cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12082887.v3
title: Diet Composition Affects Liver and Mammary Tissue Transcriptome in Primiparous Holstein Dairy Cows

description: Biopsies of liver and mammary were collected at the end of a 9-week feeding to measure mRNA profiles using a 4×44K Bovine Agilent microarray chip. Data were analyzed with SAS JMP Genomics using ANOVA with a false discovery rate correction (FDR &lt; 0.2). Dynamic Impact Approach (DIA), Database for Annotation, Visualization and Integrated Discovery (DAVID), and ClueGO were used for bioinformatic analysis of differently expressed genes (DEGs). Considering an FDR&lt;0.2, there were 299 DEG affected in both liver and mammary, 139 DEGs affected in liver, and 120 DEG affected in mammary in CS vs. MF.
DOI: 10.6084/m9.figshare.12082830
title: Additional file 1 of Review on natural products databases: where to find data in 2020

description: Additional file 1. Overlap (in percent) of compound content between open natural products databases.
DOI: 10.6084/m9.figshare.12082827
title: Additional file 5 of Genome-wide analysis of wheat DNA-binding with one finger (Dof) transcription factor genes: evolutionary characteristics and diverse abiotic stress responses

description: Additional file 5: Table S1. The nomenclature, characteristics of Dof genes and their deduced proteins in Arabidopsis thaliana and Oryza sativa subsp. japonica. The data (accession numbers and amino acid sequences) of Dof transcription factor for Arabidopsis and rice are obtained from the Plant Transcription Factor Database (http://planttfdb.cbi.pku.edu.cn/family.php?sp=Ath&fam=Dof; http://planttfdb.cbi.pku.edu.cn/family.php?sp=Osj&fam=Dof). Table S2. The nomenclature, characteristics of Dof genes and their deduced proteins in Triticum aestivum L. The accession numbers and sequences (genomic, amino acid, and CDS sequences) of the 96 wheat Dof genes were obtained from Triticum aestivum genome data (IWGSC) in Ensemble Plants (http://plants.ensembl.org/Triticum_aestivum/Info/Index). Table S3. Coevolution sites in TaDofs. Table S4. Cis-element analysis of 1500 bp nucleotide sequences data upstream of the translation initiation codon of TaDof genes. Table S5. The number of each cis-acting element contained in the subfamily. Table S6. The RNA-Seq atlas data of the TaDof genes. Table S7. Primers used for qRT-PCR of Dof genes in wheat. Table S8. The relative expression values in qRT-PCR and RNA-Seq atlas data of TaDofs under abiotic stresses. (A) The relative expression values of TaDofs in qRT-PCR under abiotic stresses. (B) The RNA-Seq atlas data of TaDofs under abiotic stresses.
DOI: 10.6084/m9.figshare.12082830.v1
title: Additional file 1 of Review on natural products databases: where to find data in 2020

description: Additional file 1. Overlap (in percent) of compound content between open natural products databases.
DOI: 10.6084/m9.figshare.12082827.v1
title: Additional file 5 of Genome-wide analysis of wheat DNA-binding with one finger (Dof) transcription factor genes: evolutionary characteristics and diverse abiotic stress responses

description: Additional file 5: Table S1. The nomenclature, characteristics of Dof genes and their deduced proteins in Arabidopsis thaliana and Oryza sativa subsp. japonica. The data (accession numbers and amino acid sequences) of Dof transcription factor for Arabidopsis and rice are obtained from the Plant Transcription Factor Database (http://planttfdb.cbi.pku.edu.cn/family.php?sp=Ath&fam=Dof; http://planttfdb.cbi.pku.edu.cn/family.php?sp=Osj&fam=Dof). Table S2. The nomenclature, characteristics of Dof genes and their deduced proteins in Triticum aestivum L. The accession numbers and sequences (genomic, amino acid, and CDS sequences) of the 96 wheat Dof genes were obtained from Triticum aestivum genome data (IWGSC) in Ensemble Plants (http://plants.ensembl.org/Triticum_aestivum/Info/Index). Table S3. Coevolution sites in TaDofs. Table S4. Cis-element analysis of 1500 bp nucleotide sequences data upstream of the translation initiation codon of TaDof genes. Table S5. The number of each cis-acting element contained in the subfamily. Table S6. The RNA-Seq atlas data of the TaDof genes. Table S7. Primers used for qRT-PCR of Dof genes in wheat. Table S8. The relative expression values in qRT-PCR and RNA-Seq atlas data of TaDofs under abiotic stresses. (A) The relative expression values of TaDofs in qRT-PCR under abiotic stresses. (B) The RNA-Seq atlas data of TaDofs under abiotic stresses.
DOI: 10.6084/m9.figshare.12082806
title: Additional file 4 of Flowering in Persian walnut: patterns of gene expression during flower development

description: Additional file 4. The raw data obtained from real-time PCR and raw data to determine chilling requirement.
DOI: 10.6084/m9.figshare.12082806.v1
title: Additional file 4 of Flowering in Persian walnut: patterns of gene expression during flower development

description: Additional file 4. The raw data obtained from real-time PCR and raw data to determine chilling requirement.
DOI: 10.6084/m9.figshare.12082752
title: Additional file 2 of Ultrasonic vocalizations in house mice depend upon genetic relatedness of mating partners and correlate with subsequent reproductive success

description: Additional file 2. Original dataset containing the raw data and variable definitions used in this article.
DOI: 10.6084/m9.figshare.12082752.v1
title: Additional file 2 of Ultrasonic vocalizations in house mice depend upon genetic relatedness of mating partners and correlate with subsequent reproductive success

description: Additional file 2. Original dataset containing the raw data and variable definitions used in this article.
DOI: 10.6084/m9.figshare.12082737
title: Additional file 9 of Visualizing metabolic network dynamics through time-series metabolomic data

description: Additional file 9 The pathway map iAB-RBC-283_Map_cell-outline.xml.gz in SBML Level 3 Version 1 format with Layout and FBC packages compressed with gzip (153 kB). Please note that the core model in this file has been reduced to the content of the pathway map and does not comprise all reactions and metabolites of the original model by [37].
DOI: 10.6084/m9.figshare.12082737.v2
title: Additional file 9 of Visualizing metabolic network dynamics through time-series metabolomic data

description: Additional file 9 The pathway map iAB-RBC-283_Map_cell-outline.xml.gz in SBML Level 3 Version 1 format with Layout and FBC packages compressed with gzip (153 kB). Please note that the core model in this file has been reduced to the content of the pathway map and does not comprise all reactions and metabolites of the original model by [37].
DOI: 10.6084/m9.figshare.12082728
title: Additional file 7 of Visualizing metabolic network dynamics through time-series metabolomic data

description: Additional file 7 The data set iAB-RBC-283_Data.zip used in the iAB-RBC-283 animation (13 kB).
DOI: 10.6084/m9.figshare.12082731
title: Additional file 8 of Visualizing metabolic network dynamics through time-series metabolomic data

description: Additional file 8 The pathway map in Escher format iAB-RBC-283_Map_cell-outline.json.gz (94 kB).
DOI: 10.6084/m9.figshare.12082737.v1
title: Additional file 9 of Visualizing metabolic network dynamics through time-series metabolomic data

description: Additional file 9 The pathway map iAB-RBC-283_Map_cell-outline.xml.gz in SBML Level 3 Version 1 format with Layout and FBC packages compressed with gzip (153 kB). Please note that the core model in this file has been reduced to the content of the pathway map and does not comprise all reactions and metabolites of the original model by [37].
DOI: 10.6084/m9.figshare.12082722
title: Additional file 5 of Visualizing metabolic network dynamics through time-series metabolomic data

description: Additional file 5 The pathway map in SBML Level 3 Version 1 format with Layout and FBC (flux balance constraints) packages iAT-PLT-636_Map.xml.gz compressed with gzip (457 kB).
DOI: 10.6084/m9.figshare.12082728.v2
title: Additional file 7 of Visualizing metabolic network dynamics through time-series metabolomic data

description: Additional file 7 The data set iAB-RBC-283_Data.zip used in the iAB-RBC-283 animation (13 kB).
DOI: 10.6084/m9.figshare.12082731.v2
title: Additional file 8 of Visualizing metabolic network dynamics through time-series metabolomic data

description: Additional file 8 The pathway map in Escher format iAB-RBC-283_Map_cell-outline.json.gz (94 kB).
DOI: 10.6084/m9.figshare.12082719
title: Additional file 4 of Visualizing metabolic network dynamics through time-series metabolomic data

description: Additional file 4 The pathway map in Escher format iAT-PLT-636_Map.json.gz compressed with gzip (200 kB).
DOI: 10.6084/m9.figshare.12082728.v1
title: Additional file 7 of Visualizing metabolic network dynamics through time-series metabolomic data

description: Additional file 7 The data set iAB-RBC-283_Data.zip used in the iAB-RBC-283 animation (13 kB).
DOI: 10.6084/m9.figshare.12082731.v1
title: Additional file 8 of Visualizing metabolic network dynamics through time-series metabolomic data

description: Additional file 8 The pathway map in Escher format iAB-RBC-283_Map_cell-outline.json.gz (94 kB).
DOI: 10.6084/m9.figshare.12082722.v2
title: Additional file 5 of Visualizing metabolic network dynamics through time-series metabolomic data

description: Additional file 5 The pathway map in SBML Level 3 Version 1 format with Layout and FBC (flux balance constraints) packages iAT-PLT-636_Map.xml.gz compressed with gzip (457 kB).
DOI: 10.6084/m9.figshare.12082710
title: Additional file 3 of Visualizing metabolic network dynamics through time-series metabolomic data

description: Additional file 3 The data set iAT-PLT-636_Data.csv used in the iAT-PLT-636 animation (15 kB).
DOI: 10.6084/m9.figshare.12082719.v2
title: Additional file 4 of Visualizing metabolic network dynamics through time-series metabolomic data

description: Additional file 4 The pathway map in Escher format iAT-PLT-636_Map.json.gz compressed with gzip (200 kB).
DOI: 10.6084/m9.figshare.12082722.v1
title: Additional file 5 of Visualizing metabolic network dynamics through time-series metabolomic data

description: Additional file 5 The pathway map in SBML Level 3 Version 1 format with Layout and FBC (flux balance constraints) packages iAT-PLT-636_Map.xml.gz compressed with gzip (457 kB).
DOI: 10.6084/m9.figshare.12082719.v1
title: Additional file 4 of Visualizing metabolic network dynamics through time-series metabolomic data

description: Additional file 4 The pathway map in Escher format iAT-PLT-636_Map.json.gz compressed with gzip (200 kB).
DOI: 10.6084/m9.figshare.12082698
title: Additional file 2 of Diet and nutrient status of legume consumers in Sweden: a descriptive cross-sectional study

description: Additional file 2: Table S1. Description of the food groups used for Principal Component Analysis (PCA). Table S2. Frequency of consumption by types of legumes and average intake (g/d) ± SD of consumers, energy-adjusted. *Meals with legumes incorporated. Figure S2. Heat map of varimax rotated loadings for the selected principal components loading positively (&gt; 0.15) on legumes. Loadings ± &gt; |0.15| are presented in bold. The color gradient indicates most negative loadings in red and most positive loadings in green. White indicates loading close to 0, meaning that the food group is not representative of the component.
DOI: 10.6084/m9.figshare.12082710.v2
title: Additional file 3 of Visualizing metabolic network dynamics through time-series metabolomic data

description: Additional file 3 The data set iAT-PLT-636_Data.csv used in the iAT-PLT-636 animation (15 kB).
DOI: 10.6084/m9.figshare.12082698.v1
title: Additional file 2 of Diet and nutrient status of legume consumers in Sweden: a descriptive cross-sectional study

description: Additional file 2: Table S1. Description of the food groups used for Principal Component Analysis (PCA). Table S2. Frequency of consumption by types of legumes and average intake (g/d) ± SD of consumers, energy-adjusted. *Meals with legumes incorporated. Figure S2. Heat map of varimax rotated loadings for the selected principal components loading positively (&gt; 0.15) on legumes. Loadings ± &gt; |0.15| are presented in bold. The color gradient indicates most negative loadings in red and most positive loadings in green. White indicates loading close to 0, meaning that the food group is not representative of the component.
DOI: 10.6084/m9.figshare.12082710.v1
title: Additional file 3 of Visualizing metabolic network dynamics through time-series metabolomic data

description: Additional file 3 The data set iAT-PLT-636_Data.csv used in the iAT-PLT-636 animation (15 kB).
DOI: 10.6084/m9.figshare.12082686
title: Additional file 14 of Visualizing metabolic network dynamics through time-series metabolomic data

description: Additional file 14 A brief Java™ program that embeds a metabolic map in the format of SBML Layout extensions into an SBML Level 3 Version 1 file.
DOI: 10.6084/m9.figshare.12082686.v2
title: Additional file 14 of Visualizing metabolic network dynamics through time-series metabolomic data

description: Additional file 14 A brief Java™ program that embeds a metabolic map in the format of SBML Layout extensions into an SBML Level 3 Version 1 file.
DOI: 10.6084/m9.figshare.12082686.v1
title: Additional file 14 of Visualizing metabolic network dynamics through time-series metabolomic data

description: Additional file 14 A brief Java™ program that embeds a metabolic map in the format of SBML Layout extensions into an SBML Level 3 Version 1 file.
DOI: 10.6084/m9.figshare.12082662
title: Additional file 9 of Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

description: Additional file 9: Data S9. The GO and KEGG pathway enrichment analysis of trans-targets for the differentially expressed lncRNAs.
DOI: 10.6084/m9.figshare.12082653
title: Additional file 7 of Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

description: Additional file 7: Data S7. The GO and KEGG pathway enrichment analysis of target genes for the differentially expressed lncRNAs.
DOI: 10.6084/m9.figshare.12082659
title: Additional file 8 of Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

description: Additional file 8: Data S8. The GO and KEGG pathway enrichment analysis of cis-target genes for the differentially expressed lncRNAs.
DOI: 10.6084/m9.figshare.12082659.v1
title: Additional file 8 of Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

description: Additional file 8: Data S8. The GO and KEGG pathway enrichment analysis of cis-target genes for the differentially expressed lncRNAs.
DOI: 10.6084/m9.figshare.12082662.v1
title: Additional file 9 of Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

description: Additional file 9: Data S9. The GO and KEGG pathway enrichment analysis of trans-targets for the differentially expressed lncRNAs.
DOI: 10.6084/m9.figshare.12082650
title: Additional file 6 of pyCancerSig: subclassifying human cancer with comprehensive single nucleotide, structural and microsatellite mutational signature deconstruction from whole genome sequencing

description: Additional file 6.
DOI: 10.6084/m9.figshare.12082653.v1
title: Additional file 7 of Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

description: Additional file 7: Data S7. The GO and KEGG pathway enrichment analysis of target genes for the differentially expressed lncRNAs.
DOI: 10.6084/m9.figshare.12082641
title: Additional file 6 of Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

description: Additional file 6: Data S6. The sponging miRNAs predicted for differentially expressed circRNAs and their potential targets.
DOI: 10.6084/m9.figshare.12082650.v1
title: Additional file 6 of pyCancerSig: subclassifying human cancer with comprehensive single nucleotide, structural and microsatellite mutational signature deconstruction from whole genome sequencing

description: Additional file 6.
DOI: 10.6084/m9.figshare.12082641.v1
title: Additional file 6 of Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

description: Additional file 6: Data S6. The sponging miRNAs predicted for differentially expressed circRNAs and their potential targets.
DOI: 10.6084/m9.figshare.12082635
title: Additional file 5 of Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

description: Additional file 5: Data S5. The cis- and trans-target genes predicted for differentially expressed lncRNAs.
DOI: 10.6084/m9.figshare.12082635.v1
title: Additional file 5 of Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

description: Additional file 5: Data S5. The cis- and trans-target genes predicted for differentially expressed lncRNAs.
DOI: 10.6084/m9.figshare.12082629
title: Additional file 4 of Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

description: Additional file 4: Data S4. The target genes predicted for differentially expressed lncRNAs.
DOI: 10.6084/m9.figshare.12082629.v1
title: Additional file 4 of Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

description: Additional file 4: Data S4. The target genes predicted for differentially expressed lncRNAs.
DOI: 10.6084/m9.figshare.12082617
title: Additional file 2 of Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

description: Additional file 2: Data S2. All the expressed mRNAs, lncRNAs and circRNAs in this study.
DOI: 10.6084/m9.figshare.12082620
title: Additional file 1 of pyCancerSig: subclassifying human cancer with comprehensive single nucleotide, structural and microsatellite mutational signature deconstruction from whole genome sequencing

description: Additional file 1.
DOI: 10.6084/m9.figshare.12082623
title: Additional file 3 of Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

description: Additional file 3: Data S3. The length distribution of lncRNAs and circRNAs.
DOI: 10.6084/m9.figshare.12082614
title: Additional file 1 of Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

description: Additional file 1: Data S1. The primers used for verification of differentially expressed mRNAs, lncRNAs and circRNAs by qRT-PCR.
DOI: 10.6084/m9.figshare.12082620.v1
title: Additional file 1 of pyCancerSig: subclassifying human cancer with comprehensive single nucleotide, structural and microsatellite mutational signature deconstruction from whole genome sequencing

description: Additional file 1.
DOI: 10.6084/m9.figshare.12082623.v1
title: Additional file 3 of Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

description: Additional file 3: Data S3. The length distribution of lncRNAs and circRNAs.
DOI: 10.6084/m9.figshare.12082611
title: Additional file 11 of Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

description: Additional file 11: Data S11. The GO and KEGG pathway enrichment analysis of sponging miRNA targets for the differentially expressed circRNAs.
DOI: 10.6084/m9.figshare.12082614.v1
title: Additional file 1 of Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

description: Additional file 1: Data S1. The primers used for verification of differentially expressed mRNAs, lncRNAs and circRNAs by qRT-PCR.
DOI: 10.6084/m9.figshare.12082617.v1
title: Additional file 2 of Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

description: Additional file 2: Data S2. All the expressed mRNAs, lncRNAs and circRNAs in this study.
DOI: 10.6084/m9.figshare.12082608
title: Additional file 10 of Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

description: Additional file 10: Data S10. The GO and KEGG pathway enrichment analysis of source genes for the differentially expressed circRNAs.
DOI: 10.6084/m9.figshare.12082611.v1
title: Additional file 11 of Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

description: Additional file 11: Data S11. The GO and KEGG pathway enrichment analysis of sponging miRNA targets for the differentially expressed circRNAs.
DOI: 10.6084/m9.figshare.12082608.v1
title: Additional file 10 of Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

description: Additional file 10: Data S10. The GO and KEGG pathway enrichment analysis of source genes for the differentially expressed circRNAs.
DOI: 10.6084/m9.figshare.12082596
title: Additional file 1 of Transcriptomic and metabolomic analyses reveal mechanisms of adaptation to salinity in which carbon and nitrogen metabolism is altered in sugar beet roots

description: Additional file 1: Table S1. Raw metabolomic data at different stages of salt stress (n = 8). Table S2. Summary of the fold changes of the metabolomic data at different stages of salt stress. Table S3. Genes used for validation of sequencing (Seq) data by qRT-PCR. Table S4. The GO terms of DEGs from the two comparison groups (S_1vsCK_1 and S_7vsCK_7). Table S5. The KEGG pathway enrichment of DEGs from the two comparison groups (S_1vsCK_1 and S_7vsCK_7). Table S6. Important DEGs detected in the roots under salt stress (P
DOI: 10.6084/m9.figshare.12082596.v1
title: Additional file 1 of Transcriptomic and metabolomic analyses reveal mechanisms of adaptation to salinity in which carbon and nitrogen metabolism is altered in sugar beet roots

description: Additional file 1: Table S1. Raw metabolomic data at different stages of salt stress (n = 8). Table S2. Summary of the fold changes of the metabolomic data at different stages of salt stress. Table S3. Genes used for validation of sequencing (Seq) data by qRT-PCR. Table S4. The GO terms of DEGs from the two comparison groups (S_1vsCK_1 and S_7vsCK_7). Table S5. The KEGG pathway enrichment of DEGs from the two comparison groups (S_1vsCK_1 and S_7vsCK_7). Table S6. Important DEGs detected in the roots under salt stress (P
DOI: 10.6084/m9.figshare.12082581
title: Additional file 5 of Integrative bioinformatics analysis reveals miR-494 and its target genes as predictive biomarkers of trastuzumab-resistant breast cancer

description: Additional file 5: Table S4. The miR-494 target prediction, analyzed using miRecords.
DOI: 10.6084/m9.figshare.12082578
title: Additional file 4 of Integrative bioinformatics analysis reveals miR-494 and its target genes as predictive biomarkers of trastuzumab-resistant breast cancer

description: Additional file 4: Table S3. DEGs from GSE66305.
DOI: 10.6084/m9.figshare.12082581.v1
title: Additional file 5 of Integrative bioinformatics analysis reveals miR-494 and its target genes as predictive biomarkers of trastuzumab-resistant breast cancer

description: Additional file 5: Table S4. The miR-494 target prediction, analyzed using miRecords.