cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6168566.v1
title: Additional file 6 of Population-based statistical inference for temporal sequence of somatic mutations in cancer genomes

description: Table S5. Enrichment genesets on C5bp for genes with negative SCORE-AN. The results were obtained by GSEApreranked on C5bp (Gene Ontology, biological process). BLCA, BRCA, COADREAD, HNSC, KIRC and LUSC were no results with nominal P value &lt;0.05. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.6168563
title: Additional file 5 of Population-based statistical inference for temporal sequence of somatic mutations in cancer genomes

description: Table S4. Enrichment genesets on C5bp for genes with positive SCORE-AN. The results were obtained by GSEApreranked on C5bp (Gene Ontology, biological process). BLCA, BRCA and KIRC were no results with nominal P value &lt;0.05. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.6168563.v1
title: Additional file 5 of Population-based statistical inference for temporal sequence of somatic mutations in cancer genomes

description: Table S4. Enrichment genesets on C5bp for genes with positive SCORE-AN. The results were obtained by GSEApreranked on C5bp (Gene Ontology, biological process). BLCA, BRCA and KIRC were no results with nominal P value &lt;0.05. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.6168560
title: Additional file 4 of Population-based statistical inference for temporal sequence of somatic mutations in cancer genomes

description: Table S3. SCORE-AN for genes observed in each tumor type. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.6168560.v1
title: Additional file 4 of Population-based statistical inference for temporal sequence of somatic mutations in cancer genomes

description: Table S3. SCORE-AN for genes observed in each tumor type. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.6168551
title: Additional file 3 of Population-based statistical inference for temporal sequence of somatic mutations in cancer genomes

description: Table S2. Ordered pairs with statistical significance in each tumor type. (XLSX 61 kb)
DOI: 10.6084/m9.figshare.6168551.v1
title: Additional file 3 of Population-based statistical inference for temporal sequence of somatic mutations in cancer genomes

description: Table S2. Ordered pairs with statistical significance in each tumor type. (XLSX 61 kb)
DOI: 10.6084/m9.figshare.6168539
title: Additional file 1 of Population-based statistical inference for temporal sequence of somatic mutations in cancer genomes

description: Table S1. SCORE-CO for the pair of genes in each tumor type. (XLSX 696 kb)
DOI: 10.6084/m9.figshare.6168539.v1
title: Additional file 1 of Population-based statistical inference for temporal sequence of somatic mutations in cancer genomes

description: Table S1. SCORE-CO for the pair of genes in each tumor type. (XLSX 696 kb)
DOI: 10.6084/m9.figshare.6168521
title: Additional file 10 of Population-based statistical inference for temporal sequence of somatic mutations in cancer genomes

description: Table S8. Common temporal orders in multiple tumor types. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6168521.v1
title: Additional file 10 of Population-based statistical inference for temporal sequence of somatic mutations in cancer genomes

description: Table S8. Common temporal orders in multiple tumor types. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6168518
title: Additional file 6: of ClustAGE: a tool for clustering and distribution analysis of bacterial accessory genomic elements

description: Comparison of ClustAGE results with pairwise gene ortholog analysis. (XLSX 54Â kb)
DOI: 10.6084/m9.figshare.6168518.v1
title: Additional file 6: of ClustAGE: a tool for clustering and distribution analysis of bacterial accessory genomic elements

description: Comparison of ClustAGE results with pairwise gene ortholog analysis. (XLSX 54Â kb)
DOI: 10.6084/m9.figshare.6168482
title: Additional file 4: of ClustAGE: a tool for clustering and distribution analysis of bacterial accessory genomic elements

description: ClustAGE output characteristics. (XLSX 58Â kb)
DOI: 10.6084/m9.figshare.6168482.v1
title: Additional file 4: of ClustAGE: a tool for clustering and distribution analysis of bacterial accessory genomic elements

description: ClustAGE output characteristics. (XLSX 58Â kb)
DOI: 10.6084/m9.figshare.6168476
title: Additional file 3: of ClustAGE: a tool for clustering and distribution analysis of bacterial accessory genomic elements

description: Unbinned accessory sequences. (XLSX 52Â kb)
DOI: 10.6084/m9.figshare.6168476.v1
title: Additional file 3: of ClustAGE: a tool for clustering and distribution analysis of bacterial accessory genomic elements

description: Unbinned accessory sequences. (XLSX 52Â kb)
DOI: 10.6084/m9.figshare.6168461
title: Additional file 4: of SpirPep: an in silico digestion-based platform to assist bioactive peptides discovery from a genome-wide database

description: Table S1. Dataset and output comparison between SpirPep and BIOPEP, the identified bioactive peptides obtained from temperature stress â expressed protein [30] digested with trypsin and no miscleavage. (XLSX 18Â kb)
DOI: 10.6084/m9.figshare.6168458
title: Additional file 2: of ClustAGE: a tool for clustering and distribution analysis of bacterial accessory genomic elements

description: Archive containing output files from ClustAGE analysis of accessory genome sequence files found in Additional file 1. (ZIP 18100Â kb)
DOI: 10.6084/m9.figshare.6168458.v1
title: Additional file 2: of ClustAGE: a tool for clustering and distribution analysis of bacterial accessory genomic elements

description: Archive containing output files from ClustAGE analysis of accessory genome sequence files found in Additional file 1. (ZIP 18100Â kb)
DOI: 10.6084/m9.figshare.6168449
title: Additional file 1: of ClustAGE: a tool for clustering and distribution analysis of bacterial accessory genomic elements

description: Archive containing relevant output files from the Spine and AGEnt analyses of the reference genomes. (ZIP 4849Â kb)
DOI: 10.6084/m9.figshare.6168449.v1
title: Additional file 1: of ClustAGE: a tool for clustering and distribution analysis of bacterial accessory genomic elements

description: Archive containing relevant output files from the Spine and AGEnt analyses of the reference genomes. (ZIP 4849Â kb)
DOI: 10.25345/c5r45m
title: MassIVE MSV000086036 - Baylor-NHP-tissue-samples-negative-mode-08-21-2020
title: The monkey tissue samples run positive and negative mode. experiment date is 8-21-2020. C8 column
DOI: 10.6084/m9.figshare.6168377
title: Additional file 7: of Comparative mitochondrial genomics of cryptophyte algae: gene shuffling and dynamic mobile genetic elements

description: Table S1. The concatenated data set of 16 protein coding genes for phylogenetic reconstruction. (XLSX 22Â kb)
DOI: 10.6084/m9.figshare.6168377.v1
title: Additional file 7: of Comparative mitochondrial genomics of cryptophyte algae: gene shuffling and dynamic mobile genetic elements

description: Table S1. The concatenated data set of 16 protein coding genes for phylogenetic reconstruction. (XLSX 22Â kb)
DOI: 10.6084/m9.figshare.6168353
title: Additional file 9: of Meta-populational demes constitute a reservoir for large MHC allele diversity in wild house mice (Mus musculus)

description: Table S8. Genbank accession numbers for new alleles (XLSX 46 kb)
DOI: 10.6084/m9.figshare.6168353.v1
title: Additional file 9: of Meta-populational demes constitute a reservoir for large MHC allele diversity in wild house mice (Mus musculus)

description: Table S8. Genbank accession numbers for new alleles (XLSX 46 kb)
DOI: 10.6084/m9.figshare.6168338
title: Additional file 8: of Meta-populational demes constitute a reservoir for large MHC allele diversity in wild house mice (Mus musculus)

description: Table S7. Microsatellite alleles in demes (XLSX 20 kb)
DOI: 10.6084/m9.figshare.6168338.v1
title: Additional file 8: of Meta-populational demes constitute a reservoir for large MHC allele diversity in wild house mice (Mus musculus)

description: Table S7. Microsatellite alleles in demes (XLSX 20 kb)
DOI: 10.6084/m9.figshare.6168320
title: Additional file 7: of Meta-populational demes constitute a reservoir for large MHC allele diversity in wild house mice (Mus musculus)

description: Table S6. H2-Eb alleles in demes (XLSX 24 kb)
DOI: 10.6084/m9.figshare.6168320.v1
title: Additional file 7: of Meta-populational demes constitute a reservoir for large MHC allele diversity in wild house mice (Mus musculus)

description: Table S6. H2-Eb alleles in demes (XLSX 24 kb)
DOI: 10.6084/m9.figshare.6168293
title: Additional file 6: of Meta-populational demes constitute a reservoir for large MHC allele diversity in wild house mice (Mus musculus)

description: Table S5. H2-Aa alleles in demes (XLSX 24 kb)
DOI: 10.6084/m9.figshare.6168293.v1
title: Additional file 6: of Meta-populational demes constitute a reservoir for large MHC allele diversity in wild house mice (Mus musculus)

description: Table S5. H2-Aa alleles in demes (XLSX 24 kb)
DOI: 10.6084/m9.figshare.6168281
title: Additional file 5: of Meta-populational demes constitute a reservoir for large MHC allele diversity in wild house mice (Mus musculus)

description: Table S4. List of all validated class II alleles found in the 454 approach (XLSX 58 kb)
DOI: 10.6084/m9.figshare.6168281.v1
title: Additional file 5: of Meta-populational demes constitute a reservoir for large MHC allele diversity in wild house mice (Mus musculus)

description: Table S4. List of all validated class II alleles found in the 454 approach (XLSX 58 kb)
DOI: 10.6084/m9.figshare.6168263
title: Additional file 4: of Meta-populational demes constitute a reservoir for large MHC allele diversity in wild house mice (Mus musculus)

description: Table S3. List of all validated class I alleles found in the 454 approach (XLSX 80 kb)
DOI: 10.6084/m9.figshare.6168263.v1
title: Additional file 4: of Meta-populational demes constitute a reservoir for large MHC allele diversity in wild house mice (Mus musculus)

description: Table S3. List of all validated class I alleles found in the 454 approach (XLSX 80 kb)
DOI: 10.6084/m9.figshare.6168251
title: Additional file 8: of Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular

description: Sequence of all primers generated for this study, together with qPCR probes, amplification efficiencies, and primer/probe combinations used. Exon content of amplicons used for Northern analyses is also shown. For additional assays, see [7]. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.6168251.v1
title: Additional file 8: of Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular

description: Sequence of all primers generated for this study, together with qPCR probes, amplification efficiencies, and primer/probe combinations used. Exon content of amplicons used for Northern analyses is also shown. For additional assays, see [7]. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.6168242
title: Additional file 3: of Meta-populational demes constitute a reservoir for large MHC allele diversity in wild house mice (Mus musculus)

description: Table S2. 454 read statistics (XLSX 38 kb)
DOI: 10.6084/m9.figshare.6168242.v1
title: Additional file 3: of Meta-populational demes constitute a reservoir for large MHC allele diversity in wild house mice (Mus musculus)

description: Table S2. 454 read statistics (XLSX 38 kb)
DOI: 10.6084/m9.figshare.6168230
title: Additional file 2: of Meta-populational demes constitute a reservoir for large MHC allele diversity in wild house mice (Mus musculus)

description: Table S1. PCR and sequencing primers (XLSX 17 kb)
DOI: 10.6084/m9.figshare.6168230.v1
title: Additional file 2: of Meta-populational demes constitute a reservoir for large MHC allele diversity in wild house mice (Mus musculus)

description: Table S1. PCR and sequencing primers (XLSX 17 kb)
DOI: 10.6084/m9.figshare.6168227
title: Additional file 7: of Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular

description: Genomic co-ordinates of all annotated and novel FIRRE exons. The position of all junctions are shown with respect to hg19, together with their current annotations where appropriate. Splice acceptor and donor junctions identified by annotation-free mapping of day 0 samples against hg19 using MapSplice are shown, together with donor exons and acceptor exons, and junction numbers in brackets. Supporting evidence for each junction is colour coded. Minor / Others â additional junctions not involving annotated exons which are present at low frequency. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.6168227.v1
title: Additional file 7: of Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular

description: Genomic co-ordinates of all annotated and novel FIRRE exons. The position of all junctions are shown with respect to hg19, together with their current annotations where appropriate. Splice acceptor and donor junctions identified by annotation-free mapping of day 0 samples against hg19 using MapSplice are shown, together with donor exons and acceptor exons, and junction numbers in brackets. Supporting evidence for each junction is colour coded. Minor / Others â additional junctions not involving annotated exons which are present at low frequency. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.6168212
title: Additional file 6: of Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular

description: FIRRE exon junctions confirmed by amplicon sequencing. All reads were mapped against hg19 without reference to transcript annotation: Amplicons using convergent primer pairs and divergent primer pairs (to amplify circRNAs only) are shown separately. Canonical junctions were mapped using MapSplice [67], circRNA (back-splice) junctions were mapped using PTESFinder [46]. For details, see methods. Exon number is according to schema in Fig. 6b. Junction position (hg19), amplicons of origin, and junction frequencies, are given for all junctions. Only splices with a frequency of 1% or higher in each amplicon, identified either by MapSplice or PTESfinder, are reported. Canonical junctions present within the current FIRRE annotation are show in blue. All others are not present within current annotation. Off target junctions (presumed to be generated by illegitimate primer binding) are also shown. Data is for confirmation of junction presence within transcripts only: Junction frequency is affected by position relative to primer, size dependent amplification bias during Nextera indexing, and size dependent bias in cluster formation/resolution efficiencies during MiSeq sequencing. (XLSX 71Â kb)
DOI: 10.6084/m9.figshare.6168212.v1
title: Additional file 6: of Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular

description: FIRRE exon junctions confirmed by amplicon sequencing. All reads were mapped against hg19 without reference to transcript annotation: Amplicons using convergent primer pairs and divergent primer pairs (to amplify circRNAs only) are shown separately. Canonical junctions were mapped using MapSplice [67], circRNA (back-splice) junctions were mapped using PTESFinder [46]. For details, see methods. Exon number is according to schema in Fig. 6b. Junction position (hg19), amplicons of origin, and junction frequencies, are given for all junctions. Only splices with a frequency of 1% or higher in each amplicon, identified either by MapSplice or PTESfinder, are reported. Canonical junctions present within the current FIRRE annotation are show in blue. All others are not present within current annotation. Off target junctions (presumed to be generated by illegitimate primer binding) are also shown. Data is for confirmation of junction presence within transcripts only: Junction frequency is affected by position relative to primer, size dependent amplification bias during Nextera indexing, and size dependent bias in cluster formation/resolution efficiencies during MiSeq sequencing. (XLSX 71Â kb)
DOI: 10.6084/m9.figshare.6168209
title: Additional file 1: of Risk factors associated with short term mortality changes over time, after arrival to the emergency department

description: DEPT triage. Vital values. (XLSX 61.8Â kb)
DOI: 10.6084/m9.figshare.6168209.v1
title: Additional file 1: of Risk factors associated with short term mortality changes over time, after arrival to the emergency department

description: DEPT triage. Vital values. (XLSX 61.8Â kb)
DOI: 10.6084/m9.figshare.6168200
title: Additional file 12: of Meta-populational demes constitute a reservoir for large MHC allele diversity in wild house mice (Mus musculus)

description: Table S11. dN/dS and K2P nucleotide distance/Poisson corrected amino acid distances (XLSX 52 kb)
DOI: 10.6084/m9.figshare.6168200.v1
title: Additional file 12: of Meta-populational demes constitute a reservoir for large MHC allele diversity in wild house mice (Mus musculus)

description: Table S11. dN/dS and K2P nucleotide distance/Poisson corrected amino acid distances (XLSX 52 kb)
DOI: 10.6084/m9.figshare.6168194
title: Additional file 5: of Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular

description: Gene Ontology analysis showing over and under-represented gene ontologies (biological process and molecular function) in parent loci of 239 significantly altered circRNAs. Analyses were performed using the Panther classification system [73], with a Bonferroni correction for multiple testing. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.6168194.v1
title: Additional file 5: of Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular

description: Gene Ontology analysis showing over and under-represented gene ontologies (biological process and molecular function) in parent loci of 239 significantly altered circRNAs. Analyses were performed using the Panther classification system [73], with a Bonferroni correction for multiple testing. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.6168182
title: Additional file 11: of Meta-populational demes constitute a reservoir for large MHC allele diversity in wild house mice (Mus musculus)

description: Table S10. Alignments of H2-Aa and H2-Eb alleles (XLSX 47 kb)
DOI: 10.6084/m9.figshare.6168182.v1
title: Additional file 11: of Meta-populational demes constitute a reservoir for large MHC allele diversity in wild house mice (Mus musculus)

description: Table S10. Alignments of H2-Aa and H2-Eb alleles (XLSX 47 kb)
DOI: 10.6084/m9.figshare.6168176
title: Additional file 4: of Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular

description: CircRNA transcripts showing significantly altered expression in both locus and sample level analyses. Normalised circRNA and canonical RNA junction read counts in all control sample replicates are shown, together with average abundance ratio (circRNA junction frequency/canonical junction frequency), genomic co-ordinates, and circbase i.d.s where available. The most significant p-values obtained in each group of pair-wise t-tests (sample DE and locus DE) are also shown for each transcript. Analyses in which transcript was identified are indicated as follows; U (untreated), I (IGF-1 treated), B (Both analyses). For details of analysis, see text and methods. (XLSX 115Â kb)
DOI: 10.6084/m9.figshare.6168176.v1
title: Additional file 4: of Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular

description: CircRNA transcripts showing significantly altered expression in both locus and sample level analyses. Normalised circRNA and canonical RNA junction read counts in all control sample replicates are shown, together with average abundance ratio (circRNA junction frequency/canonical junction frequency), genomic co-ordinates, and circbase i.d.s where available. The most significant p-values obtained in each group of pair-wise t-tests (sample DE and locus DE) are also shown for each transcript. Analyses in which transcript was identified are indicated as follows; U (untreated), I (IGF-1 treated), B (Both analyses). For details of analysis, see text and methods. (XLSX 115Â kb)
DOI: 10.6084/m9.figshare.6168158
title: Additional file 10: of Meta-populational demes constitute a reservoir for large MHC allele diversity in wild house mice (Mus musculus)

description: Table S9. Pairwise distances between demes based on microsatellites (FST) (XLSX 37 kb)
DOI: 10.6084/m9.figshare.6168158.v1
title: Additional file 10: of Meta-populational demes constitute a reservoir for large MHC allele diversity in wild house mice (Mus musculus)

description: Table S9. Pairwise distances between demes based on microsatellites (FST) (XLSX 37 kb)
DOI: 10.6084/m9.figshare.6168143
title: Additional file 4: of An integrated clinical and genomic information system for cancer precision medicine

description: Galaxy workflow file (json data format) for WTS data processing, it can be imported to another Galaxy server. (GA 23Â kb)
DOI: 10.6084/m9.figshare.6168143.v1
title: Additional file 4: of An integrated clinical and genomic information system for cancer precision medicine

description: Galaxy workflow file (json data format) for WTS data processing, it can be imported to another Galaxy server. (GA 23Â kb)
DOI: 10.6084/m9.figshare.6168134
title: Additional file 2: of Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular

description: a-d. Gene Ontology analyses showing over and under-represented gene ontologies (biological process and molecular function) in genes differentially expressed between untreated time-points. Analyses were performed using the Panther classification system [73], with a Bonferroni correction for multiple testing. e. Genes differentially expressed between IGF-1 treated and untreated samples. List includes genes identified by comparision at each timepoint, and an all v all comparison. No significant genes were identified in the day 90 analysis. (XLSX 50Â kb)
DOI: 10.6084/m9.figshare.6168134.v1
title: Additional file 2: of Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular

description: a-d. Gene Ontology analyses showing over and under-represented gene ontologies (biological process and molecular function) in genes differentially expressed between untreated time-points. Analyses were performed using the Panther classification system [73], with a Bonferroni correction for multiple testing. e. Genes differentially expressed between IGF-1 treated and untreated samples. List includes genes identified by comparision at each timepoint, and an all v all comparison. No significant genes were identified in the day 90 analysis. (XLSX 50Â kb)
DOI: 10.6084/m9.figshare.6168131
title: Additional file 3: of An integrated clinical and genomic information system for cancer precision medicine

description: Galaxy workflow file (json data format) for WES data processing, it can be imported to another Galaxy server. (GA 53Â kb)
DOI: 10.6084/m9.figshare.6168131.v1
title: Additional file 3: of An integrated clinical and genomic information system for cancer precision medicine

description: Galaxy workflow file (json data format) for WES data processing, it can be imported to another Galaxy server. (GA 53Â kb)
DOI: 10.6084/m9.figshare.6168110
title: Additional file 1: of Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular

description: Sequencing Quality Control. Data shows Illumina quality control metrics. PF = Passing chastity filter. Q30 = Phred quality score of 30 or above. (XLSX 9 kb)