Tolerance Associated Gene Expression following Allogeneic Hematopoietic Cell Transplantation
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{"title"=>"Tolerance associated gene expression following allogeneic hematopoietic cell transplantation", "type"=>"journal", "authors"=>[{"first_name"=>"Joseph", "last_name"=>"Pidala", "scopus_author_id"=>"35230759800"}, {"first_name"=>"Gregory C.", "last_name"=>"Bloom", "scopus_author_id"=>"7102667851"}, {"first_name"=>"Steven", "last_name"=>"Eschrich", "scopus_author_id"=>"6602433990"}, {"first_name"=>"Minnie", "last_name"=>"Sarwal", "scopus_author_id"=>"12780413800"}, {"first_name"=>"Steve", "last_name"=>"Enkemann", "scopus_author_id"=>"6602736734"}, {"first_name"=>"Brian C.", "last_name"=>"Betts", "scopus_author_id"=>"36698697500"}, {"first_name"=>"Francisca", "last_name"=>"Beato", "scopus_author_id"=>"57192977162"}, {"first_name"=>"Sean", "last_name"=>"Yoder", "scopus_author_id"=>"7006127884"}, {"first_name"=>"Claudio", "last_name"=>"Anasetti", "scopus_author_id"=>"56687651500"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84925264706", "doi"=>"10.1371/journal.pone.0117001", "sgr"=>"84925264706", "issn"=>"19326203", "pui"=>"603024234"}, "id"=>"f0bc325d-7836-3722-900a-955e33389878", "abstract"=>"Biologic markers of immune tolerance may facilitate tailoring of immune suppression duration after allogeneic hematopoietic cell transplantation (HCT). In a cross-sectional study, peripheral blood samples were obtained from tolerant (n = 15, median 38.5 months post-HCT) and non-tolerant (n = 17, median 39.5 post-HCT) HCT recipients and healthy control subjects (n = 10) for analysis of immune cell subsets and differential gene expression. There were no significant differences in immune subsets across groups. We identified 281 probe sets unique to the tolerant (TOL) group and 122 for non-tolerant (non-TOL). These were enriched for process networks including NK cell cytotoxicity, antigen presentation, lymphocyte proliferation, and cell cycle and apoptosis. Differential gene expression was enriched for CD56, CD66, and CD14 human lineage-specific gene expression. Differential expression of 20 probe sets between groups was sufficient to develop a classifier with > 90% accuracy, correctly classifying 14/15 TOL cases and 15/17 non-TOL cases. These data suggest that differential gene expression can be utilized to accurately classify tolerant patients following HCT. Prospective investigation of immune tolerance biologic markers is warranted.", "link"=>"http://www.mendeley.com/research/tolerance-associated-gene-expression-following-allogeneic-hematopoietic-cell-transplantation", "reader_count"=>2, "reader_count_by_academic_status"=>{"Other"=>1, "Student > Master"=>1}, "reader_count_by_user_role"=>{"Other"=>1, "Student > Master"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>1}, "reader_count_by_subdiscipline"=>{"Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>1}}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1950754"], "description"=>"<p>*CTSS—cathepsin S; FCER1G—Fc fragment of IgE, high affinity I, receptor for; gamma polypeptide; FCGR1B—Fc fragment of IgG, high affinity Ib, receptor (CD64); CD93—CD93 molecule; CR1—complement component (3b/4b) receptor 1; TLR1—toll-like receptor 1; VSIG4—V-set and immunoglobulin domain containing 4; DUSP6—dual specificity phosphatase 6; MNDA—myeloid cell nuclear differentiation antigen; GAPT—GRB2-binding adaptor protein, transmembrane; FKBP1A—FK506 binding protein 1A, 12kDa; TNFSF13B—tumor necrosis factor (ligand) superfamily, member 13b (BAFF); CDKN2B—cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4); HHEX—hematopoietically expressed homeobox; RHOB—ras homolog gene family, member B; CARD16—caspase recruitment domain family, member 16; SOD2—superoxide dismutase 2, mitochondrial.</p>", "links"=>[], "tags"=>["281 probe sets", "gene expression", "subset", "tolerance", "hct", "Allogeneic Hematopoietic Cell Transplantation Biologic markers", "differential gene expression", "Tolerance Associated Gene Expression", "20 probe sets", "tol", "NK cell cytotoxicity", "allogeneic hematopoietic cell transplantation"], "article_id"=>1337344, "categories"=>["Biological Sciences"], "users"=>["Joseph Pidala", "Gregory C. Bloom", "Steven Eschrich", "Minnie Sarwal", "Steve Enkemann", "Brian C. Betts", "Francisca Beato", "Sean Yoder", "Claudio Anasetti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0117001.g004", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Direction_and_magnitude_of_change_in_non_TOL_group_vs_TOL_and_control_Genes_with_increased_expression_in_non_TOL_group_/1337344", "title"=>"Direction and magnitude of change in non-TOL group vs. TOL and control: Genes with increased expression in non-TOL group.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-16 04:58:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1950766"], "description"=>"<p>*Numbers indicate proportion of examined PBMC with the identified phenotype.</p><p>*NK—natural killer cell; DC—dendritic cell; IEL—intra-epithelial lymphocyte; Treg—regulatory T cell; NKT—NKT cells; TOL—tolerant patients; non-TOL—non-tolerant patients</p><p>Comparison of immune cell subsets among TOL and non-TOL patients.</p>", "links"=>[], "tags"=>["281 probe sets", "gene expression", "subset", "tolerance", "hct", "Allogeneic Hematopoietic Cell Transplantation Biologic markers", "differential gene expression", "Tolerance Associated Gene Expression", "20 probe sets", "tol", "NK cell cytotoxicity", "allogeneic hematopoietic cell transplantation"], "article_id"=>1337356, "categories"=>["Biological Sciences"], "users"=>["Joseph Pidala", "Gregory C. Bloom", "Steven Eschrich", "Minnie Sarwal", "Steve Enkemann", "Brian C. Betts", "Francisca Beato", "Sean Yoder", "Claudio Anasetti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0117001.t002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_immune_cell_subsets_among_TOL_and_non_TOL_patients_/1337356", "title"=>"Comparison of immune cell subsets among TOL and non-TOL patients.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-03-16 04:58:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1950763"], "description"=>"<p>Confirmation of differential gene expression using NanoString: Genes with decreased expression in non-TOL group.</p>", "links"=>[], "tags"=>["281 probe sets", "gene expression", "subset", "tolerance", "hct", "Allogeneic Hematopoietic Cell Transplantation Biologic markers", "differential gene expression", "Tolerance Associated Gene Expression", "20 probe sets", "tol", "NK cell cytotoxicity", "allogeneic hematopoietic cell transplantation"], "article_id"=>1337353, "categories"=>["Biological Sciences"], "users"=>["Joseph Pidala", "Gregory C. Bloom", "Steven Eschrich", "Minnie Sarwal", "Steve Enkemann", "Brian C. Betts", "Francisca Beato", "Sean Yoder", "Claudio Anasetti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0117001.g009", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Confirmation_of_differential_gene_expression_using_NanoString_Genes_with_decreased_expression_in_non_TOL_group_/1337353", "title"=>"Confirmation of differential gene expression using NanoString: Genes with decreased expression in non-TOL group.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-16 04:58:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1950761"], "description"=>"<p>Confirmation of differential gene expression using NanoString: Genes with increased expression in non-TOL group.</p>", "links"=>[], "tags"=>["281 probe sets", "gene expression", "subset", "tolerance", "hct", "Allogeneic Hematopoietic Cell Transplantation Biologic markers", "differential gene expression", "Tolerance Associated Gene Expression", "20 probe sets", "tol", "NK cell cytotoxicity", "allogeneic hematopoietic cell transplantation"], "article_id"=>1337351, "categories"=>["Biological Sciences"], "users"=>["Joseph Pidala", "Gregory C. Bloom", "Steven Eschrich", "Minnie Sarwal", "Steve Enkemann", "Brian C. Betts", "Francisca Beato", "Sean Yoder", "Claudio Anasetti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0117001.g008", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Confirmation_of_differential_gene_expression_using_NanoString_Genes_with_increased_expression_in_non_TOL_group_/1337351", "title"=>"Confirmation of differential gene expression using NanoString: Genes with increased expression in non-TOL group.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-16 04:58:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1950775", "https://ndownloader.figshare.com/files/1950776", "https://ndownloader.figshare.com/files/1950777", "https://ndownloader.figshare.com/files/1950778", "https://ndownloader.figshare.com/files/1950779", "https://ndownloader.figshare.com/files/1950780"], "description"=>"<div><p>Biologic markers of immune tolerance may facilitate tailoring of immune suppression duration after allogeneic hematopoietic cell transplantation (HCT). In a cross-sectional study, peripheral blood samples were obtained from tolerant (n = 15, median 38.5 months post-HCT) and non-tolerant (n = 17, median 39.5 post-HCT) HCT recipients and healthy control subjects (n = 10) for analysis of immune cell subsets and differential gene expression. There were no significant differences in immune subsets across groups. We identified 281 probe sets unique to the tolerant (TOL) group and 122 for non-tolerant (non-TOL). These were enriched for process networks including NK cell cytotoxicity, antigen presentation, lymphocyte proliferation, and cell cycle and apoptosis. Differential gene expression was enriched for CD56, CD66, and CD14 human lineage-specific gene expression. Differential expression of 20 probe sets between groups was sufficient to develop a classifier with > 90% accuracy, correctly classifying 14/15 TOL cases and 15/17 non-TOL cases. These data suggest that differential gene expression can be utilized to accurately classify tolerant patients following HCT. Prospective investigation of immune tolerance biologic markers is warranted.</p></div>", "links"=>[], "tags"=>["281 probe sets", "gene expression", "subset", "tolerance", "hct", "Allogeneic Hematopoietic Cell Transplantation Biologic markers", "differential gene expression", "Tolerance Associated Gene Expression", "20 probe sets", "tol", "NK cell cytotoxicity", "allogeneic hematopoietic cell transplantation"], "article_id"=>1337365, "categories"=>["Biological Sciences"], "users"=>["Joseph Pidala", "Gregory C. Bloom", "Steven Eschrich", "Minnie Sarwal", "Steve Enkemann", "Brian C. Betts", "Francisca Beato", "Sean Yoder", "Claudio Anasetti"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0117001.s001", "https://dx.doi.org/10.1371/journal.pone.0117001.s002", "https://dx.doi.org/10.1371/journal.pone.0117001.s003", "https://dx.doi.org/10.1371/journal.pone.0117001.s004", "https://dx.doi.org/10.1371/journal.pone.0117001.s005", "https://dx.doi.org/10.1371/journal.pone.0117001.s006"], "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Tolerance_Associated_Gene_Expression_following_Allogeneic_Hematopoietic_Cell_Transplantation_/1337365", "title"=>"Tolerance Associated Gene Expression following Allogeneic Hematopoietic Cell Transplantation", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-03-16 04:58:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1950771"], "description"=>"<p>*TOL—tolerant; non-TOL—not tolerant; ES—enrichment score; NES—normalized enrichment score; p value—significance level; FDR—false discovery rate.</p><p>Cell lineage enrichment analysis conducted using final TOL and non-TOL gene lists.</p>", "links"=>[], "tags"=>["281 probe sets", "gene expression", "subset", "tolerance", "hct", "Allogeneic Hematopoietic Cell Transplantation Biologic markers", "differential gene expression", "Tolerance Associated Gene Expression", "20 probe sets", "tol", "NK cell cytotoxicity", "allogeneic hematopoietic cell transplantation"], "article_id"=>1337361, "categories"=>["Biological Sciences"], "users"=>["Joseph Pidala", "Gregory C. Bloom", "Steven Eschrich", "Minnie Sarwal", "Steve Enkemann", "Brian C. Betts", "Francisca Beato", "Sean Yoder", "Claudio Anasetti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0117001.t006", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cell_lineage_enrichment_analysis_conducted_using_final_TOL_and_non_TOL_gene_lists_/1337361", "title"=>"Cell lineage enrichment analysis conducted using final TOL and non-TOL gene lists.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-03-16 04:58:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1950756"], "description"=>"<p>*ROC plot for diagnostic accuracy presents true positive rate vs. false positive rate (or sensitivity x 1-specificity) for gene expression-based phenotypic classifier of TOL and non-TOL patient groups. AUC 0.97 (95% CI 0.82–0.97).</p>", "links"=>[], "tags"=>["281 probe sets", "gene expression", "subset", "tolerance", "hct", "Allogeneic Hematopoietic Cell Transplantation Biologic markers", "differential gene expression", "Tolerance Associated Gene Expression", "20 probe sets", "tol", "NK cell cytotoxicity", "allogeneic hematopoietic cell transplantation"], "article_id"=>1337346, "categories"=>["Biological Sciences"], "users"=>["Joseph Pidala", "Gregory C. Bloom", "Steven Eschrich", "Minnie Sarwal", "Steve Enkemann", "Brian C. Betts", "Francisca Beato", "Sean Yoder", "Claudio Anasetti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0117001.g005", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Receiver_operating_characteristic_ROC_plot_for_diagnostic_accuracy_of_gene_classifier_/1337346", "title"=>"Receiver operating characteristic (ROC) plot for diagnostic accuracy of gene classifier.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-16 04:58:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1950769"], "description"=>"<p>*Cellular process networks are ranked in descending order based on p value for magnitude of enrichment to annotated networks using MetaCore by GeneGo software (for each process network, solid organ = published solid organ transplant data,[<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0117001#pone.0117001.ref002\" target=\"_blank\">2</a>–<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0117001#pone.0117001.ref005\" target=\"_blank\">5</a>] and HCT = HCT experimental data.</p><p>Enriched cellular process networks shared between current experimental data and published tolerance-associated gene expression data in solid organ transplantation.</p>", "links"=>[], "tags"=>["281 probe sets", "gene expression", "subset", "tolerance", "hct", "Allogeneic Hematopoietic Cell Transplantation Biologic markers", "differential gene expression", "Tolerance Associated Gene Expression", "20 probe sets", "tol", "NK cell cytotoxicity", "allogeneic hematopoietic cell transplantation"], "article_id"=>1337359, "categories"=>["Biological Sciences"], "users"=>["Joseph Pidala", "Gregory C. Bloom", "Steven Eschrich", "Minnie Sarwal", "Steve Enkemann", "Brian C. Betts", "Francisca Beato", "Sean Yoder", "Claudio Anasetti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0117001.t004", "stats"=>{"downloads"=>2, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Enriched_cellular_process_networks_shared_between_current_experimental_data_and_published_tolerance_associated_gene_expression_data_in_solid_organ_transplantation_/1337359", "title"=>"Enriched cellular process networks shared between current experimental data and published tolerance-associated gene expression data in solid organ transplantation.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-03-16 04:58:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1950770"], "description"=>"<p>Top probe sets and corresponding genes selected in classifier construction and leave-10%-out cross-validation.</p>", "links"=>[], "tags"=>["281 probe sets", "gene expression", "subset", "tolerance", "hct", "Allogeneic Hematopoietic Cell Transplantation Biologic markers", "differential gene expression", "Tolerance Associated Gene Expression", "20 probe sets", "tol", "NK cell cytotoxicity", "allogeneic hematopoietic cell transplantation"], "article_id"=>1337360, "categories"=>["Biological Sciences"], "users"=>["Joseph Pidala", "Gregory C. Bloom", "Steven Eschrich", "Minnie Sarwal", "Steve Enkemann", "Brian C. Betts", "Francisca Beato", "Sean Yoder", "Claudio Anasetti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0117001.t005", "stats"=>{"downloads"=>2, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Top_probe_sets_and_corresponding_genes_selected_in_classifier_construction_and_leave_10_out_cross_validation_/1337360", "title"=>"Top probe sets and corresponding genes selected in classifier construction and leave-10%-out cross-validation.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-03-16 04:58:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1950751"], "description"=>"<p>*TNIK—TRAF2 and NCK interacting kinase; FCRL3—Fc receptor-like 3; NKG7—natural killer cell group 7 sequence; GZMH—granzyme H (cathepsin G-like 2, protein h-CCPX); CD8A—CD8a molecule; LAG3—lymphocyte-activation gene 3; TOX—thymocyte selection-associated high mobility group box; TBX21—T-box 21 (T-bet); EOMES—eomesodermin; TGFBR3—transforming growth factor, beta receptor III; IFNγ—interferon, gamma; IL-28RA—interleukin 28 receptor, alpha (interferon, lambda receptor); CCL5—chemokine (C-C motif) ligand 5; PLEKHF1—pleckstrin homology domain containing, family F (with FYVE domain) member 1; GZMH—granzyme H (cathepsin G-like 2, protein h-CCPX); CDK17—cyclin-dependent kinase 17; CEP78—centrosomal protein 78kDa.</p>", "links"=>[], "tags"=>["281 probe sets", "gene expression", "subset", "tolerance", "hct", "Allogeneic Hematopoietic Cell Transplantation Biologic markers", "differential gene expression", "Tolerance Associated Gene Expression", "20 probe sets", "tol", "NK cell cytotoxicity", "allogeneic hematopoietic cell transplantation"], "article_id"=>1337341, "categories"=>["Biological Sciences"], "users"=>["Joseph Pidala", "Gregory C. Bloom", "Steven Eschrich", "Minnie Sarwal", "Steve Enkemann", "Brian C. Betts", "Francisca Beato", "Sean Yoder", "Claudio Anasetti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0117001.g002", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Direction_and_magnitude_of_change_in_TOL_group_vs_non_TOL_and_control_Genes_with_increased_expression_in_TOL_group_/1337341", "title"=>"Direction and magnitude of change in TOL group vs. non-TOL and control: Genes with increased expression in TOL group.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-16 04:58:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1950768"], "description"=>"<p>*Cellular process networks are ranked in descending order based on p value for magnitude of enrichment of experimental data to annotated networks using MetaCore by GeneGo software (limited to those with p < 0.05)</p><p>Enriched cellular process networks from TOL vs. non-TOL comparison.</p>", "links"=>[], "tags"=>["281 probe sets", "gene expression", "subset", "tolerance", "hct", "Allogeneic Hematopoietic Cell Transplantation Biologic markers", "differential gene expression", "Tolerance Associated Gene Expression", "20 probe sets", "tol", "NK cell cytotoxicity", "allogeneic hematopoietic cell transplantation"], "article_id"=>1337358, "categories"=>["Biological Sciences"], "users"=>["Joseph Pidala", "Gregory C. Bloom", "Steven Eschrich", "Minnie Sarwal", "Steve Enkemann", "Brian C. Betts", "Francisca Beato", "Sean Yoder", "Claudio Anasetti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0117001.t003", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Enriched_cellular_process_networks_from_TOL_vs_non_TOL_comparison_/1337358", "title"=>"Enriched cellular process networks from TOL vs. non-TOL comparison.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-03-16 04:58:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1950765"], "description"=>"<p>*categorical data compared with Fisher’s exact test or Chi-square, continuous data utilized wilcoxon rank sum test</p><p>* AA—aplastic anemia; ALL—acute lymphoblastic leukemia; AML—acute myelogenous leukemia; CML—chronic myelogenous leukemia; FL—follicular lymphoma; HD—Hodgkin lymphoma; IMF—idiopathic myelofibrosis; MCL—mantle cell lymphoma; MDS—myelodysplastic syndrome; MM—multiple myeloma; MPD—myeloproliferative neoplasm; PBSC—peripheral blood stem cells; BM—bone marrow harvested stem cells; MMUD—mismatched unrelated donor; MRD—matched sibling donor; MUD—matched unrelated donor; HLA—human leukocyte antigen; CMV—cytomegalovirus; neg—negative; pos—positive; Bu—busulfan; Cy—cyclophosphamide; Flu—fludarabine; ATG—anti-thymocyte globulin; R—rituximab; BCNU—carmustine; VP16—etoposide; TBI—total body irradiation; pento—pentostatin; CSA—cyclosporine; TAC—tacrolimus; MMF—mycophenolate mofetil; MTX—methotrexate; aGVHD—acute graft vs. host disease; pred—prednisone; rapa—rapamycin (sirolimus); ECP—extra-corporeal photopheresis; cGVHD—chronic graft vs. host disease</p><p>Comparison of patient, transplantation, and GVHD variables across tolerant and non-tolerant groups.</p>", "links"=>[], "tags"=>["281 probe sets", "gene expression", "subset", "tolerance", "hct", "Allogeneic Hematopoietic Cell Transplantation Biologic markers", "differential gene expression", "Tolerance Associated Gene Expression", "20 probe sets", "tol", "NK cell cytotoxicity", "allogeneic hematopoietic cell transplantation"], "article_id"=>1337355, "categories"=>["Biological Sciences"], "users"=>["Joseph Pidala", "Gregory C. Bloom", "Steven Eschrich", "Minnie Sarwal", "Steve Enkemann", "Brian C. Betts", "Francisca Beato", "Sean Yoder", "Claudio Anasetti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0117001.t001", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_patient_transplantation_and_GVHD_variables_across_tolerant_and_non_tolerant_groups_/1337355", "title"=>"Comparison of patient, transplantation, and GVHD variables across tolerant and non-tolerant groups.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-03-16 04:58:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1950750"], "description"=>"<p>*TLR4—toll-like receptor 4; TLR8—toll-like receptor 8; PELI2—pellino homolog 2; IRAK3—interleukin-1 receptor-associated kinase 3; LILRA2—leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 2; LILRA5—leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 5; PDLIM5—PDZ and LIM domain 5; ARRB1—arrestin, beta 1; PAK1—p21 protein (Cdc42/Rac)-activated kinase 1; SOCS2—suppressor of cytokine signaling 2; RHOA—ras homolog gene family, member A; IL-13RA—interleukin 13 receptor, alpha 1; TNFSF13B—tumor necrosis factor (ligand) superfamily, member 13b (BAFF); TNFSF12—tumor necrosis factor (ligand) superfamily, member 12 (APRIL); GSN—gelsolin; SMAD1—SMAD family member 1; VNN1—vanin 1; PPT1—palmitoyl-protein thioesterase 1; SOD2—superoxide dismutase 2, mitochondrial; DAPK1—death-associated protein kinase 1; EVI5—ecotropic viral integration site 5; CCNY—cyclin Y.</p>", "links"=>[], "tags"=>["281 probe sets", "gene expression", "subset", "tolerance", "hct", "Allogeneic Hematopoietic Cell Transplantation Biologic markers", "differential gene expression", "Tolerance Associated Gene Expression", "20 probe sets", "tol", "NK cell cytotoxicity", "allogeneic hematopoietic cell transplantation"], "article_id"=>1337340, "categories"=>["Biological Sciences"], "users"=>["Joseph Pidala", "Gregory C. Bloom", "Steven Eschrich", "Minnie Sarwal", "Steve Enkemann", "Brian C. Betts", "Francisca Beato", "Sean Yoder", "Claudio Anasetti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0117001.g001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Direction_and_magnitude_of_change_in_TOL_group_vs_non_TOL_and_control_Genes_with_decreased_expression_in_TOL_group_/1337340", "title"=>"Direction and magnitude of change in TOL group vs. non-TOL and control: Genes with decreased expression in TOL group.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-16 04:58:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1950759"], "description"=>"<p>Confirmation of differential gene expression using NanoString: Genes with decreased expression in TOL group.</p>", "links"=>[], "tags"=>["281 probe sets", "gene expression", "subset", "tolerance", "hct", "Allogeneic Hematopoietic Cell Transplantation Biologic markers", "differential gene expression", "Tolerance Associated Gene Expression", "20 probe sets", "tol", "NK cell cytotoxicity", "allogeneic hematopoietic cell transplantation"], "article_id"=>1337349, "categories"=>["Biological Sciences"], "users"=>["Joseph Pidala", "Gregory C. Bloom", "Steven Eschrich", "Minnie Sarwal", "Steve Enkemann", "Brian C. Betts", "Francisca Beato", "Sean Yoder", "Claudio Anasetti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0117001.g007", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Confirmation_of_differential_gene_expression_using_NanoString_Genes_with_decreased_expression_in_TOL_group_/1337349", "title"=>"Confirmation of differential gene expression using NanoString: Genes with decreased expression in TOL group.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-16 04:58:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1950758"], "description"=>"<p>Confirmation of differential gene expression using NanoString: Genes with increased expression in TOL group.</p>", "links"=>[], "tags"=>["281 probe sets", "gene expression", "subset", "tolerance", "hct", "Allogeneic Hematopoietic Cell Transplantation Biologic markers", "differential gene expression", "Tolerance Associated Gene Expression", "20 probe sets", "tol", "NK cell cytotoxicity", "allogeneic hematopoietic cell transplantation"], "article_id"=>1337348, "categories"=>["Biological Sciences"], "users"=>["Joseph Pidala", "Gregory C. Bloom", "Steven Eschrich", "Minnie Sarwal", "Steve Enkemann", "Brian C. Betts", "Francisca Beato", "Sean Yoder", "Claudio Anasetti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0117001.g006", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Confirmation_of_differential_gene_expression_using_NanoString_Genes_with_increased_expression_in_TOL_group_/1337348", "title"=>"Confirmation of differential gene expression using NanoString: Genes with increased expression in TOL group.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-16 04:58:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1950772"], "description"=>"<p>*Data are presented for cell-lineage specific gene sets for which significant enrichment was demonstrated. Data for CD4, CD8, and CD19 not presented (p = NS).</p><p>*TOL—tolerant; non-TOL—not tolerant; ES—enrichment score; NES—normalized enrichment score; p value—significance level; FDR—false discovery rate.</p><p>Cell lineage enrichment analysis conducted using Initial 2 group SAM comparison (TOL vs. non-TOL).</p>", "links"=>[], "tags"=>["281 probe sets", "gene expression", "subset", "tolerance", "hct", "Allogeneic Hematopoietic Cell Transplantation Biologic markers", "differential gene expression", "Tolerance Associated Gene Expression", "20 probe sets", "tol", "NK cell cytotoxicity", "allogeneic hematopoietic cell transplantation"], "article_id"=>1337362, "categories"=>["Biological Sciences"], "users"=>["Joseph Pidala", "Gregory C. Bloom", "Steven Eschrich", "Minnie Sarwal", "Steve Enkemann", "Brian C. Betts", "Francisca Beato", "Sean Yoder", "Claudio Anasetti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0117001.t007", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cell_lineage_enrichment_analysis_conducted_using_Initial_2_group_SAM_comparison_TOL_vs_non_TOL_/1337362", "title"=>"Cell lineage enrichment analysis conducted using Initial 2 group SAM comparison (TOL vs. non-TOL).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-03-16 04:58:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1950753"], "description"=>"<p>*KLRC2—killer cell lectin-like receptor subfamily C, member 2 (NKG2C); KLRC3—killer cell lectin-like receptor subfamily C, member 3 (NKG2E); KLRC4—killer cell lectin-like receptor subfamily C, member 4 (NKG2F); KLRD1—killer cell lectin-like receptor subfamily D, member 1 (NKG2A); KLRK1—killer cell lectin-like receptor subfamily K, member 1 (NKG2D); GZMA—granzyme A (granzyme 1, cytotoxic T-lymphocyte-associated serine esterase 3); GZMB—granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1); GZMK—granzyme K (granzyme 3; tryptase II); GNLY—granulysin; BY55 (CD160)—CD160 molecule; PLCXD2—phosphatidylinositol-specific phospholipase C, X domain containing 2; TOX—thymocyte selection-associated high mobility group box; DUSP2—dual specificity phosphatase 2; IL-18RAP—interleukin 18 receptor accessory protein; IL-2Rβ—interleukin 2 receptor, beta; TGFBR3—transforming growth factor, beta receptor III; CXCR6—chemokine (C-X-C motif) receptor 6; CCL4 (MIP-1-β)—chemokine (C-C motif) ligand 4; DLG5—discs, large homolog 5; GZMA—granzyme A (granzyme 1, cytotoxic T-lymphocyte-associated serine esterase 3); GZMB—granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1).</p>", "links"=>[], "tags"=>["281 probe sets", "gene expression", "subset", "tolerance", "hct", "Allogeneic Hematopoietic Cell Transplantation Biologic markers", "differential gene expression", "Tolerance Associated Gene Expression", "20 probe sets", "tol", "NK cell cytotoxicity", "allogeneic hematopoietic cell transplantation"], "article_id"=>1337343, "categories"=>["Biological Sciences"], "users"=>["Joseph Pidala", "Gregory C. Bloom", "Steven Eschrich", "Minnie Sarwal", "Steve Enkemann", "Brian C. Betts", "Francisca Beato", "Sean Yoder", "Claudio Anasetti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0117001.g003", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Direction_and_magnitude_of_change_in_non_TOL_group_vs_TOL_and_control_Genes_with_decreased_expression_in_non_TOL_group_/1337343", "title"=>"Direction and magnitude of change in non-TOL group vs. TOL and control: Genes with decreased expression in non-TOL group.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-16 04:58:46"}

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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