zonzosa" style="color: black;">NAR Genomics and Bioinformatics</a> </i> &nbsp;
Sets of strictly co-expressed transcripts provide a resource for critical interpretation of single-cell RNA-seq data.  ...  To generate a comprehensive rat transcriptomic atlas, we curated and downloaded 7700 rat RNA-seq datasets from public repositories, downsampled them to a common depth and quantified expression.  ...  ACKNOWLEDGEMENTS Author contributions: S.J.B. developed the informatics pipeline and generated the primary expression data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nargab/lqac017">doi:10.1093/nargab/lqac017</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/35265836">pmid:35265836</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8900154/">pmcid:PMC8900154</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hyw6x6gkuvddjoetzpd5opnzeu">fatcat:hyw6x6gkuvddjoetzpd5opnzeu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220325114617/https://watermark.silverchair.com/lqac017.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAskwggLFBgkqhkiG9w0BBwagggK2MIICsgIBADCCAqsGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMQ5SetyGbDxQ6UKkCAgEQgIICfBzF4cTGGolZvWVBv6fbxCsF39vj_ZVyq4ArS3xjX9C1DrkJ7_nUfFZrCrxQcBILGr9bh9AYG-jQRmpr44dwA70V5EmgZXJM-56YuVmwf7oNg_bKyHiPxNoCTnPaYwLnnuHhiDV4DbAa-aUERMjCYHOF1_Dp4ZhffZ-eVfBXquNlyvl5cBy9lQV92XEJNTeswHIC7DDzbLjgHRIn5HnYQeW129e0dmzAsKmik_2KED4cfjWzA0_sW6XCfHOkH_N90S-3Wg3JOl2tKpmfMdIF9QV91zEIBHi9YGgFImKNH5TTpT-ShrCHyRVGjFtkKalnmeUjTgBauPXhIM7BwKjytBeT56hcDe7ZNqeqwI-3wFKB5wliTiTFXRBSb-HwbJDllEHWBQ1tVzPSwLyz5RcThU0RAqBQTqL2XP06ao5mj32OckN_mqXLNCzrrMJpTshzYqpc5I0Z5C4hUmtGxVAqMsiyW-jx8O_0iyFwlNyQIoAeq1xxXlhzi6tFdi13qck7krX4Mjdr3v7B8-AzJ4J28_NTSlMWx2MMMV-wx_kPGaMd6ni_Ck5x4lJVJHLVugk08JrmCV8QvdxjckAx0aKlnCUJ-Z_FYZTo2eAp_adVz7zPk_leWYngnlvIaJAO1mf4W0_HnpFw5T5dpAGg1UvvJIICIbjokaBTafS0t0gE1DG4ErcSUJNNANK0tmQibMdZugsyTm3jnEY3rLTuCDnnOTYGAk8RlCl43V_-P8TCClCxI-0-M-IkR4HtMqrSlxbnkJb342S5IcFfWfk7anFiKCKNEiawuCq9uWS4pKX99-oBDgWtX30wkGT0XRPcFxf5I0jT3tkdSa0goMbqtQ" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/bd/6a/bd6a55dc00455f797690d691765dab104be2f916.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nargab/lqac017"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8900154" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Identification of novel cyclin gene fusion transcripts in endometrioid ovarian carcinomas

Antonio Agostini, Marta Brunetti, Ben Davidson, Claes Göran Tropé, Sverre Heim, Ioannis Panagopoulos, Francesca Micci
<span title="2018-04-25">2018</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/vm5lxrfefrc3ziqzlhk6jlqxre" style="color: black;">International Journal of Cancer</a> </i> &nbsp;
(Image from Wikimedia commons) Bellerophon was one of the most ancient heroes of Greek mythology and a monster hunter.  ...  Since then many other fusion genes were discovered and found to be primary events in the pathogenesis of different types of cancer.  ...  Availability of data and materials The exon microarray data set is available at the Gene Expression Omnibus (GEO) data repository (http://www.ncbi.nlm.nih.gov/geo/), Series GSE83111.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/ijc.31418">doi:10.1002/ijc.31418</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29633253">pmid:29633253</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6099316/">pmcid:PMC6099316</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2zqqkcebavd2pi3gen5be3vneu">fatcat:2zqqkcebavd2pi3gen5be3vneu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190430064002/https://www.duo.uio.no/bitstream/handle/10852/62012/PhD-Agostini--2018.pdf?sequence=3" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/08/62/0862842f0d154eb9533f3fac59fe54c576c84c4f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/ijc.31418"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> wiley.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6099316" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
&laquo; Previous Showing results 1 &mdash; 15 out of 38 results