cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8062616
title: Additional file 1: of Investigation of lipid metabolism dysregulation and the effects on immune microenvironments in pan-cancer using multiple omics data

description: Lipid metabolism pathways. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.8062658
title: Additional file 6: of Investigation of lipid metabolism dysregulation and the effects on immune microenvironments in pan-cancer using multiple omics data

description: Candidate lipid metabolismÂ genes. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.7538429
title: Additional file 10: of CRlncRC: a machine learning-based method for cancer-related long noncoding RNA identification using integrated features

description: Cancer-related lncRNA Papers. (XLSX 326 kb)
DOI: 10.6084/m9.figshare.7538456.v1
title: Additional file 4: of CRlncRC: a machine learning-based method for cancer-related long noncoding RNA identification using integrated features

description: TANRIC lncRNA dataset. (XLSX 176 kb)
DOI: 10.6084/m9.figshare.8062640.v1
title: Additional file 2: of Plant lamin-like proteins mediate chromatin tethering at the nuclear periphery

description: Table S1. BAC vectors used for making FISH probes. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.8062643
title: Additional file 4: of Investigation of lipid metabolism dysregulation and the effects on immune microenvironments in pan-cancer using multiple omics data

description: The correlation of transcripition factor and target pairs in key lipidÂ metabolism pathways. (XLSX 52 kb)
DOI: 10.6084/m9.figshare.8062646
title: Additional file 3: of Plant lamin-like proteins mediate chromatin tethering at the nuclear periphery

description: Table S2. Statistics of Hi-C reads. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8062733.v1
title: Additional file 7: of Genetic variation of HvXYN1 associated with endoxylanase activity and TAX content in barley (Hordeum vulgare L.)

description: Table S4. 210 barley accessions from 34 countries. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8062745
title: Additional file 9: of Genetic variation of HvXYN1 associated with endoxylanase activity and TAX content in barley (Hordeum vulgare L.)

description: Table S6. 35 SSR markers on 7 chromosomes. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7538435
title: Additional file 1: of CRlncRC: a machine learning-based method for cancer-related long noncoding RNA identification using integrated features

description: Positive lncRNA dataset. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7538429.v1
title: Additional file 10: of CRlncRC: a machine learning-based method for cancer-related long noncoding RNA identification using integrated features

description: Cancer-related lncRNA Papers. (XLSX 326 kb)
DOI: 10.6084/m9.figshare.7538435.v1
title: Additional file 1: of CRlncRC: a machine learning-based method for cancer-related long noncoding RNA identification using integrated features

description: Positive lncRNA dataset. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8062652
title: Additional file 4: of Plant lamin-like proteins mediate chromatin tethering at the nuclear periphery

description: Table S3. Differential accessible chromatin regions in morc6 2C nuclei. (XLSX 80 kb)
DOI: 10.6084/m9.figshare.7538444
title: Additional file 2: of CRlncRC: a machine learning-based method for cancer-related long noncoding RNA identification using integrated features

description: Negative lncRNA dataset. (XLSX 64 kb)
DOI: 10.6084/m9.figshare.7538450
title: Additional file 3: of CRlncRC: a machine learning-based method for cancer-related long noncoding RNA identification using integrated features

description: Features importance. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8062733
title: Additional file 7: of Genetic variation of HvXYN1 associated with endoxylanase activity and TAX content in barley (Hordeum vulgare L.)

description: Table S4. 210 barley accessions from 34 countries. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7538501
title: Additional file 1 of Single-cell gene expression analysis reveals β-cell dysfunction and deficit mechanisms in type 2 diabetes

description: Table S1. Genes used in cellular condition (i.e. healthy or T2D) prediction. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8062682
title: Additional file 8: of Plant lamin-like proteins mediate chromatin tethering at the nuclear periphery

description: Table S7. Oligos used for ChIP-qPCR. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.7538456
title: Additional file 4: of CRlncRC: a machine learning-based method for cancer-related long noncoding RNA identification using integrated features

description: TANRIC lncRNA dataset. (XLSX 176 kb)
DOI: 10.6084/m9.figshare.7538507.v1
title: Additional file 2 of Single-cell gene expression analysis reveals β-cell dysfunction and deficit mechanisms in type 2 diabetes

description: Tables S2-S3. Entropy, joint entropy and mutual information between TEDECs and the genes in the apoptosis pathway. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8062745.v1
title: Additional file 9: of Genetic variation of HvXYN1 associated with endoxylanase activity and TAX content in barley (Hordeum vulgare L.)

description: Table S6. 35 SSR markers on 7 chromosomes. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.12246659.v1
title: Additional file 2 of The metabolome as a link in the genotype-phenotype map for peroxide resistance in the fruit fly, Drosophila melanogaster

description: Additional file 2: Table S2. Summary of Mummichog Analysis. Description: Metabolic pathways identified by mummichog from the features detected in either positive or negative LC-MS (mode) that were significant from group comparisons (e.g., resistant H2O2 vs. resistant Control, sensitive H2O2 vs. sensitive Control, resistant H2O2 vs. sensitive H2O2, resistant Control vs. sensitive Control, and interaction) in the linear model. BioCyc pathways (pathway) were identified, and the significance of enrichment was assessed, in part by the number of LC-MS features in a given pathway (overlap_size) and the size of the pathway (pathway_size), by permutation (n = 100) to give a P-value.
DOI: 10.6084/m9.figshare.7538489.v1
title: Additional file 9: of CRlncRC: a machine learning-based method for cancer-related long noncoding RNA identification using integrated features

description: Predict results. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.8062793
title: Additional file 2: of Joint analyses of multi-tissue Hi-C and eQTL data demonstrate close spatial proximity between eQTLs and their target genes

description: Additional results. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.12246659
title: Additional file 2 of The metabolome as a link in the genotype-phenotype map for peroxide resistance in the fruit fly, Drosophila melanogaster

description: Additional file 2: Table S2. Summary of Mummichog Analysis. Description: Metabolic pathways identified by mummichog from the features detected in either positive or negative LC-MS (mode) that were significant from group comparisons (e.g., resistant H2O2 vs. resistant Control, sensitive H2O2 vs. sensitive Control, resistant H2O2 vs. sensitive H2O2, resistant Control vs. sensitive Control, and interaction) in the linear model. BioCyc pathways (pathway) were identified, and the significance of enrichment was assessed, in part by the number of LC-MS features in a given pathway (overlap_size) and the size of the pathway (pathway_size), by permutation (n = 100) to give a P-value.
DOI: 10.6084/m9.figshare.8062793.v1
title: Additional file 2: of Joint analyses of multi-tissue Hi-C and eQTL data demonstrate close spatial proximity between eQTLs and their target genes

description: Additional results. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.12246665.v1
title: Additional file 3 of The metabolome as a link in the genotype-phenotype map for peroxide resistance in the fruit fly, Drosophila melanogaster

description: Additional file 3: Table S3. Summary of XCMS metabolite feature data. Description: Untargeted LC-MS features analyzed in this study. Features were given names (e.g. M438T2) based on their median mass-charge ratio (mzmed) and median retention time, in minutes (rtmed). The minimum (mzmin) and maximum (mzmax) mass-charge ratios for each feature are given, along with their minimum and maximum retention time (rtmin, rtmax, respectively). When a tentative identification was made by XCMS, the matching compound (id) is given along with the matching ion (match_form) and the difference in mass (mz_difference) between the LC-MS feature and the matching ion. These data are from positive and negative modes (mode), each data mode was analyzed separately and combined on this table.
DOI: 10.6084/m9.figshare.7538408
title: Additional file 9: of Vaginal microbiome variances in sample groups categorized by clinical criteria of bacterial vaginosis

description: PICRUSt predictive functional profiling (KEGG databases at level 3) between the A–N– and A–N* groups (Table S3), the A–N– and A + N+ groups (Table S4), the A–N– and A + N* groups (Table S5), the A + N– and A + N* groups (Table S6), the A + N– and A + N+ (Table S7), the A + N* and A + N+ groups (Table S8). Table S9: 32 predictive functional categories which differed significantly between any two of the A − N−, A − N*, A + N−, A + N* and A + N+ groups (XLSX 43 kb)
DOI: 10.6084/m9.figshare.7538540
title: Additional file 5 of Network-based logistic regression integration method for biomarker identification

description: KEGG pathway enrichment results of the subnetwork biomarkers. The enrichment of KEGG pathway is included. (XLSX 36 kb)
DOI: 10.6084/m9.figshare.7538522
title: Additional file 2 of Network-based logistic regression integration method for biomarker identification

description: GO:BP enrichment results of the subnetwork biomarkers. The enrichment of GO: BP is included. (XLSX 220 kb)
DOI: 10.6084/m9.figshare.7538528
title: Additional file 3 of Network-based logistic regression integration method for biomarker identification

description: GO:CC enrichment results of the subnetwork biomarkers. The enrichment of GO: CC is included. (XLSX 46 kb)
DOI: 10.6084/m9.figshare.7538549
title: Additional file 3: of Condition-specific gene co-expression network mining identifies key pathways and regulators in the brain tissue of Alzheimerâ s disease patients

description: Table S2. List of 30â AD-specific modules and 31 normal-specific modules. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.7538447.v1
title: Additional file 2 of Hot spot prediction in protein-protein interactions by an ensemble system

description: All relevant MATLAB code. A simple Matlab implement of our predictor. (ZIP 19,742 kb)
DOI: 10.6084/m9.figshare.7538510.v1
title: Additional file 1 of Network-based logistic regression integration method for biomarker identification

description: The identified subnetwork biomarkers. The identified subnetwork biomarkers using network-based integrative logistic regression with Abs-Network penalty. (TXT 2 kb)
DOI: 10.6084/m9.figshare.7538534.v1
title: Additional file 4 of Network-based logistic regression integration method for biomarker identification

description: GO:MF enrichment results of the subnetwork biomarkers. The enrichment of GO: MF is included. (XLSX 69 kb)
DOI: 10.6084/m9.figshare.7538555
title: Additional file 4: of Condition-specific gene co-expression network mining identifies key pathways and regulators in the brain tissue of Alzheimerâ s disease patients

description: Table S3. Enriched GO terms (p-value&lt;0.01) of all condition-specific modules. Table S4. Enriched KEGG pathway terms (p-value&lt;0.01) of all condition-specific modules. (XLSX 325 kb)
DOI: 10.6084/m9.figshare.12781438
title: Additional file 2 of Meta-analysis of genome-wide association study identifies FBN2 as a novel locus associated with systemic lupus erythematosus in Thai population

description: Additional file 2. Supplementary Table 1: List of significant variants at individual locus from meta-analysis (p-value &lt; 5E-5)
DOI: 10.6084/m9.figshare.12781444
title: Additional file 3 of Meta-analysis of genome-wide association study identifies FBN2 as a novel locus associated with systemic lupus erythematosus in Thai population

description: Additional file 3. Supplementary Table 2: List of HWE of significant variants (p-value &lt; 5E-5)
DOI: 10.6084/m9.figshare.7538561.v1
title: Additional file 1 of Predicting adverse drug reactions of combined medication from heterogeneous pharmacologic databases

description: â Table S1: Drug pairs are sorted in a descending order of their interaction scores. â Table S2: Drug pairs are sorted ascendingly according to their interaction scores. (XLSX 25,647 kb)
DOI: 10.6084/m9.figshare.12246722
title: Additional file 2 of Cytochrome P450 1A1 enhances inflammatory responses and impedes phagocytosis of bacteria in macrophages during sepsis

description: Additional file 1: Figure S1. Confirmation of transfections. Figure S2. Relative expression levels of inflammatory factors in overactivated macrophages. Figure S3. The inhibitory effects of Rhapontigenin on LPS-induced TNF-α and IL-6 secretion in PMs. Figure S4. Validation of the NF-κB signalling pathway and different MAPK signalling pathways in LPS-stimulated CYP1A1/RAW and NC/RAW. Figure S5. The levels of 12(S)-HETE in PLFs from E.coli- and CLP-induced septic mice. Figure S6. Detection of lentivirus infection rate in PMs. Figure S7. The regulation of CYP1A1-JNK-AP-1 axis in septic mice. Figure S8. Platelet count in PLFs from CYP1A1-overexpressed macrophages transferred septic mice. Figure S9. CYP1A1 is involved in phagocytosis of bacteria in macrophages during sepsis.
DOI: 10.6084/m9.figshare.7538522.v1
title: Additional file 2 of Network-based logistic regression integration method for biomarker identification

description: GO:BP enrichment results of the subnetwork biomarkers. The enrichment of GO: BP is included. (XLSX 220 kb)
DOI: 10.6084/m9.figshare.7538576
title: Additional file 3 of Predicting adverse drug reactions of combined medication from heterogeneous pharmacologic databases

description: The disease-gene associations. This file contains the researched diseases and their associated genes extracted from CTD. (CSV 7229 kb)
DOI: 10.6084/m9.figshare.7538594.v1
title: Additional file 3 of FKL-Spa-LapRLS: an accurate method for identifying human microRNA-disease association

description: Table S3. The top 50 predicted miRNAs related to Pancreatic Neoplasms. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.12246689.v1
title: Additional file 3 of Transcriptome analysis reveals rapid defence responses in wheat induced by phytotoxic aphid Schizaphis graminum feeding

description: Additional file 3. All of the differentially expressed genes (DEGs) of wheat leaves in response to S. graminum feeding at 2, 6, 12, 24 and 48 hpi.
DOI: 10.6084/m9.figshare.23590079
title: Prodigiosin as an antibiofilm agent against multidrug-resistant <i>Staphylococcus aureus</i>

description: <i>Staphylococcus aureus</i> is known for forming bacterial biofilms that confer increased antimicrobial resistance. Combining antibiotics with antibiofilm agents is an alternative approach, but the antibiofilm ability of prodigiosin (PG), a potential antibiotic synergist, against antimicrobial-resistant (AMR) <i>S. aureus</i> remains to be understood. The antibiofilm activity of PG against 29 clinical AMR <i>S. aureus</i> strains was evaluated using crystal violet staining, and its synergistic effects with vancomycin (VAN) was confirmed using the checkerboard test. The viability and metabolic activity of biofilms and planktonic cells were also assessed. The results revealed that PG exhibited promising inhibitory activity against biofilm formation and synergistic activity with VAN. It effectively reduced the metabolic activity of biofilms and suppressed the production of exopolysaccharides, which might be attributed to the downregulation of biofilm-related genes such as <i>sarA</i>, <i>agrA</i>, and <i>icaA</i>. These findings suggest that PG could be used as a preventive coating or adjuvant against biofilms in clinical settings.
DOI: 10.6084/m9.figshare.7538534
title: Additional file 4 of Network-based logistic regression integration method for biomarker identification

description: GO:MF enrichment results of the subnetwork biomarkers. The enrichment of GO: MF is included. (XLSX 69 kb)
DOI: 10.6084/m9.figshare.7538582
title: Additional file 1 of FKL-Spa-LapRLS: an accurate method for identifying human microRNA-disease association

description: Table S1. The top 50 predicted miRNAs related to Colon Neoplasms. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7538606
title: Additional file 5 of FKL-Spa-LapRLS: an accurate method for identifying human microRNA-disease association

description: Table S5. The top 50 predicted miRNAs related to Esophageal Neoplasms. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.12246650
title: Additional file 1 of The metabolome as a link in the genotype-phenotype map for peroxide resistance in the fruit fly, Drosophila melanogaster

description: Additional file 1: Table S1. Variants Associated with Peroxide Resistance all 14 SNPs associated with peroxide resistance below FDR = 0.2. Annotations are based on gene models from FlyBase version 5.48 and SNPs more than 1 kb from an annotated gene are assigned NA. Asterisks indicate SNPS associated with more than one gene.
DOI: 10.6084/m9.figshare.7538585.v1
title: Additional file 4 of Predicting adverse drug reactions of combined medication from heterogeneous pharmacologic databases

description: 1,155,755 known drug-drug-ADR associations which are extracted from the Tatonetti Lab. Drugs are labeled using their DrugBank IDs, and ADRs are labeled with their UMLS IDs. (CSV 29,346 kb)
DOI: 10.6084/m9.figshare.7538510
title: Additional file 1 of Network-based logistic regression integration method for biomarker identification

description: The identified subnetwork biomarkers. The identified subnetwork biomarkers using network-based integrative logistic regression with Abs-Network penalty. (TXT 2 kb)
DOI: 10.6084/m9.figshare.7538555.v1
title: Additional file 4: of Condition-specific gene co-expression network mining identifies key pathways and regulators in the brain tissue of Alzheimerâ s disease patients

description: Table S3. Enriched GO terms (p-value&lt;0.01) of all condition-specific modules. Table S4. Enriched KEGG pathway terms (p-value&lt;0.01) of all condition-specific modules. (XLSX 325 kb)
DOI: 10.6084/m9.figshare.7538564
title: Additional file 5: of Condition-specific gene co-expression network mining identifies key pathways and regulators in the brain tissue of Alzheimerâ s disease patients

description: Table S5. Modules with targets of specific differentially expressed TF enriched in certain pathways. At least two TF targets are in the corresponding enriched pathway. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7538564.v1
title: Additional file 5: of Condition-specific gene co-expression network mining identifies key pathways and regulators in the brain tissue of Alzheimerâ s disease patients

description: Table S5. Modules with targets of specific differentially expressed TF enriched in certain pathways. At least two TF targets are in the corresponding enriched pathway. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7538570
title: Additional file 2 of Predicting adverse drug reactions of combined medication from heterogeneous pharmacologic databases

description: â Table S3: List of 1048 drugs studied in this work. DrugBank ID, Mesh ID, drug names, drug SMILES strings, drug target proteins, substituents, enriched pathways, associated CTD diseases, and associated CTD genes are included as well. â Table S4: List of 1276 adverse drug reaction terms studied in this work. UMLS ID, UMLS name and positive drug pair number are also included. (XLSX 2644 kb)
DOI: 10.6084/m9.figshare.7538585
title: Additional file 4 of Predicting adverse drug reactions of combined medication from heterogeneous pharmacologic databases

description: 1,155,755 known drug-drug-ADR associations which are extracted from the Tatonetti Lab. Drugs are labeled using their DrugBank IDs, and ADRs are labeled with their UMLS IDs. (CSV 29,346 kb)
DOI: 10.6084/m9.figshare.7538594
title: Additional file 3 of FKL-Spa-LapRLS: an accurate method for identifying human microRNA-disease association

description: Table S3. The top 50 predicted miRNAs related to Pancreatic Neoplasms. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.12781438.v1
title: Additional file 2 of Meta-analysis of genome-wide association study identifies FBN2 as a novel locus associated with systemic lupus erythematosus in Thai population

description: Additional file 2. Supplementary Table 1: List of significant variants at individual locus from meta-analysis (p-value &lt; 5E-5)
DOI: 10.6084/m9.figshare.7538549.v1
title: Additional file 3: of Condition-specific gene co-expression network mining identifies key pathways and regulators in the brain tissue of Alzheimerâ s disease patients

description: Table S2. List of 30â AD-specific modules and 31 normal-specific modules. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.7538570.v1
title: Additional file 2 of Predicting adverse drug reactions of combined medication from heterogeneous pharmacologic databases

description: â Table S3: List of 1048 drugs studied in this work. DrugBank ID, Mesh ID, drug names, drug SMILES strings, drug target proteins, substituents, enriched pathways, associated CTD diseases, and associated CTD genes are included as well. â Table S4: List of 1276 adverse drug reaction terms studied in this work. UMLS ID, UMLS name and positive drug pair number are also included. (XLSX 2644 kb)
DOI: 10.6084/m9.figshare.7538609
title: Additional file 6 of FKL-Spa-LapRLS: an accurate method for identifying human microRNA-disease association

description: Table S6. The top 50 predicted miRNAs related to Kidney Neoplasms. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7538609.v1
title: Additional file 6 of FKL-Spa-LapRLS: an accurate method for identifying human microRNA-disease association

description: Table S6. The top 50 predicted miRNAs related to Kidney Neoplasms. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7538615
title: Additional file 7 of FKL-Spa-LapRLS: an accurate method for identifying human microRNA-disease association

description: Table S7. The top 50 predicted miRNAs related to Breast Neoplasms. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7538615.v1
title: Additional file 7 of FKL-Spa-LapRLS: an accurate method for identifying human microRNA-disease association

description: Table S7. The top 50 predicted miRNAs related to Breast Neoplasms. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7538597.v1
title: Additional file 5 of Predicting adverse drug reactions of combined medication from heterogeneous pharmacologic databases

description: Supplementary codes and data. The Python codes of HCNS-ADR and the source data. (ZIP 10,129 kb)
DOI: 10.6084/m9.figshare.7538624
title: Additional file 8 of FKL-Spa-LapRLS: an accurate method for identifying human microRNA-disease association

description: Table S8. The top 50 predicted miRNAs related to Lymphoma. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7538528.v1
title: Additional file 3 of Network-based logistic regression integration method for biomarker identification

description: GO:CC enrichment results of the subnetwork biomarkers. The enrichment of GO: CC is included. (XLSX 46 kb)
DOI: 10.6084/m9.figshare.7538597
title: Additional file 5 of Predicting adverse drug reactions of combined medication from heterogeneous pharmacologic databases

description: Supplementary codes and data. The Python codes of HCNS-ADR and the source data. (ZIP 10,129 kb)
DOI: 10.6084/m9.figshare.7538633
title: Additional file 3: of Comparative chloroplast genomes of Paris Sect. Marmorata: insights into repeat regions and evolutionary implications

description: Table S6. Number of SSRs in fifteen chloroplast genomes of Paris species. Table S7. Polymorphism of SSRs in chloroplast genomes of Sect. Marmorata. (XLSX 17 kb)