cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3637172_d3
title: Additional file 10: Table S3. of Graded gene expression changes determine phenotype severity in mouse models of CRX-associated retinopathies

description: Compiled table of results from GO analysis on rod- or cone-enriched genes from Fig.Â 6a. (XLSX 50 kb)
DOI: 10.15468/dl.9axk5f
title: Occurrence Download

description: A dataset containing 53 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anoplophora glabripennis (Motschulsky, 1854)",
 "Country is United States of America",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 53 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034322-241126133413365/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.3638411_d1
title: Additional file 2: of General continuous-time Markov model of sequence evolution via insertions/deletions: local alignment probability computation

description: A package (the version used for the analyses in this paper), which contains Perl modules that implement the key algorithms and formulas, as well as some main Perl scripts that we used for the actual data analyses. (The package is available under the GNU General Public License. The modules and scripts will run on a Mac OS X terminal, and were confirmed to run also on Red Had Enterprise Linux (6.4). And they will probably run on other UNIX platforms as well, although we have not tested whether they indeed do.) The package also contains Dawg control files necessary for creating the simulated MSA sets 1A, 1B, 2, 3P, 3M and 3F. The latest version of the package (“FA_LOLIPOG_P.verxxx”) will be available from the “LOLIPOG” (LOg-LIkelihood for the Pattern Of Gaps) project at the FTP repository of the Bioinformatics Organization [58]. (ZIP 7548 kb)
DOI: 10.6084/m9.figshare.c.3638456_d1
title: Additional file 2: Table S1. of Chromatin-wide and transcriptome profiling integration uncovers p38α MAPK as a global regulator of skeletal muscle differentiation

description: List of genes regulated and bound by p38α. (XLSX 686 kb)
DOI: 10.6084/m9.figshare.c.3638456_d2
title: Additional file 1: Table S2. of Chromatin-wide and transcriptome profiling integration uncovers p38α MAPK as a global regulator of skeletal muscle differentiation

description: List of primers used in the study. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3638462_d2
title: Additional file 1: Supplementary Tables S1-S6. of Rapid evolution of chemosensory receptor genes in a pair of sibling species of orchid bees (Apidae: Euglossini)

description: (XLSX 3214 kb)
DOI: 10.6084/m9.figshare.c.3638495_d2
title: Additional file 3: Table S3. of Consensus computational network analysis for identifying candidate outer membrane proteins from Borrelia spirochetes

description: Orthologous clusters. List of predicted orthologous clusters utilized to generate heat maps. (XLSX 667 kb)
DOI: 10.6084/m9.figshare.c.3639725_d4
title: Additional file 2: of Focal exposure of limited lung volumes to high-dose irradiation down-regulated organ development-related functions and up-regulated the immune response in mouse pulmonary tissues

description: The full list of genes include in each pattern and associated with enriched pathways. (XLSX 1669 kb)
DOI: 10.6084/m9.figshare.c.3639731_d1
title: Additional file 2: Table S2. of Genetic variation of naturally growing olive trees in Israel: from abandoned groves to feral and wild?

description: Raw microsatellite data. The fragment sizes (in base pairs) of the two alleles per individual for each locus are given as a and b (0 represents missing data). (XLSX 38 kb)
DOI: 10.6084/m9.figshare.c.3639731_d4
title: Additional file 3: Table S3. of Genetic variation of naturally growing olive trees in Israel: from abandoned groves to feral and wild?

description: Number of olive trees assigned to different multi-locus lineages (MLLs). (XLSX 18 kb)
DOI: 10.34740/kaggle/dsv/10198593
title: Global Genomic Neurofibromatosis Neoplasia
DOI: 10.34740/kaggle/dsv/10198603
title: UNET Lung Segmentation Weights for Chest X Rays
DOI: 10.6084/m9.figshare.c.3641612_d4
title: MOESM1 of Identification of genetic variation in the swine toll-like receptors and development of a porcine TLR genotyping array

description: Additional file 1. Genomic information from the 49 TLR exons that are annotated in the genome Sscrofa10.2.69 database. Columns A and B (general information) supply general information on the TLR gene related to sense of transcription (phase +1: sense; −1: antisense), number of transcripts, protein ID and length. Detailed information on exons order and length of coding sequence and UTR is only supplied for RefSeq exons. RefSeq transcripts are highlighted in bold in column “Ensembl transcript ID”.
DOI: 10.6084/m9.figshare.c.3641612_d5
title: MOESM2 of Identification of genetic variation in the swine toll-like receptors and development of a porcine TLR genotyping array

description: Additional file 2. Target TLR genomic regions. The coordinates correspond to the Sscrofa10.2 genome assembly. The column “portion without sequence information (bp)” indicates the number of bp that were sequenced to a depth of less than 1000. The column “cds and UTR content” indicates whether that genomic portion correspond to coding sequence or/and to UTR. The column “cause of missing sequence information” indicates the reason for lack of sequence information for the corresponding segment. There are two legends: “missing capture baits” indicate that Agilent capture baits that cover this segment could not be designed; “homologous region in the swine genome” indicates that although the baits were designed and the segment was sequenced, the corresponding sequence reads could not be unambiguously mapped to that region.
DOI: 10.6084/m9.figshare.c.3641612_d7
title: MOESM6 of Identification of genetic variation in the swine toll-like receptors and development of a porcine TLR genotyping array

description: Additional file 6. List of the 306 TLR variants identified in this study. Breed specificity indicates the variants that are present in only that breed and at a pAAF higher than 0.5. In this column, the number between brackets indicates the pAAF in the breed with the variant allele.
DOI: 10.6084/m9.figshare.c.3641621_d1
title: Additional file 1: of Origin and evolution of the enhancer of split complex

description: Table of bHLH Orange domain genes used in this analysis. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.c.3641621_d2
title: Additional file 2: of Origin and evolution of the enhancer of split complex

description: Alignments used for phylogenetic analyses. (TXT 111 kb)
DOI: 10.15468/dl.7akdys
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anoplophora glabripennis (Motschulsky, 1854)",
 "Country is Canada",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 13 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034323-241126133413365/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.3642233_d1
title: Additional file 1: of MIA: Mutual Information Analyzer, a graphic user interface program that calculates entropy, vertical and horizontal mutual information of molecular sequence sets

description: Drosophila-Adh data. (XLSX 153 kb)
DOI: 10.6084/m9.figshare.c.3642257_d1
title: Additional file 5 of Testing for carryover effects after cessation of treatments: a design approach

description: Was used to simulate crossover trials where diagnosis is defined using the BP measurements without error. (R 5 kb)
DOI: 10.6084/m9.figshare.c.3642257_d2
title: Additional file 4 of Testing for carryover effects after cessation of treatments: a design approach

description: Was used to simulate crossover trials. (R 5 kb)
DOI: 10.6084/m9.figshare.c.3642257_d3
title: Additional file 7 of Testing for carryover effects after cessation of treatments: a design approach

description: Was used to simulate trials which included both crossover, parallel, and control arms when diagnosis is determined by using the BP measurements without error. (R 5 kb)
DOI: 10.6084/m9.figshare.c.3642257_d4
title: Additional file 1 of Testing for carryover effects after cessation of treatments: a design approach

description: Was used to simulate parallel trials. (R 5 kb)
DOI: 10.6084/m9.figshare.c.3642257_d5
title: Additional file 6 of Testing for carryover effects after cessation of treatments: a design approach

description: Was used to simulate trials which included both crossover, parallel, and control arms. (R 3 kb)
DOI: 10.6084/m9.figshare.c.3642257_d6
title: Additional file 2 of Testing for carryover effects after cessation of treatments: a design approach

description: Was used to simulate parallel trials where diagnosis is defined using the BP measurements without error. (R 5 kb)
DOI: 10.6084/m9.figshare.c.3642257_d7
title: Additional file 3 of Testing for carryover effects after cessation of treatments: a design approach

description: Was used to simulate parallel trials where the lower bound of the inclusion criteria varied. (R 4 kb)
DOI: 10.6084/m9.figshare.c.3642656_d1
title: Additional file 2: Table S1. of Promoter hypermethylation of SHOX2 and SEPT9 is a potential biomarker for minimally invasive diagnosis in adenocarcinomas of the biliary tract

description: Clinicopathological data of the 20 biliary tract cancer cases and 100 gender- and age-matched controls included in plasma study. (XLSX 116 kb)
DOI: 10.6084/m9.figshare.c.3642659_d2
title: Additional file 5: Table S2. of Low-power photodynamic therapy induces survival signaling in perihilar cholangiocarcinoma cells

description: Overview of primer sequences and resulting amplicon sizes (in bp) that were used for the validation of microarray expression levels using qRT-PCR. The primers are listed in the 5â ˛ to 3â ˛ direction. Primers were derived from RTPrimerDB ( http://www.rtprimerdb.org/ ), NCBI primer Blast ( http://www.ncbi.nlm.nih.gov/tools/primer-blast/ ), and qPrimerDepot ( http://primerdepot.nci.nih.gov/ ). Sequencing of the qRT-PCR products, which were analyzed using NCBI Blast ( http://blast.ncbi.nlm.nih.gov/Blast.cgi ), confirmed the correct identity of each product. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.c.3642659_d5
title: Additional file 3: Table S1. of Low-power photodynamic therapy induces survival signaling in perihilar cholangiocarcinoma cells

description: Overview of transcriptional targets of the five survival pathways. Official gene names are listed that were derived from the Hugo Gene Nomenclature Committee (HGNC) along with their Genbank accession numbers (Gene ID). (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.c.3642665_d2
title: Additional file 4: of Effective strategies to reduce commercial tobacco use in Indigenous communities globally: A systematic review

description: Title of data: Intervention Activity and Outcome Efficacy Data. Description of data: Summary comparison of intervention characteristics and efficacy data for the seven outcomes. (XLSX 18 kb)
DOI: 10.15468/dl.577tqe
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anoplophora glabripennis (Motschulsky, 1854)",
 "Country is Austria",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034325-241126133413365/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.3643217_d1
title: Additional file 5: of Snail-induced epithelial-to-mesenchymal transition of MCF-7 breast cancer cells: systems analysis of molecular changes and their effect on radiation and drug sensitivity

description: List of 164 network objects from the MetaCore human protein interactome that are statistically significantly over-connected to the genes differentially expressed between MCF-7-Snail and MCF-7-Control cells. (XLS 71 kb)
DOI: 10.6084/m9.figshare.c.3643217_d3
title: Additional file 1: of Snail-induced epithelial-to-mesenchymal transition of MCF-7 breast cancer cells: systems analysis of molecular changes and their effect on radiation and drug sensitivity

description: List of 71 genes relevant to EMT and 53 genes relevant to anticancer drug resistance assembled by manual curation from appended references. (XLSX 54 kb)
DOI: 10.6084/m9.figshare.c.3643217_d2
title: Additional file 3: of Snail-induced epithelial-to-mesenchymal transition of MCF-7 breast cancer cells: systems analysis of molecular changes and their effect on radiation and drug sensitivity

description: List of 12,104 probe sets corresponding to differentially expressed transcripts between MCF-7-Snail and MCF-7-Control cells identified by Significance Analysis of Microarray (FDR = 2.12 % and |FC| ≥1.5). (XLSX 2199 kb)
DOI: 10.6084/m9.figshare.c.3643217_d5
title: Additional file 8: of Snail-induced epithelial-to-mesenchymal transition of MCF-7 breast cancer cells: systems analysis of molecular changes and their effect on radiation and drug sensitivity

description: List of differentially expressed genes between MCF-7-Snail and MCF-7-Control cells known to MetaCore knowledgebase to be directly transcriptionally regulated by ESR-1. (XLS 339 kb)
DOI: 10.6084/m9.figshare.c.3643217_d6
title: Additional file 9: of Snail-induced epithelial-to-mesenchymal transition of MCF-7 breast cancer cells: systems analysis of molecular changes and their effect on radiation and drug sensitivity

description: List of gene sets from C2: Curated Gene Sets and C6: Oncogenic Signatures gene sets ( http://www.broadinstitute.org/gsea/msigdb/collections.jsp ) significantly enriched in MCF-7-Snail or MCF-7-Control phenotypes. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.c.3643217_d7
title: Additional file 6: of Snail-induced epithelial-to-mesenchymal transition of MCF-7 breast cancer cells: systems analysis of molecular changes and their effect on radiation and drug sensitivity

description: List of 31 significant networks centered on transcription factors built from genes differentially expressed between MCF-7-Snail and MCF-7-Control cells. (XLS 39 kb)
DOI: 10.6084/m9.figshare.c.3643217_d9
title: Additional file 4: of Snail-induced epithelial-to-mesenchymal transition of MCF-7 breast cancer cells: systems analysis of molecular changes and their effect on radiation and drug sensitivity

description: List of 7602 unique annotated genes differentially expressed between MCF-7-Snail and MCF-7-Control cells. (XLSX 178 kb)
DOI: 10.6084/m9.figshare.c.3643217_d8
title: Additional file 7: of Snail-induced epithelial-to-mesenchymal transition of MCF-7 breast cancer cells: systems analysis of molecular changes and their effect on radiation and drug sensitivity

description: List of differentially expressed genes between MCF-7-Snail and MCF-7-Control cells known to MetaCore knowledgebase to be directly transcriptionally regulated by c-Myc. (XLS 610 kb)
DOI: 10.6084/m9.figshare.c.3643220_d2
title: Additional file 3: Table S1. of A clone-free, single molecule map of the domestic cow (Bos taurus) genome

description: Tabulation of discordances between BtOM1.0 and UMD3.1. (XLSX 399Â kb)
DOI: 10.6084/m9.figshare.c.3643613_d1
title: MOESM2 of Chicken interferome: avian interferon-stimulated genes identified by microarray and RNA-seq of primary chick embryo fibroblasts treated with a chicken type I interferon (IFN-α)

description: Additional file 2. Detailed information on ChISGs identified by RNA-seq, and microarray technologies (1). Technologies identifying significant IRGs are listed as “1” RNA-seq (using Kal’s Z test); “2” Affymetrix 32K GeneChip Chicken Genome Array and “3” Chicken Gene 1.0 ST Array’. ChISGs significant by one or both microarrays and RNA-seq using Kal’s Z test under relaxed criteria (FC &gt; 2.5 or FDR
DOI: 10.15468/dl.ncvkk6
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anoplophora glabripennis (Motschulsky, 1854)",
 "Country is France",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 8 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034326-241126133413365/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.3644072_d4
title: Additional file 4: of Simulation study of activities of daily living functions using online computerized adaptive testing

description: The file layouts of data used for gathering feedback from patients using online CAT. (XLS 58Â kb)
DOI: 10.6084/m9.figshare.c.3644078_d1
title: Additional file 6: Table S6. of Integrative analyses of proteomics and RNA transcriptomics implicate mitochondrial processes, protein folding pathways and GWAS loci in Parkinson disease

description: This file contains ten tables: (1) Proteomics GO BP: GO Biological Pathways that showed an enrichment p-value smaller than 0.05 in any of the performed analyses for the proteomics results (using the top 25, 50, 100, or 283 genes with multiple comparison corrected significance); (2) Proteomics GO CC: GO Cellular Components that showed an enrichment p-value smaller than 0.05 in any of the performed analyses for the proteomics results; (3) Proteomics GO MF: GO Molecular Functions that showed an enrichment p-value smaller than 0.05 in any of the performed analyses for the proteomics results; (4) Proteomics MSigDB CP: MSigDB Canonical Pathways that showed an enrichment p-value smaller than 0.05 in any of the performed analyses for the proteomics results; (5) RNA-Seq GO BP: GO Biological Pathways that showed an enrichment p-value smaller than 0.05 in any of the performed analyses for the RNA-Seq results (using the top 25, 50, 100, 350, 600, 850, or 1095 genes with multiple comparison corrected significance); (6) RNA-Seq GO CC: GO Cellular Components that showed an enrichment p-value smaller than 0.05 in any of the performed analyses for the RNA-Seq results; (7) RNA-Seq GO MF: GO Molecular Functions that showed an enrichment p-value smaller than 0.05 in any of the performed analyses for the RNA-Seq results; (8) RNA-Seq MSigDB CP: MSigDB Canonical Pathways that showed an enrichment p-value smaller than 0.05 in any of the performed analyses for the RNA-Seq results; (9) Common Genes GO: GO terms that showed an enrichment p-value smaller than 0.05 in the 77 genes with common evidence in the RNA-Seq and proteomics results (multiple comparison corrected significance in one experiment and nominal significance in the other one); (10) Common Genes MSigDB CP: MSigDB Canonical Pathways that showed an enrichment p-value smaller than 0.05 in the 77 genes with common evidence in the RNA-Seq and Proteomics results. (XLSX 110Â kb)
DOI: 10.6084/m9.figshare.c.3644078_d2
title: Additional file 3: Table S3. of Integrative analyses of proteomics and RNA transcriptomics implicate mitochondrial processes, protein folding pathways and GWAS loci in Parkinson disease

description: Results for the mRNA abundance comparison between 29 PD and 44 control samples for the 17,580 protein-coding genes from the RNA-Seq study. (XLSX 2337Â kb)
DOI: 10.6084/m9.figshare.c.3644078_d3
title: Additional file 4: Table S4. of Integrative analyses of proteomics and RNA transcriptomics implicate mitochondrial processes, protein folding pathways and GWAS loci in Parkinson disease

description: Proteomics and RNA-Seq results for the 77 genes/proteins with common evidence (multiple comparison corrected significance in one of the experiments and nominal significance in the other). (XLSX 58Â kb)
DOI: 10.6084/m9.figshare.c.3644078_d4
title: Additional file 5: Table S5. of Integrative analyses of proteomics and RNA transcriptomics implicate mitochondrial processes, protein folding pathways and GWAS loci in Parkinson disease

description: Results for the mRNA abundance comparison between 19 PD and 24 control samples present in the microarray expression dataset E-MTAB-812 from ArrayExpress and also included in the RNA-Seq study. (XLSX 3194Â kb)
DOI: 10.6084/m9.figshare.c.3644078_d6
title: Additional file 1: Table S1. of Integrative analyses of proteomics and RNA transcriptomics implicate mitochondrial processes, protein folding pathways and GWAS loci in Parkinson disease

description: Detailed information for the entire set of 29 PD cases and 44 controls studied by MS3 proteomics, RNA-Seq, and expression microarray. (XLSX 59Â kb)
DOI: 10.6084/m9.figshare.c.3644078_d5
title: Additional file 7: Table S7. of Integrative analyses of proteomics and RNA transcriptomics implicate mitochondrial processes, protein folding pathways and GWAS loci in Parkinson disease

description: MS3 proteomics and RNA-Seq PD/control comparison results for the 166 genes that were present within 100 kb (based on Annovar annotation) of the 551 genome-wide significant SNPs identified in the Nalls et al. study [7]. When the proteomics or mRNA dataset does not contain a particular gene, “NA” values are displayed in the corresponding columns. (XLSX 62 kb)
DOI: 10.6084/m9.figshare.c.3644078_d7
title: Additional file 2: Table S2. of Integrative analyses of proteomics and RNA transcriptomics implicate mitochondrial processes, protein folding pathways and GWAS loci in Parkinson disease

description: Results for the protein abundance comparison between 12 PD and 12 control samples for the 3558 proteins from the MS3 proteomics study. (XLSX 336Â kb)
DOI: 10.6084/m9.figshare.c.3644084_d1
title: Additional file 1: Table S1. of Past seawater experience enhances seawater adaptability in medaka, Oryzias latipes

description: Primers used for cloning and real-time qPCR analyses. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3644096_d2
title: Additional file 7: of The polymyxin B-induced transcriptomic response of a clinical, multidrug-resistant Klebsiella pneumoniae involves multiple regulatory elements and intracellular targets

description: Modules of co-expressed genes as revealed by weighted gene correlation network analysis. Description: Reported are the modules (labeled by different colours) to which each gene belongs, as well as the associated Gene Ontology terms. (XLS 734 kb)
DOI: 10.6084/m9.figshare.c.3644096_d7
title: Additional file 2: of The polymyxin B-induced transcriptomic response of a clinical, multidrug-resistant Klebsiella pneumoniae involves multiple regulatory elements and intracellular targets

description: Differentially expressed genes in polymyxin in comparison with five environmental conditions. (XLS 1099 kb)
DOI: 10.6084/m9.figshare.c.3644099_d1
title: Additional file 8: Table S8. of Comparative transcriptome profiling of resistant and susceptible rice genotypes in response to the seedborne pathogen Fusarium fujikuroi

description: Up-regulated and down-regulated peroxidase genes. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.c.3644480_d5
title: MOESM5 of Biomass traits and candidate genes for bioenergy revealed through association genetics in coppiced European Populus nigra (L.)

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

description: Additional file 2. containing the SNP marker set derived from the 12Â K Illumina array genotyping and employed here for GWAS.
DOI: 10.6084/m9.figshare.c.3644486_d1
title: Additional file 1: Table S1. of Molecular and phenotypic distinction of the very recently evolved insular subspecies Mus musculus helgolandicus ZIMMERMANN, 1953

description: Details of the primers used for M. m. domesticus versus M. m. musculus assignment. (XLS 31 kb)