cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3644486_d2
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_d3
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
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.3644486_d4
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_d6
title: Additional file 5: Table S5. of Molecular and phenotypic distinction of the very recently evolved insular subspecies Mus musculus helgolandicus ZIMMERMANN, 1953

description: Details of the primers used for microsatellite loci typing. (XLS 29 kb)
DOI: 10.6084/m9.figshare.c.3644486_d8
title: Additional file 8: Table S8. of Molecular and phenotypic distinction of the very recently evolved insular subspecies Mus musculus helgolandicus ZIMMERMANN, 1953

description: List of mandible landmarks raw coordinates. (XLS 48 kb)
DOI: 10.6084/m9.figshare.c.3644486_d7
title: Additional file 6: Table S6. of Molecular and phenotypic distinction of the very recently evolved insular subspecies Mus musculus helgolandicus ZIMMERMANN, 1953

description: Primers used for mtDNA genome amplification and sequencing. (XLS 37 kb)
DOI: 10.6084/m9.figshare.c.3644936_d3
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
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
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
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
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_d5
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
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_d7
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_d9
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
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
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
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: 10.15468/dl.kf6abq
title: Occurrence Download

description: A dataset containing 39671 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cossus cossus Linnaeus, 1758"
 ]
}

 The dataset includes 39671 records from 462 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034328-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.td3n54
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anoplophora glabripennis (Motschulsky, 1854)",
 "Country is Germany",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034329-241126133413365/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.3645428_d3
title: Additional file 7: Table S3. of Genome-wide methylation profiling of ovarian cancer patient-derived xenografts treated with the demethylating agent decitabine identifies novel epigenetically regulated genes and pathways

description: Table for GO enrichment and pathway analysis. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.c.3645428_d4
title: Additional file 3: Table S1. of Genome-wide methylation profiling of ovarian cancer patient-derived xenografts treated with the demethylating agent decitabine identifies novel epigenetically regulated genes and pathways

description: All ovarian cancer cell lines and their culture conditions. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3645434_d6
title: Additional file 3: Table S3. of Resistance related metabolic pathways for drug target identification in Mycobacterium tuberculosis

description: The 24 sequenced Mycobacterium strains. Data can be viewed in Microsoft excel. (XLS 34 kb)
DOI: 10.6084/m9.figshare.c.3645434_d8
title: Additional file 8: Table S5. of Resistance related metabolic pathways for drug target identification in Mycobacterium tuberculosis

description: KEGG pathway descriptors for M. tuberculosis genes retained after prioritization. Data can be viewed in Microsoft excel. (XLS 7 kb)
DOI: 10.6084/m9.figshare.c.3645434_d7
title: Additional file 4: Table S4. of Resistance related metabolic pathways for drug target identification in Mycobacterium tuberculosis

description: Blast hits obtained for Rv1712, Rv2984, Rv2194, Rv1311, Rv1305, Rv2195, Rv1622c, Rv1456c and Rv2421c against three host intestinal bacteria. Bacterial species highlighted in bold showed homology to the query gene. Data can be viewed in Microsoft excel. (XLS 13 kb)
DOI: 10.6084/m9.figshare.c.3645434_d9
title: Additional file 15: Table S6. of Resistance related metabolic pathways for drug target identification in Mycobacterium tuberculosis

description: Docking scores and number of interactions for the top ten compounds to Rv1712. The residues highlighted in bold are conserved catalytic residues while ligand C5P is highlighted in red. The numbers inside the () indicate the number of interactions formed between residue and the compound atom. Data can be viewed in Microsoft excel. (XLS 8 kb)
DOI: 10.6084/m9.figshare.c.3645434_d13
title: Additional file 2: Table S2. of Resistance related metabolic pathways for drug target identification in Mycobacterium tuberculosis

description: Criteria used to filter high priority M.tuberculosis drug targets. The genes highlighted in bold satisfied all the selection criteria. The hyphen (â  ) indicates exclusion from further analysis. Abbreviations used: NUI- Not under investigation, PDB- Protein Data Bank, TBSGC- TB Structural Genome Consortium. References 12-Sassetti et al., 2003; 34-Lamichhane et al., 2003. Data can be viewed in Microsoft excel. (XLS 12 kb)
DOI: 10.6084/m9.figshare.c.3645437_d3
title: Additional file 1: Table S1. of Isolation, selection and culture methods to enhance clonogenicity of mouse bone marrow derived mesenchymal stromal cell precursors

description: Presenting a summary of monoclonal antibodies used in the experiments. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.c.3645869_d1
title: Additional file 2: of A new high-throughput screening-compatible gap junctional intercellular communication assay

description: Determination of the optimal ratio of donor and acceptor cells. This is the raw data (fluorescence intensity reads) in Fig.Â 3a (Microsoft Excel format). (XLS 51Â kb)
DOI: 10.6084/m9.figshare.c.3645890_d1
title: MOESM1 of Bitpacking techniques for indexing genomes: I. Hash tables

description: Additional file 1. Source code. Source code in an archive format, using tar and bzip2, for all bitpackingÂ implementations of hash tables, based on a modification of the SDSL 2.0 package. Package also includes the benchmarking programs used for timing experiments. This is the same package as provided in our companion paper on bitpacking for enhanced suffix arrays.
DOI: 10.6084/m9.figshare.c.3645890_d2
title: MOESM2 of Bitpacking techniques for indexing genomes: I. Hash tables

description: Additional file 2. Source code for constructing benchmarks. Source code in an archive format, using tar and bzip2, for users to generate their own benchmarks for any genomic text in FASTA format. This is the same package as provided in our companion paper on bitpacking for enhanced suffix arrays.
DOI: 10.6084/m9.figshare.c.3645893_d1
title: Additional file 12: Table S7. of Extensive identification and analysis of conserved small ORFs in animals

description: Summary of datasets used in Additional file 13: Figure S6A and B (RNA-seq). (ODS 11 kb)
DOI: 10.6084/m9.figshare.c.3645893_d2
title: Additional file 2: Table S1. of Extensive identification and analysis of conserved small ORFs in animals

description: All sORF information for human. (TXT 6997 kb)
DOI: 10.6084/m9.figshare.c.3645893_d4
title: Additional file 25: Table S14. of Extensive identification and analysis of conserved small ORFs in animals

description: Experimental evidence for C. elegans sORFs. (ODS 43 kb)
DOI: 10.6084/m9.figshare.c.3645893_d5
title: Additional file 5: Table S4. of Extensive identification and analysis of conserved small ORFs in animals

description: All sORF information for fly. (TXT 535 kb)
DOI: 10.6084/m9.figshare.c.3645893_d6
title: Additional file 21: Table S10. of Extensive identification and analysis of conserved small ORFs in animals

description: Experimental evidence for human sORFs. (ODS 85 kb)
DOI: 10.15468/dl.sx5wah
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anoplolepis gracilipes (Smith, 1857)",
 "Country is Christmas Island",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 21 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034330-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14472303
title: paraliparis_penicillus_spades_01.fasta.gz
DOI: 10.5281/zenodo.14472304
title: paraliparis_penicillus_spades_01.fasta.gz
DOI: 10.6084/m9.figshare.c.3646358_d1
title: Additional file 7: Table S6. of Structure and variation of the mitochondrial genome of fishes

description: Proportion of invariable amino acid sites in 13 protein-coding genes in the mt genomes of 250 fishes. (XLSX 41Â kb)
DOI: 10.6084/m9.figshare.c.3646358_d2
title: Additional file 5: Table S5. of Structure and variation of the mitochondrial genome of fishes

description: Variation in overlap length between protein-coding genes in the mt genomes of 250 fishes. (XLSX 41Â kb)
DOI: 10.6084/m9.figshare.c.3646358_d3
title: Additional file 2: Table S2. of Structure and variation of the mitochondrial genome of fishes

description: Start codons in 13 protein-coding genes in the mt genomes of 250 fishes. (XLSX 64Â kb)
DOI: 10.6084/m9.figshare.c.3646358_d4
title: Additional file 13: Table S10. of Structure and variation of the mitochondrial genome of fishes

description: Potential base pairing properties of stem regions in the 16S rRNA gene in the mt genomes of 250 fishes. (XLSX 86Â kb)
DOI: 10.6084/m9.figshare.c.3646358_d5
title: Additional file 3: Table S3. of Structure and variation of the mitochondrial genome of fishes

description: Stop codons in 13 protein-coding genes in the mt genomes of 250 fishes. (XLSX 53Â kb)
DOI: 10.6084/m9.figshare.c.3646358_d6
title: Additional file 4: Table S4. of Structure and variation of the mitochondrial genome of fishes

description: Length variation in 13 protein-coding genes in the mt genomes of 250 fishes. (XLSX 53Â kb)
DOI: 10.6084/m9.figshare.c.3646358_d7
title: Additional file 9: Table S8. of Structure and variation of the mitochondrial genome of fishes

description: Occurrence of nucleotide pair types in 21 pair sites common to all 22 tRNAs in the mt genomes of 250 fishes. (XLSX 107Â kb)
DOI: 10.6084/m9.figshare.c.3646358_d9
title: Additional file 6: Figure S1-a. of Structure and variation of the mitochondrial genome of fishes

description: Aligned amino acid sequences of the ATP8 gene in mt genomes of 250 fishes. Figure S1-b. Aligned amino acid sequences of the ATP6 gene in mt genomes of 250 fishes. Figure S1-c. Aligned amino acid sequences of the COI gene in mt genomes of 250 fishes. Figure S1-d. Aligned amino acid sequences of the COII gene in mt genomes of 250 fishes. Figure S1-e. Aligned amino acid sequences of the COIII gene in mt genomes of 250 fishes. Figure S1-f. Aligned amino acid sequences of the Cyt b gene in mt genomes of 250 fishes. Figure S1-g. Aligned amino acid sequences of the ND1 gene in mt genomes of 249 fishes. Figure S1-h. Aligned amino acid sequences of the ND2 gene in mt genomes of 250 fishes. Figure S1-i. Aligned amino acid sequences of the ND3 gene in mt genomes of 250 fishes. Figure S1-j. Aligned amino acid sequences of the ND4L gene in mt genomes of 250 fishes. Figure S1-k. Aligned amino acid sequences of the ND4 gene in mt genomes of 250 fishes. Figure S1-l. Aligned amino acid sequences of the ND5 gene in mt genomes of 250 fishes. Figure S1-m. Aligned amino acid sequences of the ND6 gene in mt genomes of 249 fishes. (ZIP 3250Â kb)
DOI: 10.6084/m9.figshare.c.3646358_d11
title: Additional file 14: Table S11. of Structure and variation of the mitochondrial genome of fishes

description: Differences between previous and present rRNA secondary structure models. (XLSX 59Â kb)
DOI: 10.6084/m9.figshare.c.3646358_d12
title: Additional file 15: Figure S4-a. of Structure and variation of the mitochondrial genome of fishes

description: Aligned nucleotide sequences of the conserved sequence blocks-D and -I in the control region (CR) in mt genomes of 182 fishes. Figure S4-b. Aligned nucleotide sequences of the conserved sequence blocks-II and -III in the control region (CR) in mt genomes of 182 fishes. (ZIP 87Â kb)
DOI: 10.6084/m9.figshare.c.3646358_d13
title: Additional file 12: Table S9. of Structure and variation of the mitochondrial genome of fishes

description: Potential base pairing properties of stem regions in the 12S rRNA gene in the mt genomes of 250 fishes. (XLSX 76Â kb)
DOI: 10.6084/m9.figshare.c.3646358_d15
title: Additional file 1: Table S1. of Structure and variation of the mitochondrial genome of fishes

description: List of species examined in this study with DDBJ/EMBL/GenBank accession numbers. (XLS 83Â kb)
DOI: 10.6084/m9.figshare.c.3646358_d16
title: Additional file 8: Table S7. of Structure and variation of the mitochondrial genome of fishes

description: Base frequencies for 83 nucleotide positions of 22 tRNA genes in the mt genomes of 250 fishes. (XLS 13112Â kb)
DOI: 10.6084/m9.figshare.c.3646361_d1
title: Additional file 1: of A method for assessing efficiency of bacterial cell disruption and DNA release

description: Spreadsheet for converting nanomoles or nanograms of adenine to nanograms of DNA. (XLSX 17Â kb)
DOI: 10.6084/m9.figshare.c.3649814_d3
title: Additional file 1: Table S1. of Resilient microorganisms in dust samples of the International Space Station—survival of the adaptation specialists

description: DADA2 output including negative controls (universal primer set); Highlighted RSVs were also found in the negative controls "RISS-LB-incubation-NC" and "RISS-protocol-NC" and were therefore removed from the dataset for further analysis. (XLSX 212 kb)
DOI: 10.6084/m9.figshare.c.3649829_d2
title: Additional file 2 of Skeleton-based cerebrovascular quantitative analysis

description: Normal047-segmentation.obj. This file is the segmentation result of the NO.47 data based on the Additional file 1: Normal047-MRA.mha. (OBJ 2846.72 kb)
DOI: 10.6084/m9.figshare.c.3649817_d3
title: MOESM7 of Mapping the membrane proteome of anaerobic gut fungi identifies a wealth of carbohydrate binding proteins and transporters

description: Additional file 7: Table S1. The transporter classification database (TCDB) hits identified in this study.
DOI: 10.6084/m9.figshare.c.3649796_d4
title: MOESM1 of Janus kinase inhibition suppresses PKC-induced cytokine release without affecting HIV-1 latency reversal ex vivo

description: Additional file 1: Table 1. Compounds screened in the kinase inhibitor library. Compounds are listed by Chemical Abstracts Service (CAS) number in the order shown in Fig. 2 along with the compound’s common names, known functions, and if they were observed to reduce IC IL-6 levels by ≥fourfold.