cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3644480_d4.v1
title: MOESM4 of Biomass traits and candidate genes for bioenergy revealed through association genetics in coppiced European Populus nigra (L.)

description: Additional file 4. containing supplementary table S2; depicting the top 1Â % loading SNPs for the first 2 principal components of the genetic variation.
DOI: 10.6084/m9.figshare.c.3644480_d3.v1
title: MOESM6 of Biomass traits and candidate genes for bioenergy revealed through association genetics in coppiced European Populus nigra (L.)

description: Additional file 6. containing supplementary TableÂ 1096 S4; reporting the raw and normalised RNAseq count data used for supplementary Figure S12.
DOI: 10.6084/m9.figshare.c.3644480_d5.v1
title: MOESM5 of Biomass traits and candidate genes for bioenergy revealed through association genetics in coppiced European Populus nigra (L.)

description: Additional file 5. containing supplementary table S3; showing the BIC values for optimal model selection for GWAS.
DOI: 10.6084/m9.figshare.c.3644480_d6.v1
title: MOESM2 of Biomass traits and candidate genes for bioenergy revealed through association genetics in coppiced European Populus nigra (L.)

description: Additional file 2. containing the SNP marker set derived from the 12Â K Illumina array genotyping and employed here for GWAS.
DOI: 10.6084/m9.figshare.c.3644486_d2.v1
title: Additional file 2: Table S2. of Molecular and phenotypic distinction of the very recently evolved insular subspecies Mus musculus helgolandicus ZIMMERMANN, 1953

description: Introgressed regions in the genome of house mouse from Heligoland and their frequencies. (XLS 88 kb)
DOI: 10.6084/m9.figshare.c.3644486_d1.v1
title: Additional file 1: Table S1. of Molecular and phenotypic distinction of the very recently evolved insular subspecies Mus musculus helgolandicus ZIMMERMANN, 1953

description: Details of the primers used for M. m. domesticus versus M. m. musculus assignment. (XLS 31 kb)
DOI: 10.6084/m9.figshare.c.3644486_d4.v1
title: Additional file 4: Table S4. of Molecular and phenotypic distinction of the very recently evolved insular subspecies Mus musculus helgolandicus ZIMMERMANN, 1953

description: Details of weight, body and tail lengths and scored dorsal and ventral color for Heligoland house mice. (XLS 29 kb)
DOI: 10.6084/m9.figshare.c.3644486_d3.v1
title: Additional file 7: Table S7. of Molecular and phenotypic distinction of the very recently evolved insular subspecies Mus musculus helgolandicus ZIMMERMANN, 1953

description: List of mice skull specimens for the mice used for this study. (XLS 36 kb)
DOI: 10.6084/m9.figshare.c.3644486_d5.v1
title: Additional file 3: Table S3. of Molecular and phenotypic distinction of the very recently evolved insular subspecies Mus musculus helgolandicus ZIMMERMANN, 1953

description: Output of GOrilla showing Gene Ontology term enrichment for the biological process in the gene list overlapping the introgressed regions into M. m. helgolandicus. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3644561_d4.v1
title: Additional file 7: Table S6. of Next generation sequencing of triple negative breast cancer to find predictors for chemotherapy response

description: Specific mutations within affected pathways. This file shows all pathways with KEGG IDs, and mutations affecting the different pathways. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3644561_d8.v1
title: Additional file 4: Table S3. of Next generation sequencing of triple negative breast cancer to find predictors for chemotherapy response

description: List of all mutations. This file shows all mutations passing thresholds as explained in “Methods”. The column “confirmed” shows mutations that have been confirmed by either Sanger Sequencing or deep whole exome sequencing in another research project (unpublished data). The column “included in analysis” shows the mutations that passed our threshold for putative driver mutations, based on effect, SIFT, polyphen scores and COSMIC (see “Methods”). The column “dubious” shows the mutations that might be dubious based on gene length, expression or replication time [20]. (XLSX 64 kb)
DOI: 10.6084/m9.figshare.c.3644561_d9.v1
title: Additional file 2: Table S1. of Next generation sequencing of triple negative breast cancer to find predictors for chemotherapy response

description: 1977 Cancer Gene Panel. This file lists all 1,977 genes in the Cancer Gene Panel, used in this study. (XLS 111 kb)
DOI: 10.6084/m9.figshare.c.3644564_d1.v1
title: Additional file 1: of Gene expression in the brain of a migratory songbird during breeding and migration

description: The distribution of positive probes per probe set is shown in Figure S1. The hierarchical clustering including the discarded samples is shown in Figure S2. Gene IDs, fold-change differences and FDR P-values for each of the 22,109 probe sets are available in Table S1. Microarray data are available in the ArrayExpress database ( www.ebi.ac.uk/arrayexpress ) under accession number E-MTAB-4102. (ZIP 1810Â kb)
DOI: 10.6084/m9.figshare.c.3644567_d3.v1
title: Additional file 3: of Higher expression of TNFα-induced genes in the synovium of patients with early rheumatoid arthritis correlates with disease activity, and predicts absence of response to first line therapy

description: Numbers of probe sets displaying a positive correlation with global disease activity indices and each of their individual variables. Overlap between probe sets displaying a Pearson r correlation coefficient &gt;0.5 between tender joint count, swollen joint count, patient’s global assessment, physician’s global assessment, C-reactive protein (CRP) and global disease activity scores. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.c.3644567_d2.v1
title: Additional file 4: of Higher expression of TNFα-induced genes in the synovium of patients with early rheumatoid arthritis correlates with disease activity, and predicts absence of response to first line therapy

description: Genes over-expressed in poor responders to therapy at baseline. Lists of probe sets differentially expressed at baseline in synovial biopsies from patients with early rheumatoid arthritis (RA) in good versus poor responders to first line therapy at 3 and 6 months. (XLSX 293 kb)
DOI: 10.6084/m9.figshare.c.3644576_d1.v1
title: Additional file 1: Table S1. of The Cancer Genome Atlas Clinical Explorer: a web and mobile interface for identifying clinicalâ  genomic driver associations

description: List of patients with inconsistent clinical outcomes. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3644576_d3.v1
title: Additional file 3: Table S3. of The Cancer Genome Atlas Clinical Explorer: a web and mobile interface for identifying clinicalâ  genomic driver associations

description: The number of genes selected from TCGA studies by type of genetic alterations and cancer type. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3644576_d2.v1
title: Additional file 5: Table S5. of The Cancer Genome Atlas Clinical Explorer: a web and mobile interface for identifying clinicalâ  genomic driver associations

description: List of genes that cannot be updated properly. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.c.3644576_d4.v1
title: Additional file 4: Table S4. of The Cancer Genome Atlas Clinical Explorer: a web and mobile interface for identifying clinicalâ  genomic driver associations

description: List of genes/miRs/proteins selected for elastic-net analysis. (XLSX 160 kb)
DOI: 10.6084/m9.figshare.c.3644576_d6.v1
title: Additional file 6: Table S6. of The Cancer Genome Atlas Clinical Explorer: a web and mobile interface for identifying clinicalâ  genomic driver associations

description: Conversion of clinical parameters into integer values. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3644576_d5.v1
title: Additional file 2: Table S2. of The Cancer Genome Atlas Clinical Explorer: a web and mobile interface for identifying clinicalâ  genomic driver associations

description: List of cancer genes by COSMIC and TARGET. (XLSX 36 kb)
DOI: 10.6084/m9.figshare.c.3644579_d1.v1
title: Additional file 1: of The leukemogenic fusion gene MLL-AF9 alters microRNA expression pattern and inhibits monoblastic differentiation via miR-511 repression

description: All (non-filtered) gene ontology results of known miRNAs targets. DAVID gene ontology analysis was performed for all THP1-expressed, validated direct targets (extracted from miRTarBase) of MLL-AF9 knockdown associated miRNAs. This file includes all extracted MTIs extracted from miRTarBase as well as all gene ontology results from DAVID analysis (clustered and non-clustered terms). (XLSX 125 kb)
DOI: 10.6084/m9.figshare.c.3644579_d2.v1
title: Additional file 4: of The leukemogenic fusion gene MLL-AF9 alters microRNA expression pattern and inhibits monoblastic differentiation via miR-511 repression

description: Functional disease ontology (FunDO) analysis results of genes differentially regulated by miR-511 mimic treatment. Analysis was used to extract leukemia and cancer related genes. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.c.3644684_d6.v1
title: Additional file 6: of Travelling at a slugâ  s pace: possible invertebrate vectors of Caenorhabditis nematodes

description: Original data for the third field screen in Kiel, Northern Germany, in 2014. 544 slugs and 123 substrate samples were collected between July and October 2014 from 21 locations in Kiel and the surroundings.
DOI: 10.6084/m9.figshare.c.3644804_d3.v1
title: MOESM4 of BIDCHIPS: bias decomposition and removal from ChIP-seq data clarifies true binding signal and its functional correlates

description: Additional file 4: Table S3. This Excel sheet lists the percentages of variance explained by individual predictors for the K562 cell line (relates to main Fig.Â 2)
DOI: 10.6084/m9.figshare.c.3644804_d4.v1
title: MOESM6 of BIDCHIPS: bias decomposition and removal from ChIP-seq data clarifies true binding signal and its functional correlates

description: Additional file 6: Table S5. This Excel sheet presents a comparative table of Pearsonâ  s correlation coefficients between different binding-signal metrics and DNA-binding motif occurrences under two conditions: (1) when looking at just the motif presence/absence and (2) when looking at the actual motif counts
DOI: 10.6084/m9.figshare.c.3644804_d6.v1
title: MOESM2 of BIDCHIPS: bias decomposition and removal from ChIP-seq data clarifies true binding signal and its functional correlates

description: Additional file 2: Table S1 . This Excel sheet lists the percentages of variance explained by individual predictors for the Gm12878 cell line (relates to main Fig.Â 2)
DOI: 10.6084/m9.figshare.c.3644933_d1.v1
title: Additional file 1: of A reliability assessment of a direct-observation park evaluation tool: the Parks, activity and recreation among kids (PARK) tool

description: The Parks, Activity and Recreation among Kids (PARK) Tool. This contains the complete and final direct observation tool developed and tested for reliability in Montreal, Canada. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.c.3644933_d2.v1
title: Additional file 3: of A reliability assessment of a direct-observation park evaluation tool: the Parks, activity and recreation among kids (PARK) tool

description: Test-retest results for intra-observer reliability. This contains the intra-observer reliability estimates for 41 items on the PARK Tool. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3644933_d3.v1
title: Additional file 2: of A reliability assessment of a direct-observation park evaluation tool: the Parks, activity and recreation among kids (PARK) tool

description: Kappa and percent agreement results for all items on the PARK Tool. This contains the kappa and percent agreement estimates for all the items on the PARK Tool. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.c.3644936_d1.v1
title: Additional file 3: of 
                     De novo assembly and analysis of changes in the protein-coding transcriptome of the freshwater shrimp Paratya australiensis (Decapoda: Atyidae) in response to acid sulfate drainage water

description: Differential abundance analysis results, functional annotations and putative descriptions of transcripts passing the minimum abundance threshold. (XLSX 2717Â kb)
DOI: 10.6084/m9.figshare.c.3644936_d3.v1
title: Additional file 4: of 
                     De novo assembly and analysis of changes in the protein-coding transcriptome of the freshwater shrimp Paratya australiensis (Decapoda: Atyidae) in response to acid sulfate drainage water

description: Functional enrichment analysis results including p-values and false discovery rates. (XLSX 36Â kb)
DOI: 10.6084/m9.figshare.c.3644942_d1.v1
title: Additional file 11: of The molecular landscape of premenopausal breast cancer

description: Gene list for clustering premenopausal (preM) estrogen receptor-positive (ER+) tumors. Table S1. Gene list selected by sparse k-means algorithm in The Cancer Genome Atlas (TCGA) data. Table S2. Genes selected based on TCGA data that are also in the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) data for validation. Table S3. Fixed number of genes (n = 21), gene list being selected from sparse k-means in TCGA. Table S4. Gene list selected by semi-supervised algorithm in METABRIC. Table S5. Fixed number of genes (n = 21), gene list being selected by semi-supervised algorithm in TCGA. Table S6. Genes (n = 28) in the LumA cluster that are significantly different between clusters 1 and 3. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.c.3644942_d2.v1
title: Additional file 5: of The molecular landscape of premenopausal breast cancer

description: Ingenuity pathway analysis (IPA) in The Cancer Genome Atlas (TCGA) union of RNA seq and Agilent data. Top canonical pathways detected by IPA using the union of differentially expressed genes in Agilent and RNA-Seq expression platforms in TCGA. Four columns correspond to Ingenuity canonical pathway names, â  log(p value), percentage of genes detected in this pathway, and molecules in this pathway. (XLS 15 kb)
DOI: 10.6084/m9.figshare.c.3644942_d3.v1
title: Additional file 2: of The molecular landscape of premenopausal breast cancer

description: Stratified analysis TCGA. Table S1 and Table S2: Gene expression-Agilent (ER-pos) (Table S1) and RNA-Seq (ER-pos) (Table S2). Output from R package “limma” for ER+ tumors. Table S3: Methylation (ER-pos). Table S4: Copy Number Variation (ER-pos). Table S5: RPPA (ER-pos). Table S6: Somatic Mutation (ER-pos) (MutSig). Table S7: Power Analysis for comparison of two mutation rates with fixed sample size (n1 = 102, n2 = 384), and alpha = 0.05. Table S8: Gene expression-Agilent (ER-neg). Output from R package “limma” for ER- tumors. No genes were significant when FDR was controlled at 5 %. Table S9: Gene expression-RNA-Seq(ER-neg). Output from R package “limma” for ER- tumors. No genes were significant when FDR was controlled at 5 %. For all tabs, genes highlighted in yellow are significant when FDR is controlled at 5 %. For methylation analysis, there was additional requirement for absolute difference between average beta-value of two groups to be &gt; 0.1. (XLSX 25246 kb)
DOI: 10.6084/m9.figshare.c.3644942_d4.v1
title: Additional file 7: of The molecular landscape of premenopausal breast cancer

description: PARADIGM analysis in The Cancer Genome Atlas (TCGA). Table S1. Pathways detected by gene set enrichment analysis (GSEA) with input of gene expression and copy number variation data for the PARADIGM algorithm. The nine columns correspond to the pathway name, size of the pathway, Enrichment score (ES) score, Normalized enrichment score (NES) score, nominal p value, false discovery rate (FDR) q value, Family-wise error rate (FWER) p value, and leading edge (typical GSEA output). Table S2. Pathways detected by GSEA with input of gene expression, copy number variation and methylation data for the PARADIGM algorithm. The nine columns correspond to the pathway name, the size of pathway, ES score, NES score, nominal p value, FDR q value, FWER p value, and leading edge (typical GSEA output). (XLSX 88 kb)
DOI: 10.6084/m9.figshare.c.3644942_d7.v1
title: Additional file 1: of The molecular landscape of premenopausal breast cancer

description: The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) - clinical data summary. Descriptive statistics of important clinical variables in TCGA and METABRIC data including disease stage, histologic type, estrogen receptor (ER) status, progesterone receptor (PR) status, and human epidermal growth factor receptor 2 (Her2) status. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.c.3644942_d5.v1
title: Additional file 8: of The molecular landscape of premenopausal breast cancer

description: Stratified gene expression analysis in the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC). Gene expression-Illumina. Output from R package limma. The five columns correspond to the gene symbol, log2 fold change, t statistics, raw p value and adjusted p value. Genes (n = 2542) highlighted in yellow were significant when the false discovery rate (FDR) was controlled at 5 %. (XLSX 1323 kb)
DOI: 10.6084/m9.figshare.c.3644942_d6.v1
title: Additional file 6: of The molecular landscape of premenopausal breast cancer

description: The Cancer Genome Atlas (TCGA) Ingenuity pathway analysis (IPA) upstream regulators. Table S1., Table S2. Top upstream regulators detected by IPA using the union of differentially expressed genes in Agilent and RNA-Seq expression platforms in TCGA. Table S2. Top upstream regulators detected by IPA using the differentially expressed gene list from Agilent expression array. Four columns correspond to Ingenuity canonical pathway names, â  log(p value), percentage of genes detected in this pathway, and molecules in this pathway. Table S3. Top upstream regulators detected by IPA using the differentially expressed gene list from RNA-Seq expression array. Four columns correspond to Ingenuity canonical pathway names, â  log(p value), percentage of genes detected in this pathway, and molecules in this pathway. (XLS 177 kb)
DOI: 10.6084/m9.figshare.c.3644942_d9.v1
title: Additional file 4: of The molecular landscape of premenopausal breast cancer

description: Stratified gene expression analysis comparing estrogen-receptor-positive (ER+) premenopausal (preM) and Normal groups in The Cancer Genome Atlas (TCGA). Table S1. Gene expression-Agilent. The five columns correspond to gene symbol, log2 fold change, t statistics, raw p value and adjusted p value. Genes (n = 11,366) highlighted in yellow were significant when the false discovery rate (FDR) was controlled at 5 %. Table S2. Gene expression- RNA-Seq. The five columns correspond to gene symbol, log2 fold change, t statistics, raw p value and adjusted p value. Genes (n = 14478) highlighted in yellow were significant when the FDR was controlled at 5 %. (XLSX 2881 kb)
DOI: 10.6084/m9.figshare.c.3644942_d10.v1
title: Additional file 9: of The molecular landscape of premenopausal breast cancer

description: Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) Ingenuity pathway analysis (IPA) upstream regulators. Top canonical upstream regulators detected by IPA using the list of differentially expressed genes in METABRIC. Four columns correspond to the Ingenuity canonical pathway names, â  log(p value), percentage of genes detected in this pathway, and molecules in this pathway. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.c.3644942_d12.v1
title: Additional file 10: of The molecular landscape of premenopausal breast cancer

description: PARADIGM analysis in Molecular Taxonomy of Breast Cancer International Consortium (METABRIC). Pathways detected by gene set enrichment analysis (GSEA) with input of gene expression and copy number variation data for the PARADIGM algorithm. The nine columns correspond to the pathway name, size of the athway, ES score, NES score, nominal p value, false discovery rate (FDR) q value, FWER p value and leading edge (typical GSEA output). (XLSX 62 kb)
DOI: 10.6084/m9.figshare.c.3644942_d13.v1
title: Additional file 3: of The molecular landscape of premenopausal breast cancer

description: Copy number variation (CNV) GISTIC The Cancer Genome Atlas (TCGA). List of significant (q &lt;0.25) amplification and deletion peaks identified by GISTIC 2.0, uniquely in premenopausal (preM) and postmenopausal (postM) groups. The columns correspond to the sample group in which the peak is uniquely identified (preM or postM), type of peak (amplification or deletion), cytoband, q value, residual q value, wide peak boundaries, and number of genes in the region, followed by the list of genes falling under the wide peak boundaries. (XLSX 73 kb)
DOI: 10.6084/m9.figshare.c.3645062_d1.v1
title: Additional file 3: of Clinical and paraclinical profile, and predictors of outcome in 90 cases of scrub typhus, Meghalaya, India

description: Data spreadsheet. (XLSX 35Â kb)
DOI: 10.6084/m9.figshare.c.3645086_d1.v1
title: Additional file 2: of An analysis of three levels of scaled-up coverage for 28 interventions to avert stillbirths and maternal, newborn and child mortality in 27 countries in Latin America and the Caribbean with the Lives Saved Tool (LiST)

description: The baseline data. (XLSX 63 kb)
DOI: 10.6084/m9.figshare.c.3645179_d1.v1
title: Additional file 2: of Epidemiological surveys of, and research on, soil-transmitted helminths in Southeast Asia: a systematic review

description: Full list of the included studies. (XLSX 56Â kb)
DOI: 10.6084/m9.figshare.c.3645179_d3.v1
title: Additional file 3: of Epidemiological surveys of, and research on, soil-transmitted helminths in Southeast Asia: a systematic review

description: Preventive chemotherapy data for the Southeast Asian countries. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.c.3645185_d4.v1
title: Additional file 6: of Could the erythrocyte indices or serum ferritin predict the therapeutic response to a trial with oral iron during pregnancy? Results from the Accuracy study for Maternal Anaemia diagnosis (AMA)

description: Data set of AMA study (XLSX 64 kb)
DOI: 10.6084/m9.figshare.c.3645287_d1.v1
title: MOESM1 of Molecular epidemiological tracing of a cattle rabies outbreak lasting less than a month in Rio Grande do Sul in southern Brazil

description: Additional file 1. Primers used for RT-PCR and sequencing.
DOI: 10.6084/m9.figshare.c.3645287_d3.v1
title: MOESM2 of Molecular epidemiological tracing of a cattle rabies outbreak lasting less than a month in Rio Grande do Sul in southern Brazil

description: Additional file 2. Nucleotide sequences RABV N gene retrieved from GenBank.
DOI: 10.6084/m9.figshare.c.3645311_d2.v1
title: Additional file 6: of Differences in the skeletal muscle transcriptome profile associated with extreme values of fatty acids content

description: Normalized gene expression level and statistical results of differentially expressed genes analysis (FDR 10%) between High and Low groups based on eicosapentaenoic acid (EPA) content from Longissimus dorsi muscle of Nellore steers. (XLSX 15447 kb)
DOI: 10.6084/m9.figshare.c.3645311_d3.v1
title: Additional file 4: of Differences in the skeletal muscle transcriptome profile associated with extreme values of fatty acids content

description: Normalized gene expression level and statistical results of differentially expressed genes analysis (FDR 10%) between High and Low groups based on linoleic acid (LA) content from Longissimus dorsi muscle of Nellore steers. (XLSX 15462 kb)
DOI: 10.6084/m9.figshare.c.3645311_d6.v1
title: Additional file 5: of Differences in the skeletal muscle transcriptome profile associated with extreme values of fatty acids content

description: Normalized gene expression level and statistical results of differentially expressed genes analysis (FDR 10%) between High and Low groups based on stearic acid (SA) content from Longissimus dorsi muscle of Nellore steers. (XLSX 15406 kb)
DOI: 10.6084/m9.figshare.c.3645311_d7.v1
title: Additional file 15: of Differences in the skeletal muscle transcriptome profile associated with extreme values of fatty acids content

description: Uspstrem regulators analysis from DE genes list. (XLS 27Â kb)