cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3644576_d2
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
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_d5
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.3644576_d6
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.3644579_d1
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
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.3644579_d3
title: Additional file 3: 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 predicted miRNAs targets. DAVID gene ontology analysis was performed for all THP1-expressed targets predicted via TargetScan with a minimum context + score of 0.4 of MLL-AF9 knockdown associated miRNAs. This file includes all predicted MTIs as well as all gene ontology results from DAVID analysis (clustered and non-clustered terms) with a p-value below 0.1 and a fold enrichment above 1.5. (XLSX 475 kb)
DOI: 10.6084/m9.figshare.c.3644585_d1
title: MOESM2 of The microbiome associated with equine periodontitis and oral health

description: Additional file 2. Microbial families of higher taxa that differed significantly between the groups. The output was created in LEfSe. The same taxa are visualised in FigureÂ 5.
DOI: 10.6084/m9.figshare.c.3644585_d2
title: MOESM1 of The microbiome associated with equine periodontitis and oral health

description: Additional file 1. OTUs that differed significantly between the groups. The output was created in LEfSe.
DOI: 10.6084/m9.figshare.c.3644597_d2
title: Additional file 1: of A novel multi-tissue RNA diagnostic of healthy ageing relates to cognitive health status

description: An Excel spreadsheet containing data related to our study with six tabs: 1) analysis of the top 150 genes from age prototype classifier in PUBMED; 2) the top 670 genes from the first stage of the project; 3) phenodata for the training data set and validation data sets in our study; 4) a list of prior markers in the literature for Alzheimerâ  s disease; 5) positional gene enrichment analysis; 6) sample information for the BrainEac study. (XLSX 221 kb)
DOI: 10.6084/m9.figshare.c.3644804_d3
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
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_d5
title: MOESM3 of BIDCHIPS: bias decomposition and removal from ChIP-seq data clarifies true binding signal and its functional correlates

description: Additional file 3: Table S2 . This Excel sheet lists the percentages of variance explained by individual predictors for the H1-hESC cell line (relates to main Fig.Â 2)
DOI: 10.6084/m9.figshare.c.3644804_d6
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.3645062_d1
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
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.3645311_d2
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
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_d5
title: Additional file 2: of Differences in the skeletal muscle transcriptome profile associated with extreme values of fatty acids content

description: Test of means (t-test) between groups with high and low fatty acid content in Longissimus dorsi muscle in Nellore steers. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.c.3645311_d6
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
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)
DOI: 10.6084/m9.figshare.c.3645311_d8
title: Additional file 18: of Differences in the skeletal muscle transcriptome profile associated with extreme values of fatty acids content

description: Summary of functional enrichment analysis from a list of differentially expressed genes between High and Low groups based on conjugated linoleic acid cis9 trans11 content from Longissimus dorsi muscle of Nellore steers using Ingenuity Pathway Analysis. (IPA) (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3645311_d10
title: Additional file 9: 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 oleic acid (OA) content from Longissimus dorsi muscle of Nellore steers. (XLSX 13046 kb)
DOI: 10.6084/m9.figshare.c.3645311_d9
title: Additional file 3: of Differences in the skeletal muscle transcriptome profile associated with extreme values of fatty acids content

description: Summary of total reads before and after filtering, percentage of mapped reads against Bos taurus UMD3.1 reference genome and, information of each group according to specifically fatty acid content from Longissimus dorsi muscle of Nellore steers. (XLSX 53 kb)
DOI: 10.6084/m9.figshare.c.3645311_d11
title: Additional file 21: of Differences in the skeletal muscle transcriptome profile associated with extreme values of fatty acids content

description: qPCR validation of RNA-seq data on a random selection of nine differentially expressed genes. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.c.3645311_d13
title: Additional file 14: of Differences in the skeletal muscle transcriptome profile associated with extreme values of fatty acids content

description: IPA network analysis of differentially expressed genes analysis (FDR 10%) between High and Low groups based on oleic acid content from Longissimus dorsi muscle of Nellore steers. (XLSX 57 kb)
DOI: 10.6084/m9.figshare.c.3645311_d12
title: Additional file 1: of Differences in the skeletal muscle transcriptome profile associated with extreme values of fatty acids content

description: Phenotypic and statistical analysis description for two groups of extreme values of fatty acids content in Longissimus dorsi muscle of Nellore steers. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.c.3645311_d14
title: Additional file 7: 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 docosahexaenoic acid (DHA) content from Longissimus dorsi muscle of Nellore steers. (XLSX 13199 kb)
DOI: 10.6084/m9.figshare.c.3645311_d15
title: Additional file 20: of Differences in the skeletal muscle transcriptome profile associated with extreme values of fatty acids content

description: qPCR results of nine differentially expressed genes by random selection from DataAssist software. (XLSX 49 kb)
DOI: 10.15468/dl.wdhxh9
title: Occurrence Download

description: A dataset containing 86042 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Bombina variegata (Linnaeus, 1758)"
 ]
}

 The dataset includes 86042 records from 498 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034197-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3645551_d1
title: Additional file 2: of Single-cell profiling of human megakaryocyte-erythroid progenitors identifies distinct megakaryocyte and erythroid differentiation pathways

description: Supplementary Tables S1 - S3. Table S1. Gene assays included in multiplex RT-PCR analysis with coefficient of dilution (R2) examined over fourfold serial dilutions with technical triplicates at each dilution. Table S2. Normalized Ct values for gene expression data for all genes and cells. Table S3. Raw data for single-cell gene expression analysis (non-normalized Ct values). (XLSX 1059 kb)
DOI: 10.5281/zenodo.11203843
title: The Breeding Bird Survey of the United Kingdom
DOI: 10.5281/zenodo.13969202
title: The Breeding Bird Survey of the United Kingdom
DOI: 10.5281/zenodo.14161736
title: The Breeding Bird Survey of the United Kingdom

description: The dataset contains the data collected during the Breeding Bird Survey (BBS) of the United Kingdom, for each visit made in years from 1994 to 2023. The data may be used for many different applications, including population trend production and pure and applied ecological studies. Please refer to the associated article (Massimino et al., in press) for recommendation for use and caveats.

The present version, named "2024 (1994-2023 data)" includes the specific data related to the associated article. We envisage updating the datasets annually, therefore new versions will be uploaded in the future.
DOI: 10.6084/m9.figshare.c.3645767_d2
title: MOESM3 of A genome-wide perspective about the diversity and demographic history of seven Spanish goat breeds

description: Additional file 3: Table S2. Number of SNPs per chromosome and average, minimum and maximum distances between SNPs.
DOI: 10.6084/m9.figshare.c.3645767_d4
title: MOESM6 of A genome-wide perspective about the diversity and demographic history of seven Spanish goat breeds

description: Additional file 6: Table S4. Average ROH sizes (kb) for 12 goat populations.
DOI: 10.6084/m9.figshare.c.3645773_d1
title: Additional file 1: of The oldest described eurypterid: a giant Middle Ordovician (Darriwilian) megalograptid from the Winneshiek LagerstĂ¤tte of Iowa

description: Data matrix for the phylogenetic analysis. (NEX 35 kb)
DOI: 10.6084/m9.figshare.c.3645788_d2
title: Additional file 3: of The timing of complementary feeding in preterm infants and the effect on overweight: study protocol for a systematic review

description: Risk of Bias Assessment Tool. Risk of Bias Assessment Tool form that will be used to assess the risk of bias in included studies in this systematic review. (XLSX 14Â kb)
DOI: 10.5281/zenodo.14466972
title: MEDIENPSYCHOLOGIE: DER EINFLUSS DER MEDIEN AUF KOGNITIVE PROZESSE, EMOTIONALEN ZUSTAND UND SOZIALE BEZIEHUNGEN
DOI: 10.5281/zenodo.14466973
title: MEDIENPSYCHOLOGIE: DER EINFLUSS DER MEDIEN AUF KOGNITIVE PROZESSE, EMOTIONALEN ZUSTAND UND SOZIALE BEZIEHUNGEN
DOI: 10.6084/m9.figshare.c.3645980_d20
title: Additional file 3 of Exploring the cellular basis of human disease through a large-scale mapping of deleterious genes to cell types

description: Table S3. Performance of the GSC method when applied to interactomes created using various confidence score cutoffs and run using various restart probabilities. All diseases with two or more associated genes were used. Performance is measured using associations identified by the text-mining as true positives. Sets of diseaseâ  cell-type associations were produced by applying an FDR cutoff of 10 % to the GSC and text-mining results. (XLS 10 kb)
DOI: 10.6084/m9.figshare.c.3645980_d18
title: Additional file 13 of Exploring the cellular basis of human disease through a large-scale mapping of deleterious genes to cell types

description: Table S8. Term mappings for the diseases used in the analyses. NAME: Disease name used throughout the analyses (obtained from DisGeN ET). UMLS: UMLS identifiers mapped to the disease. MESH: MeSH term mapped to the disease used to conduct the text-mining. (XLS 66 kb)
DOI: 10.6084/m9.figshare.c.3645980_d19
title: Additional file 14 of Exploring the cellular basis of human disease through a large-scale mapping of deleterious genes to cell types

description: Table S9. Diseaseâ  cell-type association P values computed using the text-mining method. (XLS 438 kb)
DOI: 10.6084/m9.figshare.c.3645980_d21
title: Additional file 15 of Exploring the cellular basis of human disease through a large-scale mapping of deleterious genes to cell types

description: Table S10. Diseaseâ  cell-type association P values computed using the GSO method. (XLS 686 kb)
DOI: 10.6084/m9.figshare.c.3645989_d1
title: Additional file 3: Table S2. of Quantitative analyses of the hepatic proteome of methylmercury-exposed Atlantic cod (Gadus morhua) suggest oxidative stress-mediated effects on cellular energy metabolism

description: Full list of 1143 quantified proteins and associated data from label-free proteomics analysis of liver protein samples from controls (n = 10), 0.5 mg/kg BW MeHg (n = 9) and 2 mg/kg BW MeHg (n = 9) fish. (XLSX 610 kb)
DOI: 10.6084/m9.figshare.c.3645989_d2
title: Additional file 5: Table S4. of Quantitative analyses of the hepatic proteome of methylmercury-exposed Atlantic cod (Gadus morhua) suggest oxidative stress-mediated effects on cellular energy metabolism

description: Full list of significantly enriched KEGG, GO (BP, MF and CC) and Interpro protein domains from STRING network analysis. (XLS 50 kb)
DOI: 10.6084/m9.figshare.c.3645989_d4
title: Additional file 4: Table S3. of Quantitative analyses of the hepatic proteome of methylmercury-exposed Atlantic cod (Gadus morhua) suggest oxidative stress-mediated effects on cellular energy metabolism

description: Full list of significantly enriched top 50 GO BP and MF and all significant MetaCore processes network terms and the associated proteins. (XLSX 73 kb)
DOI: 10.6084/m9.figshare.c.3645989_d5
title: Additional file 2: Table S1. of Quantitative analyses of the hepatic proteome of methylmercury-exposed Atlantic cod (Gadus morhua) suggest oxidative stress-mediated effects on cellular energy metabolism

description: 125 proteins differentially regulated by MeHg. (XLSX 94 kb)
DOI: 10.6084/m9.figshare.c.3646001_d3
title: Additional file 16: of Indica rice genome assembly, annotation and mining of blast disease resistance genes

description: Number of effects of SNPs and InDels on various regions of genes. (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.c.3646001_d2
title: Additional file 2: of Indica rice genome assembly, annotation and mining of blast disease resistance genes

description: Sequence data size for rice cultivars. (XLSX 15Â kb)
DOI: 10.15468/dl.n2dc55
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Desmodium triflorum Linnaeus, 1753"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034198-241126133413365/datasets/export for details.
DOI: 10.6084/m9.figshare.c.3646253_d1
title: Additional file 4: of Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries

description: Complete edgeR results for HOMINGS taxon probes, comparing Plaque vs. WS pairs. The spreadsheet otherwise is formatted in the same way as Additional file 3.
DOI: 10.6084/m9.figshare.c.3646253_d2
title: Additional file 5: of Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries

description: Complete edgeR results for HOMINGS taxon probes, comparing WS vs. NS pairs. There were no probes with an adjusted p value â ¤0.05, so the rows only were sorted according to the number of samples in which the relative abundance of a taxon probe exceeded 1Â % of total reads (in descending order, using column H).
DOI: 10.6084/m9.figshare.c.3646253_d3
title: Additional file 12: of Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries

description: Clinical metadata for subjects. Lists each subjectâ  s age at time of sampling, gender, the universal ID code for the restored primary tooth from which the sample was taken and the clinical characteristics of the composite restoration around the margins of which plaque was collected.
DOI: 10.6084/m9.figshare.c.3646253_d4
title: Additional file 9: of Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries

description: Counts for spectra assigned to SEED ontology proteins by MEGAN5. Each row lists spectral counts assigned to a SEED protein. The spreadsheet otherwise is formatted in the same way as Additional file 6.
DOI: 10.6084/m9.figshare.c.3646253_d5
title: Additional file 11: of Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries

description: Complete edgeR results for spectra assigned to SEED proteins by MEGAN5, comparing WS vs. NS pairs. The proteins names assigned by MEGAN5 were derived from the SEED ontology database. The spreadsheet is formatted in the same way as Additional file 8, except that column H sorts the proteins by the number of microcosms in which they were detected (in descending order).
DOI: 10.6084/m9.figshare.c.3646253_d7
title: Additional file 8: of Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries

description: Complete edgeR results for spectra assigned at the species level by the MEGAN5 LCA, comparing WS vs. NS pairs. The species names assigned by MEGAN5 were derived from the NCBI taxonomy database. The spreadsheet otherwise is formatted in the same way as Additional file 3.
DOI: 10.6084/m9.figshare.c.3646253_d9
title: Additional file 3: of Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries

description: Complete edgeR results for HOMINGS taxon probes, comparing Plaque vs. NS pairs. Each row summarizes the results for a HOMINGS taxon probe that was detected in at least one plaque or NS sample. The rows were first sorted into two groups (using column G), those with an adjusted p value ≤0.05 (shown in blue) and those in which the adjusted p value exceeded that threshold. Within each group, the rows then were sorted according to the number of plaque samples in which reads for a probe were ≥1 % (as a percent of total reads), in descending order (using column H). The taxon probe names in the FDR ≤ 5 % group were shaded red when the log fold change value was positive (P &gt; NS), and green when the log fold change value was negative (NS &gt; P).
DOI: 10.6084/m9.figshare.c.3646253_d11
title: Additional file 1: of Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries

description: ProbeSeq results as received from the HOMINGS core facility. The first worksheet provides read count summaries for each sample. The second worksheet lists read counts for all HOMINGS probes (including those not detected) for each sample. The third worksheet presents the read counts as a percent of total reads for each sample, and the fourth worksheet summarizes results for each sample as stacked column plots.
DOI: 10.6084/m9.figshare.c.3646253_d12
title: Additional file 6: of Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries

description: Counts for spectra assigned at the species level by the MEGAN5 LCA. Each row lists spectral counts assigned to a NCBI species level taxon in at least one NS or WS sample. The columns are paired, so that each NS sample is matched with its WS counterpart. The rows are sorted in descending order by the number of samples in which that species was assigned (using column Z).