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CD34+THY1+ synovial fibroblast subset in arthritic joints has high osteoblastic and chondrogenic potentials in vitro

Seiji Noda, Tadashi Hosoya, Yoji Komiya, Yasuhiro Tagawa, Kentaro Endo, Keiichiro Komori, Hideyuki Koga, Yasuhiro Takahara, Kazutaka Sugimoto, Ichiro Sekiya, Tetsuya Saito, Fumitaka Mizoguchi (+1 others)
<span title="2022-02-15">2022</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/m5rx6mbo4jhzdownmvkt3dg5vq" style="color: black;">Arthritis Research &amp; Therapy</a> </i> &nbsp;
possessed the highest osteogenic and chondrogenic potential among three subsets, while the differentiation potentials to adipocytes were comparable among the subsets regarding lipid droplet formations  ...  Consistently, the expressions of differentiation markers of the osteoblasts (RUNX2, ALPL, and OCN) or chondrocytes (ACAN) were the highest in the CD34+THY1+ subset, indicating that the CD34+THY1+ subset  ...  Data were analyzed by Dunn's multiple comparison test for comparing each subset from the same samples Fig. 5 5 Fig. 5 THY1 knockdown regulated osteoblast differentiation.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13075-022-02736-7">doi:10.1186/s13075-022-02736-7</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/35168627">pmid:35168627</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8845288/">pmcid:PMC8845288</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/eahkn6l7znecdled7vhfmow5n4">fatcat:eahkn6l7znecdled7vhfmow5n4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220426100604/https://arthritis-research.biomedcentral.com/track/pdf/10.1186/s13075-022-02736-7.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/1e/91/1e91aba27c3a3d487f73ab2a8fcd81bbbf30a935.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13075-022-02736-7"> <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/PMC8845288" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Wasserstein Learning of Determinantal Point Processes [article]

Lucas Anquetil, Mike Gartrell, Alain Rakotomamonjy, Ugo Tanielian, Clément Calauzènes
<span title="2020-11-19">2020</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
In this work, by deriving a differentiable relaxation of a DPP sampling algorithm, we present a novel approach for learning DPPs that minimizes the Wasserstein distance between the model and data composed  ...  of observed subsets.  ...  a differentiable sample from a Gumbel-Softmax distribution.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2011.09712v1">arXiv:2011.09712v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/onpygopy7bge7dawfsu3grlysu">fatcat:onpygopy7bge7dawfsu3grlysu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201121024457/https://arxiv.org/pdf/2011.09712v1.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/21/1a/211a61161630e84a35da343789e6804c286b0bd3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2011.09712v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Integrated differential DNA methylation and gene expression of formalin-fixed paraffin-embedded uveal melanoma specimens identifies genes associated with early metastasis and poor prognosis

Charlotte Ness, Kirankumar Katta, Øystein Garred, Theresa Kumar, Ole Kristoffer Olstad, Goran Petrovski, Morten C. Moe, Agate Noer
<span title="2020-12-30">2020</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/yjwblbd3d5eozhd724smr52rhy" style="color: black;">Experimental Eye Research</a> </i> &nbsp;
Integrated differential DNA methylation and gene expression of two subsets of samples identified genes associated with early metastasis and poor prognosis.  ...  "Subset Early metastasis" (n = 4) vs "Subset No metastasis" (n = 4) identified 348 DMPs and 36 DMRs, and their differential gene expression by microarray showed that 14 DMPs and 2 DMRs corresponded to  ...  Additionally, we thank GeneVia Technologies, Finland for running the differential DNA methylation analyses, and Clara-Cecilie Günther at Norwegian Computing Center (NR) for valuable help running the preliminary  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.exer.2020.108426">doi:10.1016/j.exer.2020.108426</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33387485">pmid:33387485</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/j27k7uqdefeqpehpttrg54l4c4">fatcat:j27k7uqdefeqpehpttrg54l4c4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220125173408/https://www.duo.uio.no/bitstream/handle/10852/85599/Integrated+differential+DNA+methylation+and+gene+expression+of.pdf?sequence=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/58/4c/584c0c9157726279d2cdb3c617b8eb95cb12d7cd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.exer.2020.108426"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Altered Monocyte Subsets in Kawasaki Disease Revealed by Single-cell RNA-Sequencing

Zhimin Geng, Yijing Tao, Fenglei Zheng, Linlin Wu, Ying Wang, Yujia Wang, Yameng Sun, Songling Fu, Wei Wang, Chunhong Xie, Yiying Zhang, Fangqi Gong
<span title="2021-03-16">2021</span> <i title="Informa UK Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dvo255blmbh77avlw2ptc3keem" style="color: black;">Journal of Inflammation Research</a> </i> &nbsp;
Cell trajectory analysis revealed that the three monocyte subsets represent a linear differentiation, and possess different biological functions.  ...  Bio-information analysis was utilized to identify monocyte subsets and explore their functions and differentiation states. SELL+CD14+CD16- monocytes were validated using flow cytometry.  ...  Linear Differentiation of Monocyte Subsets in Healthy Infants Differentiation continuance of monocyte subsets is not clear yet in infants.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2147/jir.s293993">doi:10.2147/jir.s293993</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33758528">pmid:33758528</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7981157/">pmcid:PMC7981157</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/u3vlparnyvdc5d7fkb2vkpowv4">fatcat:u3vlparnyvdc5d7fkb2vkpowv4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210325025043/https://www.dovepress.com/front_end/cr_data/cache/pdf/download_1616640642_605bfa82f0ec8/jir-293993-altered-monocyte-subsets-in-kawasaki-disease-revealed-by-scr.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/af/5aaf827e4f238eee8264a3e677977fde86738238.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2147/jir.s293993"> <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/PMC7981157" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

CoXpress: differential co-expression in gene expression data

Michael Watson
<span title="2006-11-20">2006</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
However, these methods may miss groups of genes which form differential co-expression patterns under different subsets of experimental conditions.  ...  The software uses a re-sampling method to calculate a p-value for each group, and provides several methods for the visualisation of differentially co-expressed genes.  ...  Expression profiles for three groups of differentially co-expressed genes from the Golub dataset [21] . A) Group 3 (n = 34) in 27 ALL samples (left) and 11 AML samples (right).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-7-509">doi:10.1186/1471-2105-7-509</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17116249">pmid:17116249</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1660556/">pmcid:PMC1660556</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vpsohpdldbhilgmywpjvylw4pm">fatcat:vpsohpdldbhilgmywpjvylw4pm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180719121729/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-7-509?site=bmcbioinformatics.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/e4/ca/e4cad765dc7676b57ee685312ca9400b5bb73ef3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-7-509"> <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/PMC1660556" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Federated Model Distillation with Noise-Free Differential Privacy [article]

Lichao Sun, Lingjuan Lyu
<span title="2021-05-21">2021</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
In this paper, we propose a novel framework called FEDMD-NFDP, which applies a Noise-Free Differential Privacy (NFDP) mechanism into a federated model distillation framework.  ...  To address this issue, one naive approach is adding the differentially private random noise to the predictions, which however brings a substantial trade-off between privacy budget and model performance  ...  Sampling with replacement is (k ln n+1 n , 1 − n−1 n k )differential privacy and sampling without replacement is (ln n+1 n+1−k , k/n)-differential privacy.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2009.05537v2">arXiv:2009.05537v2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gjrxkc2jorgqfkqougzv3xojv4">fatcat:gjrxkc2jorgqfkqougzv3xojv4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210602102752/https://arxiv.org/pdf/2009.05537v2.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/a6/ea/a6ea0785d8439be18381e04cee8bef4e878aeef8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2009.05537v2" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Transcriptional programming and T cell receptor repertoires distinguish human lung and lymph node memory T cells

Nathan Schoettler, Cara L Hrusch, Kelly M Blaine, Anne I Sperling, Carole Ober
<span title="2019-11-13">2019</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/mzxttxs3pbflldxliejplve56e" style="color: black;">Communications Biology</a> </i> &nbsp;
This study focused on CD4 and CD8 memory T cells from paired human lung and lung draining lymph node (LDLN) samples and identified substantial differences in the transcriptional landscape of these subsets  ...  T cell subsets compared across tissues.  ...  according to the tissue. b Samples are colored according to donor. c Samples are colored according to whether they were CD4 or CD8 subsets. d Samples are colored according to T cell subset Fig. 4 4  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s42003-019-0657-2">doi:10.1038/s42003-019-0657-2</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31925217">pmid:31925217</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/m5vtafawfjdalh2i2jegzlsvnq">fatcat:m5vtafawfjdalh2i2jegzlsvnq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191116021727/https://www.nature.com/articles/s42003-019-0657-2.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/60/32/6032a9c01edc1c8deaf359a68ec23496b8bd61d9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s42003-019-0657-2"> <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>

GEOlimma: differential expression analysis and feature selection using pre-existing microarray data

Liangqun Lu, Kevin A. Townsend, Bernie J. Daigle
<span title="2021-02-03">2021</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Our results suggest that use of GEOlimma provides greater experimental power to detect DE genes compared to Limma, due to its increased effective sample size.  ...  Furthermore, in a supervised classification analysis using GEOlimma as a feature selection method, we observed similar or better classification performance than Limma given small, noisy subsets of an asthma  ...  Table 3 3 Distribution of effective sample sizes from applying GEOlimma to a range of data subsets (size denoted by N) for four differential expression comparisons Asthma AML-Nonleuk Nonleuk.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-020-03932-5">doi:10.1186/s12859-020-03932-5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33535967">pmid:33535967</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7vwi6zjv7baffauwovxhirynu4">fatcat:7vwi6zjv7baffauwovxhirynu4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210204124647/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03932-5.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/24/f4/24f4f3db916c9157686db90a7b850837d5e4e9ba.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-020-03932-5"> <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>

Novel Strategy for Phenotypic Characterization of Human B Lymphocytes from Precursors to Effector Cells by Flow Cytometry

Giovanna Clavarino, Noémie Delouche, Claire Vettier, David Laurin, Martine Pernollet, Tatiana Raskovalova, Jean-Yves Cesbron, Chantal Dumestre-Pérard, Marie-Christine Jacob, R. Keith Reeves
<span title="2016-09-22">2016</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;
However, phenotypic studies are often focused on a particular type of sample (bone marrow, peripheral blood, lymphoid organs, cord blood) [8] [9] [10] or on a particular B-cell subset [11] [12] [13] [14  ...  So far, a routinely usable strategy allowing the phenotypic characterization of B-cell subpopulations throughout B-cell differentiation in samples from different anatomical sites has not been reported  ...  A precise identification of human B-cell subsets in biological samples is of crucial importance in pathological conditions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0162209">doi:10.1371/journal.pone.0162209</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27657694">pmid:27657694</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5033467/">pmcid:PMC5033467</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tn3qkcoejrbuhn3azslrr5xwl4">fatcat:tn3qkcoejrbuhn3azslrr5xwl4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171012012300/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0162209&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/0b/71/0b71b98f3b391f398870a5e41efdaac5a1de800a.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.0162209"> <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/PMC5033467" 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 HIERARCHICAL BAYESIAN APPROACH FOR DETECTING DIFFERENTIAL GENE EXPRESSION IN UNREPLICATED RNA-SEQUENCING DATA

Sanvesh Srivastava, R. W. Doerge
<span title="2011-05-01">2011</span> <i title="New Prairie Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/avievh33yza7lcwsxj2z6qwryu" style="color: black;">Conference on Applied Statistics in Agriculture</a> </i> &nbsp;
It is used for detecting differential gene expression between different biological conditions.  ...  We present a simple parametric hierarchical Bayesian model for detecting differential expression in data from unreplicated RNA-Seq experiments.  ...  From this we observe that the CIs for all the sampled genes from the first subset do not contain 0, and conclude they are differentially expressed.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4148/2475-7772.1053">doi:10.4148/2475-7772.1053</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/teajlth55jalbn4t65vx3wyxo4">fatcat:teajlth55jalbn4t65vx3wyxo4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190430161405/https://newprairiepress.org/cgi/viewcontent.cgi?referer=&amp;httpsredir=1&amp;article=1053&amp;context=agstatconference" 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/cd/ee/cdeebbe7f2d573ff73c6dbade7b7e82cb801a38d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4148/2475-7772.1053"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

GEOlimma: Differential Expression Analysis and Feature Selection Using Pre-Existing Microarray Data [article]

Liangqun Lu, Kevin Townsend, Bernie Daigle
<span title="2019-07-05">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Our results suggest that use of GEOlimma provides greater experimental power to detect DE genes compared to Limma, due to its increased effective sample size.  ...  Furthermore, in a supervised classification analysis using GEOlimma as a feature selection method, we observed similar or better classification performance than Limma given small, noisy subsets of an asthma  ...  We then increased this subset size by the smallest possible sample increment and repeated the generation of subsets.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/693564">doi:10.1101/693564</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4gqzfrhdwncfnjxgfvgl7yu54e">fatcat:4gqzfrhdwncfnjxgfvgl7yu54e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200214053707/https://www.biorxiv.org/content/biorxiv/early/2019/07/05/693564.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] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/693564"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Sensitive Gene Expression Profiling of Human T Cell Subsets Reveals Parallel Post-Thymic Differentiation for CD4+ and CD8+ Lineages

V. Appay, A. Bosio, S. Lokan, Y. Wiencek, C. Biervert, D. Kusters, E. Devevre, D. Speiser, P. Romero, N. Rufer, S. Leyvraz
<span title="2007-11-19">2007</span> <i title="The American Association of Immunologists"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/pbkbyur74rdkdgx2mbqyooa75e" style="color: black;">Journal of Immunology</a> </i> &nbsp;
ϩ or CD4 ϩ T cell subsets of differentiation.  ...  Naive and highly differentiated cell samples were hybridized in a competitive manner on the microarrays (in duplicate) to provide differential gene expression profiles between these two subsets.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4049/jimmunol.179.11.7406">doi:10.4049/jimmunol.179.11.7406</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18025184">pmid:18025184</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2ur3zaporvfbhfuvay2iqiuz3a">fatcat:2ur3zaporvfbhfuvay2iqiuz3a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190426125511/http://www.jimmunol.org/content/jimmunol/179/11/7406.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/af/54/af54a6eb3bc56750acdf04eeae25b2edab271da4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4049/jimmunol.179.11.7406"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling in cancer cells

Jian-Rong Li, Chuan-Hu Sun, Wenyuan Li, Rou-Fang Chao, Chieh-Chen Huang, Xianghong Jasmine Zhou, Chun-Chi Liu
<span title="2015-11-23">2015</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;
The genome-wide transcriptome profiling of cancerous and normal tissue samples can provide insights into the molecular mechanisms of cancer initiation and progression.  ...  coding-transcript profiling, long non-coding RNA (lncRNA) profiling and coexpression networks; (ii) phenotype-oriented data organization and searching and (iii) the visualization of expression profiles, differential  ...  subsets with no overlapping samples and from the same data set.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkv1282">doi:10.1093/nar/gkv1282</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26602695">pmid:26602695</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4702907/">pmcid:PMC4702907</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7xrnmyhkergrxigab2wrxptawe">fatcat:7xrnmyhkergrxigab2wrxptawe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190226023526/http://pdfs.semanticscholar.org/77d3/e8262a98712a7aaa8552c5d2beae82967c49.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/77/d3/77d3e8262a98712a7aaa8552c5d2beae82967c49.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkv1282"> <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/PMC4702907" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Distinct transcriptional control in major immunogenetic subsets of chronic lymphocytic leukemia exhibiting subset-biased global DNA methylation profiles

Meena Kanduri, Millaray Marincevic, Anna M. Halldórsdóttir, Larry Mansouri, Katarina Junevik, Stavroula Ntoufa, Hanna Göransson Kultima, Anders Isaksson, Gunnar Juliusson, Per-Ola Andersson, Hans Ehrencrona, Kostas Stamatopoulos (+1 others)
<span title="2012-12-17">2012</span> <i title="Informa UK Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lkovtdud7bactlc5fb4ffvecii" style="color: black;">Epigenetics</a> </i> &nbsp;
Recent studies have also revealed an important association between stereotyped BcRs and clinical outcome for certain subsets. 6,10,11 For instance, subset #1 cases typically express heavy chains encoded  ...  Specifically, the expression was significantly lower in subset #1 samples compared with subset #4 samples (CD80 p = 0.0002, CD86 p = 0.002, Fig. 3A) .  ...  Recent studies have also shown that levels in subset #1 and subset #4 patient samples.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4161/epi.22901">doi:10.4161/epi.22901</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23154584">pmid:23154584</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3528698/">pmcid:PMC3528698</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nno3utmlfne2zdyagyope6eiva">fatcat:nno3utmlfne2zdyagyope6eiva</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200208125236/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3528698&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/bf/a8/bfa86f94fbbdd11bb4bceb184da717c2b1a57f3b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4161/epi.22901"> <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/PMC3528698" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

An Epigenetically Distinct Subset of Children With Autism Spectrum Disorder Resulting From Differences in Blood Cell Composition

Maryam Jangjoo, Sarah J. Goodman, Sanaa Choufani, Brett Trost, Stephen W. Scherer, Elizabeth Kelley, Muhammad Ayub, Rob Nicolson, Stelios Georgiades, Jennifer Crosbie, Russell Schachar, Evdokia Anagnostou (+2 others)
<span title="2021-04-16">2021</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4kchoxo3jrfubkck3y7nfncina" style="color: black;">Frontiers in Neurology</a> </i> &nbsp;
The CpG sites at which this subset was differentially methylated mapped to known ASD risk genes that encode proteins of the nervous and immune systems.  ...  differential methylation from both controls than the remaining ASD cases.  ...  Samples labeled with red and yellow represent the ASD subset and the remaining ASD cases, respectively, blue samples represent controls. and clinical data were assessed against DNAm in all samples for  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fneur.2021.612817">doi:10.3389/fneur.2021.612817</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33935932">pmid:33935932</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8085304/">pmcid:PMC8085304</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dnipo6gqhvc6repsp2zynynyn4">fatcat:dnipo6gqhvc6repsp2zynynyn4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210423182455/https://fjfsdata01prod.blob.core.windows.net/articles/files/612817/pubmed-zip/.versions/1/.package-entries/fneur-12-612817/fneur-12-612817.pdf?sv=2018-03-28&amp;sr=b&amp;sig=triN3mu6zU05cB68Ig%2B49ApBRmWkbjv6RJSW1twwFAM%3D&amp;se=2021-04-23T18%3A25%3A24Z&amp;sp=r&amp;rscd=attachment%3B%20filename%2A%3DUTF-8%27%27fneur-12-612817.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/d3/4c/d34cf0b2b2e4795b49b62c3609afb27073c8e951.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fneur.2021.612817"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8085304" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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