cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3642350_d27
title: Additional file 18: Table S10. of 
                     De novo transcriptome sequencing and gene expression profiling of Elymus nutans under cold stress

description: List of KEGG pathway enrichment analysis (Q value ≤ 0.05) of specifically expressed genes in DX and GN in response to 3, 24 h, and 5 d of cold stress. (XLSX 358 kb)
DOI: 10.6084/m9.figshare.c.3642350_d29
title: Additional file 15: Table S11. of 
                     De novo transcriptome sequencing and gene expression profiling of Elymus nutans under cold stress

description: Differentially expressed transcription factors (TFs) in response to cold treatment of DX and GN genotypes. DX-specific TFs are color-coded with pale yellow shaded. GN-specific TFs are color-coded with light green shaded. Common expression TFs are color-coded with gray shaded. Significant (Pâ  &gt;â  0.8) decrease of transcript abundance is highlighted in blue and bold, significant transcript increase is highlighted in red and bold. (XLSX 490 kb)
DOI: 10.6084/m9.figshare.c.3642353_d1
title: Additional file 11: Table S7. of Identification of global regulators of T-helper cell lineage specification

description: List of lineage-specific lncRNAs in the vicinity of lineage-specific protein coding genes. (XLSX 42 kb)
DOI: 10.6084/m9.figshare.c.3642353_d2
title: Additional file 7: Table S4. of Identification of global regulators of T-helper cell lineage specification

description: High confidence list of Th1- and Th2-specific genes in human. (XLSX 399 kb)
DOI: 10.6084/m9.figshare.c.3642353_d3
title: Additional file 5: Table S2. of Identification of global regulators of T-helper cell lineage specification

description: Table showing Jaccard similarity coefficients between platforms (XLSX 34 kb)
DOI: 10.6084/m9.figshare.c.3642353_d5
title: Additional file 14: Table S9. of Identification of global regulators of T-helper cell lineage specification

description: Predicted GO terms of lineage-specific lncRNAs. (XLSX 380 kb)
DOI: 10.6084/m9.figshare.c.3642353_d6
title: Additional file 1: Table S1. of Identification of global regulators of T-helper cell lineage specification

description: Reads obtained from next-generation sequencing data. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.c.3642353_d7
title: Additional file 9: Table S6. of Identification of global regulators of T-helper cell lineage specification

description: List of Th1- and Th2-specific long non-coding RNAs. (XLSX 97 kb)
DOI: 10.6084/m9.figshare.c.3642353_d10
title: Additional file 8: Table S5. of Identification of global regulators of T-helper cell lineage specification

description: Novel list of Th1- and Th2-specific genes in human. (XLSX 122 kb)
DOI: 10.6084/m9.figshare.c.3642353_d12
title: Additional file 13: Table S8. of Identification of global regulators of T-helper cell lineage specification

description: GO terms enriched in Th1- and Th2- specific lncRNAs. (XLSX 99 kb)
DOI: 10.6084/m9.figshare.c.3642452_d1
title: Additional file 3: Table S2. of The PfAlba1 RNA-binding protein is an important regulator of translational timing in Plasmodium falciparum blood stages

description: Gene Ontology (GO) analysis of transcripts that co-immunoprecipitated with PfAlba1-Ty1 complexes in trophozoites. (XLS 192 kb)
DOI: 10.6084/m9.figshare.c.3642452_d2
title: Additional file 11: Table S10. of The PfAlba1 RNA-binding protein is an important regulator of translational timing in Plasmodium falciparum blood stages

description: List of primers used in the study. (XLS 33 kb)
DOI: 10.6084/m9.figshare.c.3642452_d4
title: Additional file 6: Table S5. of The PfAlba1 RNA-binding protein is an important regulator of translational timing in Plasmodium falciparum blood stages

description: Fold-change in the steady state level of every Plasmodium falciparum transcript in 3D7+PfAlba1-Ty1 ring or trophozoite stages relative to 3D7 and 3D7+empty vector parasites. (XLS 841 kb)
DOI: 10.6084/m9.figshare.c.3642452_d6
title: Additional file 2: Table S1. of The PfAlba1 RNA-binding protein is an important regulator of translational timing in Plasmodium falciparum blood stages

description: List of transcripts that co-immunoprecipitated with PfAlba1-Ty1 complexes in trophozoite stages. (XLS 435 kb)
DOI: 10.6084/m9.figshare.c.3642452_d5
title: Additional file 10: Table S9. of The PfAlba1 RNA-binding protein is an important regulator of translational timing in Plasmodium falciparum blood stages

description: Properties of fastq files generated using RNA-seq and relevant statistics. (XLS 51 kb)
DOI: 10.6084/m9.figshare.c.3642452_d7
title: Additional file 7: Table S6. of The PfAlba1 RNA-binding protein is an important regulator of translational timing in Plasmodium falciparum blood stages

description: Gene Ontology (GO) analysis of 926 transcripts that were differentially regulated in PfAlba1-Ty1 trophozoites. (XLS 115 kb)
DOI: 10.6084/m9.figshare.c.3642452_d8
title: Additional file 4: Table S3. of The PfAlba1 RNA-binding protein is an important regulator of translational timing in Plasmodium falciparum blood stages

description: List of transcripts that bound to GST-PfAlba1 in vitro. (XLS 232 kb)
DOI: 10.6084/m9.figshare.c.3642452_d10
title: Additional file 8: Table S7. of The PfAlba1 RNA-binding protein is an important regulator of translational timing in Plasmodium falciparum blood stages

description: List of transcripts that were over twofold differentially regulated in PfAlba1-Ty1 trophozoites and that were bound directly by PfAlba1 in vivo and in vitro. (XLS 42 kb)
DOI: 10.6084/m9.figshare.c.3642452_d9
title: Additional file 5: Table S4. of The PfAlba1 RNA-binding protein is an important regulator of translational timing in Plasmodium falciparum blood stages

description: Gene Ontology (GO) analysis of transcripts that bound to GST-PfAlba1 in vitro. (XLS 266 kb)
DOI: 10.6084/m9.figshare.c.3642452_d11
title: Additional file 9: Table S8. of The PfAlba1 RNA-binding protein is an important regulator of translational timing in Plasmodium falciparum blood stages

description: List of transcripts identified by Foth et al. [16] and Caro et al. [19] as being translationally regulated in Plasmodium falciparum asexual blood stages. (XLS 80 kb)
DOI: 10.6084/m9.figshare.c.3642458_d3
title: Additional file 1: of Bicycle helmet laws and persistent racial and ethnic helmet use disparities among urban high school students: a repeated cross-sectional analysis

description: Appendix C: Analysis Code. (RTF 10Â kb)
DOI: 10.6084/m9.figshare.c.3642599_d1
title: Additional file 2: Table S2. of Gender-specific effects of intrauterine growth restriction on the adipose tissue of adult rats: a proteomic approach

description: Protein name, gene name and biological process of the proteins identified in the adipose tissue of males. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3642599_d2
title: Additional file 3: Table S3. of Gender-specific effects of intrauterine growth restriction on the adipose tissue of adult rats: a proteomic approach

description: Protein name, gene name and biological process of the proteins identified in the adipose tissue of females. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3642599_d3
title: Additional file 1: Table S1. of Gender-specific effects of intrauterine growth restriction on the adipose tissue of adult rats: a proteomic approach

description: Optic density of the spots with significant differences between the control and the restricted groups. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.28021082
title: KOMPAK:An instrument for assessing interprofessional collaboration between pharmacists and physicians in Indonesia

description: The title "KOMPAK: Translation, cross-cultural adaptation, and validation of an instrument for assessing interprofessional collaboration between pharmacists and physicians in Indonesia" represents a methodologically sophisticated research endeavour addressing a critical healthcare assessment gap. The strategically crafted acronym KOMPAK, derived from "KOlaborasi Medis Persepsi Apoteker dan doKter" (Medical Collaboration: Perceptions of Pharmacists and Physicians), transcends linguistic representation by embodying the core research objective while simultaneously reflecting the Indonesian cultural nuance of collaborative unity.This pioneering research meticulously transforms an existing Canadian-developed instrument into a culturally contextualized, scientifically validated measurement tool specifically designed for the Indonesian healthcare ecosystem. By implementing a rigorous, multi-phase methodology encompassing comprehensive translation, nuanced cross-cultural adaptation, and advanced psychometric validation, the study aims to generate a standardized, culturally sensitive instrument capable of precisely capturing interprofessional collaboration dynamics between pharmacists and physicians.
DOI: 10.6084/m9.figshare.c.3642614_d1
title: Additional file 1: of Revisiting the taxonomical classification of Porcine Circovirus type 2 (PCV2): still a real challenge

description: Spreadsheet containing the datasets used in the present study. For ORF2, the clustering according to NJ and ML phylogenetic trees is included. The list of Acc.Num of reference strains is also reported. (XLS 313 kb)
DOI: 10.6084/m9.figshare.c.3642617_d1
title: Additional file 1: of Impact of prognostic nutritional index on long-term outcomes in patients with breast cancer

description: The raw data of this study.
DOI: 10.6084/m9.figshare.c.3642623_d1
title: Additional file 6: of Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds

description: EASE systematic functional annotation for the 683 unique differentially expressed genes. Detailed functional information were obtained from EASE (Expression Analysis Systematic Explorer) from DAVID (Database for Annotation, Visualization and Integrated Discovery) is given for each known gene when available: Official Gene Symbol, Gene identifiers (the human ortholog), Gene Name, Gene Ontology for Biological Process, Cellular Component and Molecular Function, KEGG pathway and a Function Summary (XLSX 178Â kb)
DOI: 10.6084/m9.figshare.c.3642623_d2
title: Additional file 5: of Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds

description: 228 spots (171 unique genes) allow the discrimination between the five lines. These genes were identified as differentially expressed from one line against the others or were identified in the sPLS-DA or Random Forest analysis. The 15 discriminant genes with the three methods are highlighted. DU: Duroc; LWF: Large White dam line; LWM: Large White sire line; LR: Landrace; PI: PiĂŠtrain. (XLSX 69Â kb)
DOI: 10.6084/m9.figshare.c.3642623_d5
title: Additional file 1: of Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds

description: 1,859 genes were identified to be differentially expressed between five breeds according to statistical analysis. 1,703 were differentially expressed with a linear mixed model (FDR
DOI: 10.15468/dl.dwgp4x
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "TaxonKey is Quercus sessiliflora Salisb."
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034136-241126133413365/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.3642731_d1
title: Additional file 2: Figure S1. of Properties of Boolean dynamics by node classification using feedback loops in a network

description: Comparison between groups of NFD and non-NFD genes in random networks with respect to the proportions of essential genes, disease genes, and drug targets. In each subfigure, a set of 100 random networks were generated by rewiring the interactions of the signaling networks such that the in-degree and the out-degree of all nodes are conserved. (A) Result of random networks shuffled from KEGG network. The average numbers of NFD and non-NFD genes were 509 and 1150, respectively. The average proportions of essential genes in the NFD and the non-NFD groups were 0.2849 and 0.2852, respectively. The proportions of disease genes in the NFD and the non-NFD groups were 0.2417 and 0.2435, respectively. The proportions of drug-targets in the NFD and the non-NFD groups were 0.2141 and 0.2122, respectively. (B) Result of random networks shuffled from WANG network. The average numbers of NFD and non-NFD genes were 1544 and 4761, respectively. The proportions of essential genes in the NFD and the non-NFD groups were 0.2390 and 0.2413, respectively. The proportions of disease genes in the NFD and the non-NFD groups were 0.2455 and 0.2472, respectively. The proportions of drug-targets in the NFD and the non-NFD groups were 0.1768 and 0.1769, respectively. Figure S2. Changes in the proportion of functionally important genes over the threshold value of the perturbation-sustainable probability in random networks. In each subfigure, a set of 100 random networks were generated by rewiring the interactions of the signaling network such that the in-degree and the out-degree of all nodes are conserved. Given a threshold value β, the y-axis values indicate the average proportions of essential genes, disease genes, and drug targets over the set of candidate genes whose perturbation-sustainable probability is larger than or equal to β in random networks. (A) Results in random networks shuffled from KEGG network. For a reliable comparison, the maximal β was set to 0.0266 which generates 131 candidate genes on average. (B) Results in random networks shuffled from WANG network. The maximal β was set to 0.0908, which results in 121 candidate genes on average. (ZIP 362 kb)
DOI: 10.6084/m9.figshare.c.3642731_d2
title: Additional file 1: Table S1. of Properties of Boolean dynamics by node classification using feedback loops in a network

description: Dataset of KEGG network. It consists of 1659 genes and 7964 interactions constructed by integrating all the human signaling pathways in the KEGG (Kyoto Encyclopedia of Genes and Genomes) database. Table S2. Dataset of WANG network. It consists of 6306 genes and 62,937 interactions downloaded from http://www.bri.nrc.ca/wang . Table S3. Detailed analysis result of the KEGG network. It includes information about essential genes, disease genes, drug targets, NRU/NRD genes, and perturbation-sustainable probabilities in the KEGG network. Table S4. Detailed analysis result of the WANG network. It includes information about essential genes, disease genes, drug targets, NRU/NRD genes, and perturbation-sustainable probabilities in the WANG network. (ZIP 352 kb)
DOI: 10.6084/m9.figshare.c.3642752_d1
title: Additional file 5: Table S4. of A genome-wide approach to link genotype to clinical outcome by utilizing next generation sequencing and gene chip data of 6,697 breast cancer patients

description: Complete results of the random holdout analysis. The table contains the average HR and P values computed in the survival analysis, as well as their minimum and maximum values. (XLS 27 kb)
DOI: 10.6084/m9.figshare.c.3642752_d2
title: Additional file 4: Table S3. of A genome-wide approach to link genotype to clinical outcome by utilizing next generation sequencing and gene chip data of 6,697 breast cancer patients

description: Analysis results for both up- and downregulated genes whose AUC value was over 0.65 and P value below 0.01 in the ROC analysis and accepting a HR over 1.4 and a P value below 0.01 in the survival analysis. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.c.3642752_d4
title: Additional file 1: Table S1. of A genome-wide approach to link genotype to clinical outcome by utilizing next generation sequencing and gene chip data of 6,697 breast cancer patients

description: List of genes used during mutation annotation with SnpEff. (TXT 973 kb)
DOI: 10.6084/m9.figshare.c.3642752_d5
title: Additional file 2: Table S2. of A genome-wide approach to link genotype to clinical outcome by utilizing next generation sequencing and gene chip data of 6,697 breast cancer patients

description: The complete set of all genes included in the metagenes for each of the putative driver genes listed in Table 2. (XLSX 156 kb)
DOI: 10.6084/m9.figshare.c.3642863_d1
title: Additional file 2: of Gene-based SNP discovery in tepary bean (Phaseolus acutifolius) and common bean (P. vulgaris) for diversity analysis and comparative mapping

description: A) List of SNPs identified in 6 P. vulgaris and 2 P. acutifolius genotypes along with the corresponding homologues position in Pv1.0 assembly, B) SNPs exclusive to teparies, C) results of SNPs selected for KASP assay, D) Pv768 GoldenGate assay results, E) Pac768 GoldenGate assay results, and F) summary of assay results. (XLSX 20503Â kb)
DOI: 10.6084/m9.figshare.c.3642863_d2
title: Additional file 3: of Gene-based SNP discovery in tepary bean (Phaseolus acutifolius) and common bean (P. vulgaris) for diversity analysis and comparative mapping

description: A) BR-06 map with binned marker loci and corresponding P. vulgaris pseudochromosome locations and B) SNP genotypes for 158 accessions using Pac768 GoldenGate assay. (XLSX 497Â kb)
DOI: 10.6084/m9.figshare.c.3642863_d4
title: Additional file 1: of Gene-based SNP discovery in tepary bean (Phaseolus acutifolius) and common bean (P. vulgaris) for diversity analysis and comparative mapping

description: List of P. acutifolius accessions selected for phylogenetic analysis. (XLSX 19Â kb)
DOI: 10.6084/m9.figshare.c.3642989_d1
title: Additional file 1: of Proteomic analysis of Pteropus alecto kidney cells in response to the viral mimic, Poly I:C

description: Full list of identified proteins by LC-MS/MS and their ratio at each replicate time points determined by iTRAQ (Sheet1). A list of the differentially regulated proteins with a mean fold-change ofâ  â Ľâ  1.5 (Sheet2). (XLSX 486 kb)
DOI: 10.6084/m9.figshare.c.3643013_d1
title: MOESM1 of Lessons for livestock genomics from genome and transcriptome sequencing in cattle and other mammals

description: Additional file 1: Table S1. Description of tissue samples analyzed by RNA-seq by species or breed and the project associated with the analysis.
DOI: 10.6084/m9.figshare.c.3643154_d1
title: Additional file 10: Table S6. of Errors in RNA-Seq quantification affect genes of relevance to human disease

description: EdgeR results from MMGs. Differential expression results calculated by edgeR for MMG counts produced by the stage 2 analysis. Can be downloaded from [43]. (XLSX 428 kb)
DOI: 10.6084/m9.figshare.c.3643154_d2
title: Additional file 11: Table S7. of Errors in RNA-Seq quantification affect genes of relevance to human disease

description: Novel differentially expressed MMGs. The 672 differentially expressed MMGs that do not contain any genes identified as differentially expressed by the stage 1 analysis. Can be downloaded from [43]. (XLSX 67 kb)
DOI: 10.6084/m9.figshare.c.3643154_d3
title: Additional file 8: Table S4. of Errors in RNA-Seq quantification affect genes of relevance to human disease

description: Counts of multi-map groups (MMGs) from Choi et al. [35]. Counts of reads from Choi et al. that map uniquely to MMGs. Can be downloaded from [43]. (XLSX 876 kb)
DOI: 10.6084/m9.figshare.c.3643154_d4
title: Additional file 9: Table S5. of Errors in RNA-Seq quantification affect genes of relevance to human disease

description: EdgeR results from unique counts. Differential expression results calculated by edgeR for gene counts produced by the stage 1 analysis. Can be downloaded from [43]. (XLSX 2159 kb)
DOI: 10.6084/m9.figshare.c.3643154_d5
title: Additional file 1: Table S1. of Errors in RNA-Seq quantification affect genes of relevance to human disease

description: Counts and FPKM for simulated data from all genes. FPKM and read counts calculated by 12 different methods for 19,654 human protein-coding genes. Can be downloaded from [43]. (XLSX 7248 kb)
DOI: 10.6084/m9.figshare.c.3643154_d9
title: Additional file 6: Table S2. of Errors in RNA-Seq quantification affect genes of relevance to human disease

description: Counts and FPKM for simulated data from 958 problematic genes. FPKM and read counts calculated by 12 different methods for 958 problematic human protein-coding genes. Can be downloaded from [43]. (XLSX 311 kb)
DOI: 10.6084/m9.figshare.c.3643154_d11
title: Additional file 7: Table S3. of Errors in RNA-Seq quantification affect genes of relevance to human disease

description: Unique counts from Choi et al. [35]. Counts of reads from Choi et al. that map uniquely to genes using STAR and HTSeq. Can be downloaded from [43]. (XLSX 5833 kb)
DOI: 10.6084/m9.figshare.c.3643268_d1
title: Additional file 3: of Assessing breast cancer cell lines as tumour models by comparison of mRNA expression profiles

description: Top 1 % of differentially expressed genes between tumours and cell lines after filtering out genes correlated with stromal and immune scores in tumours (absolute tumour stromal and immune scores, Pearson correlation coefficient &lt;0.2, adjusted p values by t test). (XLSX 29 kb)
DOI: 10.6084/m9.figshare.c.3643268_d3
title: Additional file 4: of Assessing breast cancer cell lines as tumour models by comparison of mRNA expression profiles

description: Comparison of the frequency of select mutational events in breast cancer tumours versus cell lines. Differences in mutational frequencies of selected genes in TCGA BRCA tumours (n = 503) and CCLE breast cancer cell lines (n = 31). (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3643268_d2
title: Additional file 2: of Assessing breast cancer cell lines as tumour models by comparison of mRNA expression profiles

description: Top 1 % of differentially expressed genes between tumours and cell lines (with adjusted p values by t test). (XLSX 26 kb)
DOI: 10.6084/m9.figshare.c.3643274_d1
title: Additional file 2: of Validation of the Dutch language version of the Safety Attitudes Questionnaire (SAQ-NL)

description: Research Dataset. (XLSX 687 kb)
DOI: 10.6084/m9.figshare.c.3643277_d2
title: Additional file 8: Figure S2. of 
                     De novo transcriptomic assembly and profiling of Rigidoporus microporus during saprotrophic growth on rubber wood

description: A-C. Hierarchical cluster analysis of (A) GlycosylTransferases (GT) (B) Carbohydrate esterases (CE) and (C) Polysaccharide lyases (PL) genes up-regulated during saprotrophic growth on rubber wood. (FDR  2). Cluster analysis was constructed based on the log2 values of the fragments per kilobase per million reads (FPKM) of the unigenes. Red indicates high expression and blue indicates low expression. (ZIP 703 kb)
DOI: 10.6084/m9.figshare.c.3643277_d4
title: Additional file 14: Table S9. of 
                     De novo transcriptomic assembly and profiling of Rigidoporus microporus during saprotrophic growth on rubber wood

description: List of all differentially expressed hydrophobin genes. (XLSX 17Â kb)
DOI: 10.6084/m9.figshare.c.3643277_d6
title: Additional file 16: Figure S7. of 
                     De novo transcriptomic assembly and profiling of Rigidoporus microporus during saprotrophic growth on rubber wood

description: Aâ  C. KEGG Gene Ontology (GO) enrichment analysis of differentially expressed genes between the two conditions (W and C) showing the main enriched processes in both experimental conditions. (A) Biological process, (B) Cellular component (C) Molecular function. (ZIP 4695Â kb)
DOI: 10.6084/m9.figshare.c.3643277_d7
title: Additional file 3: Table S3. of 
                     De novo transcriptomic assembly and profiling of Rigidoporus microporus during saprotrophic growth on rubber wood

description: Annotation of all unigenes from the R. microporus transcriptome. (XLSX 9519Â kb)