cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9760784.v1
title: Additional file 2 of SigsPack, a package for cancer mutational signatures

description: Exposure estimation for synthetic data example. Exposure estimation from synthetic data. 1000 mutations have been generated at random, using frequencies from set1 (signatures 7, 13, 21, 24 & 28), and set2 (signatures 3, 5, 8, 16, & 25). A perfect reconstruction would have original exposure values very close to 0.2 for these 5 signatures, and 0 for all the others. The mutational catalogues was resampled 1000 times, and for each signature, the minimum, first quartile, median, third quartile and maximum values of exposures computed from the re-sampled data are shown. (TSV 5 kb)
DOI: 10.6084/m9.figshare.9760763
title: Additional file 4: of Correction to: Epigenetic signatures associated with imprinted paternally expressed genes in the Arabidopsis endosperm

description: Table S5. Parent-of-origin RNAseq dataset of 4 DAP INTACT-purified endosperm of Col × Ler reciprocal crosses. (XLSX 820 kb)
DOI: 10.6084/m9.figshare.9760763.v1
title: Additional file 4: of Correction to: Epigenetic signatures associated with imprinted paternally expressed genes in the Arabidopsis endosperm

description: Table S5. Parent-of-origin RNAseq dataset of 4 DAP INTACT-purified endosperm of Col × Ler reciprocal crosses. (XLSX 820 kb)
DOI: 10.6084/m9.figshare.9760640
title: Additional file 1: of The geography and economics of forgoing medical examinations or therapeutic treatments in Italy during the economic crisis

description: Table S1. Crude (OR) and adjusted Odds Ratios (aOR) with 95%CI and p-value for factors associated with forgone medical visits or specialist treatment in the preceding 12 months for any reason. Hierarchical logistic models per period. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.9760640.v1
title: Additional file 1: of The geography and economics of forgoing medical examinations or therapeutic treatments in Italy during the economic crisis

description: Table S1. Crude (OR) and adjusted Odds Ratios (aOR) with 95%CI and p-value for factors associated with forgone medical visits or specialist treatment in the preceding 12 months for any reason. Hierarchical logistic models per period. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.9760601
title: Additional file 6 of MPRAnalyze: statistical framework for massively parallel reporter assays

description: Table s4. BH-corrected p values from the Transcription Factor finding site enrichment analysis of the temporal results. (CSV 40 kb)
DOI: 10.6084/m9.figshare.9760592
title: Additional file 4 of MPRAnalyze: statistical framework for massively parallel reporter assays

description: Table s2. Transcription factor binding site enrichment analysis results: fold-enrichment scores. (CSV 82 kb)
DOI: 10.6084/m9.figshare.9760595
title: Additional file 5 of MPRAnalyze: statistical framework for massively parallel reporter assays

description: Table s3. Full RNA-seq measurements from the Inoue-Kreimer study of the timepoints T0h and T72h. (CSV 993 kb)
DOI: 10.6084/m9.figshare.9760592.v1
title: Additional file 4 of MPRAnalyze: statistical framework for massively parallel reporter assays

description: Table s2. Transcription factor binding site enrichment analysis results: fold-enrichment scores. (CSV 82 kb)
DOI: 10.6084/m9.figshare.9760595.v1
title: Additional file 5 of MPRAnalyze: statistical framework for massively parallel reporter assays

description: Table s3. Full RNA-seq measurements from the Inoue-Kreimer study of the timepoints T0h and T72h. (CSV 993 kb)
DOI: 10.6084/m9.figshare.9760601.v1
title: Additional file 6 of MPRAnalyze: statistical framework for massively parallel reporter assays

description: Table s4. BH-corrected p values from the Transcription Factor finding site enrichment analysis of the temporal results. (CSV 40 kb)
DOI: 10.6084/m9.figshare.9760577
title: MOESM7 of Integrating genome-wide co-association and gene expression to identify putative regulators and predictors of feed efficiency in pigs

description: Additional file 7: Table S6. Description of the SNPs significantly associated with the gene expression according to the expression genome-wide association studies (eGWAS).
DOI: 10.6084/m9.figshare.9760583
title: Additional file 3 of MPRAnalyze: statistical framework for massively parallel reporter assays

description: Table s1. Transcription factor binding site enrichment analysis results: BH-corrected p values. (CSV 48 kb)
DOI: 10.6084/m9.figshare.9760577.v1
title: MOESM7 of Integrating genome-wide co-association and gene expression to identify putative regulators and predictors of feed efficiency in pigs

description: Additional file 7: Table S6. Description of the SNPs significantly associated with the gene expression according to the expression genome-wide association studies (eGWAS).
DOI: 10.6084/m9.figshare.9760583.v1
title: Additional file 3 of MPRAnalyze: statistical framework for massively parallel reporter assays

description: Table s1. Transcription factor binding site enrichment analysis results: BH-corrected p values. (CSV 48 kb)
DOI: 10.6084/m9.figshare.9760565
title: MOESM4 of Integrating genome-wide co-association and gene expression to identify putative regulators and predictors of feed efficiency in pigs

description: Additional file 4: Table S3. Description of the genes identified in the partial least squares discriminant analysis (sPLS-DA).
DOI: 10.6084/m9.figshare.9760562
title: MOESM3 of Integrating genome-wide co-association and gene expression to identify putative regulators and predictors of feed efficiency in pigs

description: Additional file 3: Table S2. Description of genes identified as differentially expressed between the high and low feed efficiency groups (HFE and LFE).
DOI: 10.6084/m9.figshare.9760568
title: MOESM5 of Integrating genome-wide co-association and gene expression to identify putative regulators and predictors of feed efficiency in pigs

description: Additional file 5: Table S4. Description of the genes identified in the regularized canonical correlation analysis (rCCA).
DOI: 10.6084/m9.figshare.9760565.v1
title: MOESM4 of Integrating genome-wide co-association and gene expression to identify putative regulators and predictors of feed efficiency in pigs

description: Additional file 4: Table S3. Description of the genes identified in the partial least squares discriminant analysis (sPLS-DA).
DOI: 10.6084/m9.figshare.9760571
title: MOESM6 of Integrating genome-wide co-association and gene expression to identify putative regulators and predictors of feed efficiency in pigs

description: Additional file 6: Table S5. Functional annotation of the identified candidate genes.
DOI: 10.6084/m9.figshare.9760562.v1
title: MOESM3 of Integrating genome-wide co-association and gene expression to identify putative regulators and predictors of feed efficiency in pigs

description: Additional file 3: Table S2. Description of genes identified as differentially expressed between the high and low feed efficiency groups (HFE and LFE).
DOI: 10.6084/m9.figshare.9760568.v1
title: MOESM5 of Integrating genome-wide co-association and gene expression to identify putative regulators and predictors of feed efficiency in pigs

description: Additional file 5: Table S4. Description of the genes identified in the regularized canonical correlation analysis (rCCA).
DOI: 10.6084/m9.figshare.9760571.v1
title: MOESM6 of Integrating genome-wide co-association and gene expression to identify putative regulators and predictors of feed efficiency in pigs

description: Additional file 6: Table S5. Functional annotation of the identified candidate genes.
DOI: 10.6084/m9.figshare.9760547
title: Additional file 2: of Phylogenetic analysis of Bacillus anthracis strains from Western Siberia reveals a new genetic cluster in the global population of the species

description: Table S2. Base of sites of nucleotide polymorphisms of 195 Bacillus strains. (XLSX 9461 kb)
DOI: 10.6084/m9.figshare.9760556
title: MOESM2 of Integrating genome-wide co-association and gene expression to identify putative regulators and predictors of feed efficiency in pigs

description: Additional file 2: Table S1. Annotation of the 829 SNPs that were selected in the association weight matrix (AWM) procedure.
DOI: 10.6084/m9.figshare.9760547.v1
title: Additional file 2: of Phylogenetic analysis of Bacillus anthracis strains from Western Siberia reveals a new genetic cluster in the global population of the species

description: Table S2. Base of sites of nucleotide polymorphisms of 195 Bacillus strains. (XLSX 9461 kb)
DOI: 10.6084/m9.figshare.9760556.v1
title: MOESM2 of Integrating genome-wide co-association and gene expression to identify putative regulators and predictors of feed efficiency in pigs

description: Additional file 2: Table S1. Annotation of the 829 SNPs that were selected in the association weight matrix (AWM) procedure.
DOI: 10.6084/m9.figshare.9760544
title: Additional file 1: of Phylogenetic analysis of Bacillus anthracis strains from Western Siberia reveals a new genetic cluster in the global population of the species

description: Table S1. Strain metadata. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.9760544.v1
title: Additional file 1: of Phylogenetic analysis of Bacillus anthracis strains from Western Siberia reveals a new genetic cluster in the global population of the species

description: Table S1. Strain metadata. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.9760520
title: Additional file 5: of Peripheral blood DNA methylation differences in twin pairs discordant for Alzheimer’s disease

description: Gene expression level of candidate genes in blood of non-twin subjects with Alzheimer’s disease in comparison to reference subjects. Gene expression levels of the candidate genes from Additional file 2c in GEO NCBI data from blood (GSE63061) of non-twin subjects with Alzheimer’s disease in comparison to reference subjects. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.9760520.v1
title: Additional file 5: of Peripheral blood DNA methylation differences in twin pairs discordant for Alzheimer’s disease

description: Gene expression level of candidate genes in blood of non-twin subjects with Alzheimer’s disease in comparison to reference subjects. Gene expression levels of the candidate genes from Additional file 2c in GEO NCBI data from blood (GSE63061) of non-twin subjects with Alzheimer’s disease in comparison to reference subjects. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.9760505
title: Additional file 2: of Peripheral blood DNA methylation differences in twin pairs discordant for Alzheimer’s disease

description: Table of differentially methylated sites associated with Alzheimer’s disease. Differentially methylated sites in Alzheimer’s disease discordant a) monozygotic, b) dizygotic and in c) both twin pair groups and d) in brain of non-twin subjects with Alzheimer’s disease in comparison to reference subjects. (XLSX 415 kb)
DOI: 10.6084/m9.figshare.9760505.v1
title: Additional file 2: of Peripheral blood DNA methylation differences in twin pairs discordant for Alzheimer’s disease

description: Table of differentially methylated sites associated with Alzheimer’s disease. Differentially methylated sites in Alzheimer’s disease discordant a) monozygotic, b) dizygotic and in c) both twin pair groups and d) in brain of non-twin subjects with Alzheimer’s disease in comparison to reference subjects. (XLSX 415 kb)
DOI: 10.6084/m9.figshare.9760496
title: Additional file 1: of Peripheral blood DNA methylation differences in twin pairs discordant for Alzheimer’s disease

description: Table of APOE genotypes of the study individuals. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.9760496.v1
title: Additional file 1: of Peripheral blood DNA methylation differences in twin pairs discordant for Alzheimer’s disease

description: Table of APOE genotypes of the study individuals. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.9760412
title: Additional file 9: of Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird

description: Table S9. Significant GO terms associated with the time point main effect model gene clusters in ovary. Results based on human GO-database. (XLSX 489 kb)
DOI: 10.6084/m9.figshare.9760406
title: Additional file 7: of Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird

description: Table S7. Significant GO terms associated with the time point - temperature interaction model gene clusters in hypothalamus. Results based on human GO-database. (XLSX 120 kb)
DOI: 10.6084/m9.figshare.9760409
title: Additional file 8: of Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird

description: Table S8. Significant GO terms associated with the time point main effect model gene clusters in liver. Results based on human GO-database. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.9760412.v1
title: Additional file 9: of Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird

description: Table S9. Significant GO terms associated with the time point main effect model gene clusters in ovary. Results based on human GO-database. (XLSX 489 kb)
DOI: 10.6084/m9.figshare.9760397
title: Additional file 5: of Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird

description: Table S5. The Likelihood Ratio Test results of the nine models and annotations for the transcripts in ovary. Log2 fold changes are reported in the Log2FC â columns and P-values were adjusted for multiple comparisons using Benjamini-Hochberg method. Annotations were based on the Parus major annotation release 101 in NCBI. Clusters and modules from the hierarchical clustering analysis and WGCNA are also reported. In the time point main effect model the log2 fold change is between time points 3 vs 1. (XLSX 5693 kb)
DOI: 10.6084/m9.figshare.9760403
title: Additional file 6: of Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird

description: Table S6. Significant GO terms associated with the time point main effect model gene clusters in hypothalamus. Results based on human GO-database. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.9760394
title: Additional file 4: of Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird

description: Table S4. The Likelihood Ratio Test results of the nine models and annotations for the transcripts in liver. Log2 fold changes are reported in the Log2FC â columns and P-values were adjusted for multiple comparisons using Benjamini-Hochberg method. Annotations were based on the Parus major annotation release 101 in NCBI. Clusters and modules from the hierarchical clustering analysis and WGCNA are also reported. In the time point main effect model the log2 fold change is between time points 3 vs 1. (XLSX 4342 kb)
DOI: 10.6084/m9.figshare.9760406.v1
title: Additional file 7: of Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird

description: Table S7. Significant GO terms associated with the time point - temperature interaction model gene clusters in hypothalamus. Results based on human GO-database. (XLSX 120 kb)
DOI: 10.6084/m9.figshare.9760409.v1
title: Additional file 8: of Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird

description: Table S8. Significant GO terms associated with the time point main effect model gene clusters in liver. Results based on human GO-database. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.9760403.v1
title: Additional file 6: of Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird

description: Table S6. Significant GO terms associated with the time point main effect model gene clusters in hypothalamus. Results based on human GO-database. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.9760391
title: Additional file 3: of Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird

description: Table S3. The Likelihood Ratio Test results of the nine models and annotations for the transcripts in hypothalamus. Log2 fold changes are reported in the Log2FC â columns and P-values were adjusted for multiple comparisons using Benjamini-Hochberg method. Annotations were based on the Parus major annotation release 101 in NCBI. Clusters and modules from the hierarchical clustering analysis and WGCNA are also reported. In the time point main effect model the log2 fold change is between time points 3 vs 1. (XLSX 4991 kb)
DOI: 10.6084/m9.figshare.9760397.v1
title: Additional file 5: of Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird

description: Table S5. The Likelihood Ratio Test results of the nine models and annotations for the transcripts in ovary. Log2 fold changes are reported in the Log2FC â columns and P-values were adjusted for multiple comparisons using Benjamini-Hochberg method. Annotations were based on the Parus major annotation release 101 in NCBI. Clusters and modules from the hierarchical clustering analysis and WGCNA are also reported. In the time point main effect model the log2 fold change is between time points 3 vs 1. (XLSX 5693 kb)
DOI: 10.6084/m9.figshare.9760391.v1
title: Additional file 3: of Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird

description: Table S3. The Likelihood Ratio Test results of the nine models and annotations for the transcripts in hypothalamus. Log2 fold changes are reported in the Log2FC â columns and P-values were adjusted for multiple comparisons using Benjamini-Hochberg method. Annotations were based on the Parus major annotation release 101 in NCBI. Clusters and modules from the hierarchical clustering analysis and WGCNA are also reported. In the time point main effect model the log2 fold change is between time points 3 vs 1. (XLSX 4991 kb)
DOI: 10.6084/m9.figshare.9760394.v1
title: Additional file 4: of Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird

description: Table S4. The Likelihood Ratio Test results of the nine models and annotations for the transcripts in liver. Log2 fold changes are reported in the Log2FC â columns and P-values were adjusted for multiple comparisons using Benjamini-Hochberg method. Annotations were based on the Parus major annotation release 101 in NCBI. Clusters and modules from the hierarchical clustering analysis and WGCNA are also reported. In the time point main effect model the log2 fold change is between time points 3 vs 1. (XLSX 4342 kb)
DOI: 10.6084/m9.figshare.9760379
title: Additional file 2: of Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird

description: Table S2. The number of genes showing significant differential expression in the time point comparisons and interaction models for the three tissues. Time1 is comparison of time point 1 to time point 2 and 3, Time2 is comparison of time point 2 to time point 1 and 3, Time3 is comparison of time point 3 to time point 1 and 2. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.9760379.v1
title: Additional file 2: of Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird

description: Table S2. The number of genes showing significant differential expression in the time point comparisons and interaction models for the three tissues. Time1 is comparison of time point 1 to time point 2 and 3, Time2 is comparison of time point 2 to time point 1 and 3, Time3 is comparison of time point 3 to time point 1 and 2. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.9760343
title: Additional file 2: of Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7Â years in a single center

description: Table S1. Accession numbers, isolation site, study month of isolation, detected acquired resistance genes, antimicrobial resistance phenotypes, of Klebsiella pneumoniae in this study. Table S2. Accession numbers and metadata for the global K. pneumoniae collection [7]. Table S3. Accession numbers and metadata for UK K. pneumoniae and E. cloacae [14, 16]. Table S4. Accession numbers, isolation site, study month of isolation, detected acquired resistance genes, antimicrobial resistance phenotypes, of Enterobacter cloacae in this study. Table S5. Accession numbers and metadata for the global E. cloacae collection [11]. (XLSX 176 kb)
DOI: 10.6084/m9.figshare.9760343.v1
title: Additional file 2: of Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7Â years in a single center

description: Table S1. Accession numbers, isolation site, study month of isolation, detected acquired resistance genes, antimicrobial resistance phenotypes, of Klebsiella pneumoniae in this study. Table S2. Accession numbers and metadata for the global K. pneumoniae collection [7]. Table S3. Accession numbers and metadata for UK K. pneumoniae and E. cloacae [14, 16]. Table S4. Accession numbers, isolation site, study month of isolation, detected acquired resistance genes, antimicrobial resistance phenotypes, of Enterobacter cloacae in this study. Table S5. Accession numbers and metadata for the global E. cloacae collection [11]. (XLSX 176 kb)
DOI: 10.6084/m9.figshare.9760331
title: Additional file 1: of Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird

description: Table S1. Summary of the sequencing and alignment of the three tissue types and 12 pools. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.9760331.v1
title: Additional file 1: of Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird

description: Table S1. Summary of the sequencing and alignment of the three tissue types and 12 pools. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.9760304
title: Additional file 16: of Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird

description: Table S16. List of highly connected module genes in ovary that have at least one connection degree in the PPI network. (XLSX 100 kb)
DOI: 10.6084/m9.figshare.9760313
title: Additional file 17: of Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird

description: Table S17. Significant GO terms associated with the real hub genes. Results based on human GO-database. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.9760313.v1
title: Additional file 17: of Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird

description: Table S17. Significant GO terms associated with the real hub genes. Results based on human GO-database. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.9760295
title: Additional file 15: of Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird

description: Table S15. List of highly connected module genes in liver that have at least one connection degree in the PPI network. (XLSX 13 kb)