cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3769577_d6
title: Additional file 5: Table S3. of Integrated data analysis reveals potential drivers and pathways disrupted by DNA methylation in papillary thyroid carcinomas

description: Integrative analysis between methylation and expression data in PTC samples. Legend. FGD functional genomic distribution, CHR chromosome, DMR differential methylation region, RDMR reprogramming-specific differentially methylated region, CDMR cancer-specific differentially methylated region, NA not available, NS not significant, FC fold change, FDR false discovery rate, R inverse correlation. (XLSX 122 kb)
DOI: 10.6084/m9.figshare.c.3769577_d7
title: Additional file 6: Table S4. of Integrated data analysis reveals potential drivers and pathways disrupted by DNA methylation in papillary thyroid carcinomas

description: Disease, biological functions, and canonical pathways potentially regulated by methylation in PTC samples. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3769577_d10.v1
title: Additional file 9: Table S7. of Integrated data analysis reveals potential drivers and pathways disrupted by DNA methylation in papillary thyroid carcinomas

description: Integrative analysis between methylation and expression data according to the BRAF mutation. Legend. FGD functional genomic distribution, CHR chromosome, DMR differential methylation region, RDMR reprogramming-specific differentially methylated region, CDMR cancer-specific differentially methylated region, NA not available, NS not significant, FC fold change, FDR false discovery rate, R inverse correlation. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.c.3769577_d10
title: Additional file 9: Table S7. of Integrated data analysis reveals potential drivers and pathways disrupted by DNA methylation in papillary thyroid carcinomas

description: Integrative analysis between methylation and expression data according to the BRAF mutation. Legend. FGD functional genomic distribution, CHR chromosome, DMR differential methylation region, RDMR reprogramming-specific differentially methylated region, CDMR cancer-specific differentially methylated region, NA not available, NS not significant, FC fold change, FDR false discovery rate, R inverse correlation. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.c.3769643_d1
title: Additional file 1: of Post-operative atrial fibrillation examined using whole-genome RNA sequencing in human left atrial tissue

description: All cis eQTL relationships in LA at false discovery rate (FDR)-adjusted p-value &lt;0.05. Location is in hg19 coordinates. Mean gene expression is in normalized FPM (fragments per million mapped fragments). (TXT 2516 kb)
DOI: 10.6084/m9.figshare.c.3769628_d2
title: Additional file 2: Table S1. of Zipper plot: visualizing transcriptional activity of genomic regions

description: Summary table for the set of 36 well-characterized lncRNAs using CAGE-seq data. (XLS 69Â kb)
DOI: 10.6084/m9.figshare.c.3769628_d6.v1
title: Additional file 6: Table S5. of Zipper plot: visualizing transcriptional activity of genomic regions

description: Cancer type and barcode for each sample from TCGA. (XLS 138Â kb)
DOI: 10.6084/m9.figshare.c.3769628_d6
title: Additional file 6: Table S5. of Zipper plot: visualizing transcriptional activity of genomic regions

description: Cancer type and barcode for each sample from TCGA. (XLS 138Â kb)
DOI: 10.6084/m9.figshare.c.3769661_d4.v1
title: Additional file 4: of A high quality assembly of the Nile Tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regions

description: Extended repeat annotations of O_niloticus_UMD1 and Orenil1.1. RepeatMasker results for each TE family and other repeats for both assemblies and the differences between the two. (XLSX 60 kb)
DOI: 10.6084/m9.figshare.c.3769628_d7
title: Additional file 7: Table S6. of Zipper plot: visualizing transcriptional activity of genomic regions

description: HGNC, Ensembl ID, PMID, chromosome location, TSS and strand information for the set of 36 well-characterized lncRNAs. (XLS 26Â kb)
DOI: 10.6084/m9.figshare.c.3769661_d4
title: Additional file 4: of A high quality assembly of the Nile Tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regions

description: Extended repeat annotations of O_niloticus_UMD1 and Orenil1.1. RepeatMasker results for each TE family and other repeats for both assemblies and the differences between the two. (XLSX 60 kb)
DOI: 10.15468/dl.bzb9ry
title: Occurrence Download

description: A dataset containing 15079543 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is South America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Aves",
 "Year 1979-2016"
 ]
}

 The dataset includes 15079543 records from 279 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038675-241126133413365/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.3769724_d2
title: Additional file 11: of Transcriptome analysis of smut fungi reveals widespread intergenic transcription and conserved antisense transcript expression

description: Trinotate results for U. hordei intergenic transcripts. (XLSX 247 kb)
DOI: 10.6084/m9.figshare.c.3769733_d1
title: Additional file 1: Table S1. of ICoVeR â   an interactive visualization tool for verification and refinement of metagenomic bins

description: List of contigs and their bin assignments for the automated binning tools used in this study and for the subset of ICoVeR-refined genome bins for AD microbiome dataset. (XLS 2861Â kb)
DOI: 10.6084/m9.figshare.c.3769733_d2.v1
title: Additional file 2: Table S2. of ICoVeR â   an interactive visualization tool for verification and refinement of metagenomic bins

description: CheckM results for the genome bins generated with the automated binning tools used in this study and for the subset of ICoVeR-refined genome bins for AD microbiome dataset. (XLS 109Â kb)
DOI: 10.6084/m9.figshare.c.3769733_d2
title: Additional file 2: Table S2. of ICoVeR â   an interactive visualization tool for verification and refinement of metagenomic bins

description: CheckM results for the genome bins generated with the automated binning tools used in this study and for the subset of ICoVeR-refined genome bins for AD microbiome dataset. (XLS 109Â kb)
DOI: 10.6084/m9.figshare.c.3769724_d3.v1
title: Additional file 12: of Transcriptome analysis of smut fungi reveals widespread intergenic transcription and conserved antisense transcript expression

description: Trinotate results for S. reilianum intergenic transcripts. (XLSX 242 kb)
DOI: 10.6084/m9.figshare.c.3769730_d3.v1
title: Additional file 3: of Comparative costs and activity from a sample of UK clinical trials units

description: Tasks by role â   all CTUs. (XLSX 129 kb)
DOI: 10.6084/m9.figshare.c.3769724_d3
title: Additional file 12: of Transcriptome analysis of smut fungi reveals widespread intergenic transcription and conserved antisense transcript expression

description: Trinotate results for S. reilianum intergenic transcripts. (XLSX 242 kb)
DOI: 10.6084/m9.figshare.c.3769733_d3.v1
title: Additional file 3: Table S3. of ICoVeR â   an interactive visualization tool for verification and refinement of metagenomic bins

description: CheckM results for ICoVeR-refined genome bins for Sharonâ  s dataset. (XLS 56Â kb)
DOI: 10.6084/m9.figshare.c.3769724_d4.v1
title: Additional file 13: of Transcriptome analysis of smut fungi reveals widespread intergenic transcription and conserved antisense transcript expression

description: BLASTn results find intergenic transcripts with similar sequences in smuts. (XLSX 285 kb)
DOI: 10.6084/m9.figshare.c.3769730_d3
title: Additional file 3: of Comparative costs and activity from a sample of UK clinical trials units

description: Tasks by role â   all CTUs. (XLSX 129 kb)
DOI: 10.6084/m9.figshare.c.3769724_d8
title: Additional file 17: of Transcriptome analysis of smut fungi reveals widespread intergenic transcription and conserved antisense transcript expression

description: U. maydis detected antisense and putative orthologs with detected antisense. (XLSX 386 kb)
DOI: 10.6084/m9.figshare.c.3769724_d8.v1
title: Additional file 17: of Transcriptome analysis of smut fungi reveals widespread intergenic transcription and conserved antisense transcript expression

description: U. maydis detected antisense and putative orthologs with detected antisense. (XLSX 386 kb)
DOI: 10.6084/m9.figshare.c.3769760_d3
title: Additional file 3: Table S3. of Volatile organic compounds associated with Plasmodium falciparum infection in vitro

description: Detection of VOCs in SNUs. Raw data show the abundance area of each VOC in each sample from all volunteers. The total area sample was summed up for each sample. (XLSX 20Â kb)
DOI: 10.6084/m9.figshare.c.3769784_d1.v1
title: MOESM1 of Development of a core Clostridium thermocellum kinetic metabolic model consistent with multiple genetic perturbations

description: Additional file 1. The genome-scale model iCth446 with GPRs and metabolite information in COBRA toolbox compatible SBML format.
DOI: 10.6084/m9.figshare.c.3769784_d1
title: MOESM1 of Development of a core Clostridium thermocellum kinetic metabolic model consistent with multiple genetic perturbations

description: Additional file 1. The genome-scale model iCth446 with GPRs and metabolite information in COBRA toolbox compatible SBML format.
DOI: 10.6084/m9.figshare.c.3769724_d9
title: Additional file 18: of Transcriptome analysis of smut fungi reveals widespread intergenic transcription and conserved antisense transcript expression

description: U. hordei detected antisense and putative orthologs with detected antisense. (XLSX 332 kb)
DOI: 10.6084/m9.figshare.c.3769784_d2.v1
title: MOESM2 of Development of a core Clostridium thermocellum kinetic metabolic model consistent with multiple genetic perturbations

description: Additional file 2. The genome-scale model iCth446 with GPRs and metabolite information, list of TICs.
DOI: 10.6084/m9.figshare.c.3769784_d2
title: MOESM2 of Development of a core Clostridium thermocellum kinetic metabolic model consistent with multiple genetic perturbations

description: Additional file 2. The genome-scale model iCth446 with GPRs and metabolite information, list of TICs.
DOI: 10.15468/dl.gpfpwe
title: Occurrence Download

description: A dataset containing 113354 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is South America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Mammalia",
 "Year 1979-2016"
 ]
}

 The dataset includes 113354 records from 265 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038676-241126133413365/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.3769724_d10
title: Additional file 19: of Transcriptome analysis of smut fungi reveals widespread intergenic transcription and conserved antisense transcript expression

description: S. reilianum detected antisense and putative orthologs with detected antisense. (XLSX 351 kb)
DOI: 10.6084/m9.figshare.c.3769805_d3.v1
title: Additional file 12: of Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range

description: Summary of small, secreted proteins (SSPs) similar to proteins present in the Pathogen-Host Interactions database. Filled grey boxes in columns indicate presence of a similar protein(s) in that secretome identified by OrthoMCL clustering. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3769805_d2
title: Additional file 11: of Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range

description: Classification of proteases in the secretomes of the Venturia pathogens. Filled grey boxes in columns indicate presence of similar proteins in that secretome identified by OrthoMCL clustering: aspartate and serine (including those annotated as subtilases) proteases, metalloproteases and unclassified peptidases. Several of the proteases were similar (
DOI: 10.6084/m9.figshare.c.3769724_d13
title: Additional file 21: of Transcriptome analysis of smut fungi reveals widespread intergenic transcription and conserved antisense transcript expression

description: Primers used in this study. (XLSX 244 kb)
DOI: 10.6084/m9.figshare.c.3769724_d14.v1
title: Additional file 2: of Transcriptome analysis of smut fungi reveals widespread intergenic transcription and conserved antisense transcript expression

description: RNA-seq library information. (XLSX 316 kb)
DOI: 10.6084/m9.figshare.c.3769805_d3
title: Additional file 12: of Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range

description: Summary of small, secreted proteins (SSPs) similar to proteins present in the Pathogen-Host Interactions database. Filled grey boxes in columns indicate presence of a similar protein(s) in that secretome identified by OrthoMCL clustering. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3769724_d14
title: Additional file 2: of Transcriptome analysis of smut fungi reveals widespread intergenic transcription and conserved antisense transcript expression

description: RNA-seq library information. (XLSX 316 kb)
DOI: 10.6084/m9.figshare.c.3769724_d15
title: Additional file 3: of Transcriptome analysis of smut fungi reveals widespread intergenic transcription and conserved antisense transcript expression

description: U. maydis GFF3-formatted annotation file. (TXT 12298 kb)
DOI: 10.6084/m9.figshare.c.3769805_d6.v1
title: Additional file 15: of Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range

description: The genomes used in this study (non-Venturia). Sources of the genomes downloaded or accessed (with permission) from the Joint Genome Institute (JGI)/MycoCosm. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.c.3769724_d16
title: Additional file 4: of Transcriptome analysis of smut fungi reveals widespread intergenic transcription and conserved antisense transcript expression

description: U. hordei GFF3-formatted annotation file. (TXT 11903 kb)
DOI: 10.6084/m9.figshare.c.3769805_d5.v1
title: Additional file 14: of Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range

description: Details of the small (â ¤200 amino acids in length) secreted proteins in the Venturia infection secretome (VIS) gene set. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.c.3769805_d12
title: Additional file 4: of Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range

description: Core Eukaryotic Gene Model Analysis (CEGMA) of the Venturia inaequalis and V. pirina genomes. The 248 most highly-conserved core eukaryotic genes were used in the CEGMA to assess genome completeness. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3769805_d13
title: Additional file 5: of Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range

description: Benchmarking Universal Single-Copy Orthologs (BUSCO_v1.1b) analysis of the Venturia inaequalis and V. pirina genomes. BUSCO analysis was used to assess completeness of the Venturia genome assemblies. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3769805_d15.v1
title: Additional file 7: of Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range

description: The predicted secretomes and small, secreted proteins (SSPs) encoded by the genomes of Venturia and representative related pathogens. The genomes for Parastagonospora nodorum, Cladosporium fulvum and Puccinia graminis f. sp. tritici were downloaded via the Mycocosm portal at the Joint Genome Institute (JGI; see details in Additional file 15). These pathogens were representatives of necrotrophic, facultative and obligate biotrophic fungi, respectively. The pipeline outlined in Additional file 6 was employed to identify the secretome and SSPs in each of the genomes. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3769805_d15
title: Additional file 7: of Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range

description: The predicted secretomes and small, secreted proteins (SSPs) encoded by the genomes of Venturia and representative related pathogens. The genomes for Parastagonospora nodorum, Cladosporium fulvum and Puccinia graminis f. sp. tritici were downloaded via the Mycocosm portal at the Joint Genome Institute (JGI; see details in Additional file 15). These pathogens were representatives of necrotrophic, facultative and obligate biotrophic fungi, respectively. The pipeline outlined in Additional file 6 was employed to identify the secretome and SSPs in each of the genomes. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3769805_d17.v1
title: Additional file 9: of Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range

description: The CAZyme domains present in proteins encoded by the Venturia secretomes. CAZyme domains were identified using the CAZymes analysis toolkit (CAT) server. Domains: CBM: carbohydrate binding module; CE: carbohydrate esterase; GH: glycoside hydrolase; GT: glycosyltransferase; PL: polysaccharide lyase. The known substrates for the CAZyme domains were taken from Zhao et al. PCW: plant cell wall. FCW: fungal cell wall. CW: cell wall. ESR: energy storage and recovery. PG: protein glycosylation. dpi: days post inoculation. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3769805_d17
title: Additional file 9: of Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range

description: The CAZyme domains present in proteins encoded by the Venturia secretomes. CAZyme domains were identified using the CAZymes analysis toolkit (CAT) server. Domains: CBM: carbohydrate binding module; CE: carbohydrate esterase; GH: glycoside hydrolase; GT: glycosyltransferase; PL: polysaccharide lyase. The known substrates for the CAZyme domains were taken from Zhao et al. PCW: plant cell wall. FCW: fungal cell wall. CW: cell wall. ESR: energy storage and recovery. PG: protein glycosylation. dpi: days post inoculation. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3770717_d1.v1
title: MOESM1 of Multiple genotypes within aecial clusters in Puccinia graminis and Puccinia coronata: improved understanding of the biology of cereal rust fungi

description: Additional file 1. SSR allele sizes of all aecia within aecial clusters for Puccinia coronata, sampled from the hosts Rhamnus cathartica and Frangula alnus.
DOI: 10.6084/m9.figshare.c.3770717_d1
title: MOESM1 of Multiple genotypes within aecial clusters in Puccinia graminis and Puccinia coronata: improved understanding of the biology of cereal rust fungi

description: Additional file 1. SSR allele sizes of all aecia within aecial clusters for Puccinia coronata, sampled from the hosts Rhamnus cathartica and Frangula alnus.
DOI: 10.6084/m9.figshare.c.3770717_d2.v1
title: MOESM2 of Multiple genotypes within aecial clusters in Puccinia graminis and Puccinia coronata: improved understanding of the biology of cereal rust fungi

description: Additional file 2. SSR allele sizes of all aecia within aecial clusters for Puccinia graminis, sampled from the host Berberis vulgaris.
DOI: 10.6084/m9.figshare.c.3770717_d2
title: MOESM2 of Multiple genotypes within aecial clusters in Puccinia graminis and Puccinia coronata: improved understanding of the biology of cereal rust fungi

description: Additional file 2. SSR allele sizes of all aecia within aecial clusters for Puccinia graminis, sampled from the host Berberis vulgaris.
DOI: 10.6084/m9.figshare.c.3770771_d1.v1
title: Additional file 10: of Genome-wide DNA methylation analysis reveals loci that distinguish different types of adipose tissue in obese individuals

description: Annotated data for the 4900 CpG sites with a positive merit score in the combinatorial algorithm analysis before weight loss analysis. Illumina probe ID, gene symbol, gene region and chromosomal location (as Illumina 450K manifest) are shown along with methylation statistics. OM_mean_beta and AB_mean_beta present mean beta values for omental (OM) and abdominal subcutaneous (AB) adipose, respectively. Merit score and ranking are also provided. (CSV 310 kb)
DOI: 10.6084/m9.figshare.c.3770771_d1
title: Additional file 10: of Genome-wide DNA methylation analysis reveals loci that distinguish different types of adipose tissue in obese individuals

description: Annotated data for the 4900 CpG sites with a positive merit score in the combinatorial algorithm analysis before weight loss analysis. Illumina probe ID, gene symbol, gene region and chromosomal location (as Illumina 450K manifest) are shown along with methylation statistics. OM_mean_beta and AB_mean_beta present mean beta values for omental (OM) and abdominal subcutaneous (AB) adipose, respectively. Merit score and ranking are also provided. (CSV 310 kb)
DOI: 10.6084/m9.figshare.c.3770771_d2.v1
title: Additional file 11: of Genome-wide DNA methylation analysis reveals loci that distinguish different types of adipose tissue in obese individuals

description: Annotated data for the 8624 CpG sites with a positive merit score in the combinatorial algorithm analysis after weight loss. Illumina probe ID, gene symbol, gene region and chromosomal location (as Illumina 450K manifest) are shown along with methylation statistics. OM_mean_beta and AB_mean_beta present mean beta values for omental (OM) and abdominal subcutaneous (AB) adipose, respectively. Merit score and ranking are also provided. (CSV 655 kb)
DOI: 10.6084/m9.figshare.c.3770780_d2
title: Additional file 2: of Seasonal influenza vaccination in patients with COPD: a systematic literature review

description: Summary tables Safety results. Table S1 COPD Exacerbations after seasonal influenza vaccination. Table S2 Spirometric results before, 1Â week and 3â  4 weeks after seasonal influenza vaccination. Table S3: Local and systemic effects after seasonal influenza vaccination (most frequent effects). (XLSX 93 kb)