cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22609675
title: Additional file 13 of Methylation in MAD1L1 is associated with the severity of suicide attempt and phenotypes of depression

description: Additional file 13: Table S5. 5.1 Genetic variants used for mQTL analysis. The column headers correspond to the IMPUTE2 output. 5.2 The mQTL analysis in the adolescent screening sample. The statistics were calculated in the package MatrixEQTL. P values were adjusted with false discovery rate method. 5.3 Statistics of the candidate CpG sites in screening. Depr. SNP placement column indicates a relative placement of a MAD1L1 depression-related SNP in the CpG-specific mQTL table (sorted by FDR). Depr. SNP name column indicates the name of the MAD1L1 depression-related SNP in the column with placement. Top 10 Variants column shows the Top 10 variants associated with a CpG in the CpG-specific mQTL table (sorted by FDR). LD with depr.SNPs column shows if the SNP in the Top 10 list is in LD with at least one MAD1L1 depression-related SNP. 5.4 Statistics of the MAD1L1 depression-related SNPs in screening. The Top CpG placement column shows a relative placement of a candidate CpG site in the SNP-specific mQTL table (sorted by FDR). The CpG name column shows the name of the CpG associated with its placement in the previous column. 5.5 The mQTL analysis in the adolescent recall sample. The statistics were calculated in the package MatrixEQTL. P values were adjusted with the false discovery rate method. 5.6 Statistics of the candidate CpG sites in the recall. Depr. SNP placement column indicates a relative placement of a MAD1L1 depression-related SNP in the CpG-specific mQTL table (sorted by FDR). Depr. SNP name column indicates the name of the MAD1L1 depression-related SNP in the column with placement. Top 10 Variants column shows the Top 10 variants associated with a CpG in the CpG-specific mQTL table (sorted by FDR). LD with depr.SNPs column shows if the SNP in the Top 10 list is in LD with at least one MAD1L1 depression-related SNP. 5.7 Statistics of the MAD1L1 depression-related SNPs in the recall. The Top CpG placement column shows a relative placement of a candidate CpG site in the SNP-specific mQTL table (sorted by FDR). The CpG name column shows the name of the CpG associated with its placement in the previous column.
DOI: 10.6084/m9.figshare.22609675.v1
title: Additional file 13 of Methylation in MAD1L1 is associated with the severity of suicide attempt and phenotypes of depression

description: Additional file 13: Table S5. 5.1 Genetic variants used for mQTL analysis. The column headers correspond to the IMPUTE2 output. 5.2 The mQTL analysis in the adolescent screening sample. The statistics were calculated in the package MatrixEQTL. P values were adjusted with false discovery rate method. 5.3 Statistics of the candidate CpG sites in screening. Depr. SNP placement column indicates a relative placement of a MAD1L1 depression-related SNP in the CpG-specific mQTL table (sorted by FDR). Depr. SNP name column indicates the name of the MAD1L1 depression-related SNP in the column with placement. Top 10 Variants column shows the Top 10 variants associated with a CpG in the CpG-specific mQTL table (sorted by FDR). LD with depr.SNPs column shows if the SNP in the Top 10 list is in LD with at least one MAD1L1 depression-related SNP. 5.4 Statistics of the MAD1L1 depression-related SNPs in screening. The Top CpG placement column shows a relative placement of a candidate CpG site in the SNP-specific mQTL table (sorted by FDR). The CpG name column shows the name of the CpG associated with its placement in the previous column. 5.5 The mQTL analysis in the adolescent recall sample. The statistics were calculated in the package MatrixEQTL. P values were adjusted with the false discovery rate method. 5.6 Statistics of the candidate CpG sites in the recall. Depr. SNP placement column indicates a relative placement of a MAD1L1 depression-related SNP in the CpG-specific mQTL table (sorted by FDR). Depr. SNP name column indicates the name of the MAD1L1 depression-related SNP in the column with placement. Top 10 Variants column shows the Top 10 variants associated with a CpG in the CpG-specific mQTL table (sorted by FDR). LD with depr.SNPs column shows if the SNP in the Top 10 list is in LD with at least one MAD1L1 depression-related SNP. 5.7 Statistics of the MAD1L1 depression-related SNPs in the recall. The Top CpG placement column shows a relative placement of a candidate CpG site in the SNP-specific mQTL table (sorted by FDR). The CpG name column shows the name of the CpG associated with its placement in the previous column.
DOI: 10.6084/m9.figshare.22609678
title: Additional file 14 of Methylation in MAD1L1 is associated with the severity of suicide attempt and phenotypes of depression

description: Additional file 14: Table S6. Coefficients for binary logistic regression models, where depression diagnosis is a dependent outcome variable depending on methylation at cg02825527 (M value) or cg18302629 (M value) in glial cells adjusted for confounders. Statistics for the models were calculated using a native implementation of the binary logistic regression model in the R programming language.
DOI: 10.6084/m9.figshare.22609678.v1
title: Additional file 14 of Methylation in MAD1L1 is associated with the severity of suicide attempt and phenotypes of depression

description: Additional file 14: Table S6. Coefficients for binary logistic regression models, where depression diagnosis is a dependent outcome variable depending on methylation at cg02825527 (M value) or cg18302629 (M value) in glial cells adjusted for confounders. Statistics for the models were calculated using a native implementation of the binary logistic regression model in the R programming language.
DOI: 10.15156/bio/sh1138066.09fu
title: SH1138066.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.6084/m9.figshare.22609681
title: Additional file 15 of Methylation in MAD1L1 is associated with the severity of suicide attempt and phenotypes of depression

description: Additional file 15: Table S7. Results for gene ontology analysis for MAD1L interacting partners based on the STRING database data. For further information, please refer to the STRING database. Analysis was conducted with default settings. Abbreviations: TFAMP1, transcription factor A, mitochondrial pseudogene 1; ELFN1, extracellular leucine-rich repeat and fibronectin type III domain containing 1; ELFN1-AS1, ELFN1 antisense RNA 1; MAD1L1, mitotic arrest deficient 1 like 1; SNORA114, small nucleolar RNA, H/ACA Box 114; LOC105375303, homo sapiens uncharacterized LOC105375303; MIR4655, microRNA 4655; MRM2, mitochondrial RRNA methyltransferase 2; NUDT1, nudix hydrolase 1; MIR6836, microRNA 6836; SNX8, sorting nexin 8; EIF3B, eukaryotic translation initiation factor 3 subunit B; CHST12, carbohydrate sulfotransferase 12; GRIFIN, galectin-related inter-fiber protein; PAX5, paired box 5; EP300, E1A binding protein p300; SP4, sp4 transcription factor; BRAG, brain angular gyrus; BRAC, brain anterior caudate; BRCG, brain cingulate gyrus; BRGM, brain germinal matrix; BRHM, brain hippocampus middle; BITL, brain inferior temporal lobe; BDPC, brain dorsolateral prefrontal cortex; BRSN, brain substantia nigra.
DOI: 10.6084/m9.figshare.22609681.v1
title: Additional file 15 of Methylation in MAD1L1 is associated with the severity of suicide attempt and phenotypes of depression

description: Additional file 15: Table S7. Results for gene ontology analysis for MAD1L interacting partners based on the STRING database data. For further information, please refer to the STRING database. Analysis was conducted with default settings. Abbreviations: TFAMP1, transcription factor A, mitochondrial pseudogene 1; ELFN1, extracellular leucine-rich repeat and fibronectin type III domain containing 1; ELFN1-AS1, ELFN1 antisense RNA 1; MAD1L1, mitotic arrest deficient 1 like 1; SNORA114, small nucleolar RNA, H/ACA Box 114; LOC105375303, homo sapiens uncharacterized LOC105375303; MIR4655, microRNA 4655; MRM2, mitochondrial RRNA methyltransferase 2; NUDT1, nudix hydrolase 1; MIR6836, microRNA 6836; SNX8, sorting nexin 8; EIF3B, eukaryotic translation initiation factor 3 subunit B; CHST12, carbohydrate sulfotransferase 12; GRIFIN, galectin-related inter-fiber protein; PAX5, paired box 5; EP300, E1A binding protein p300; SP4, sp4 transcription factor; BRAG, brain angular gyrus; BRAC, brain anterior caudate; BRCG, brain cingulate gyrus; BRGM, brain germinal matrix; BRHM, brain hippocampus middle; BITL, brain inferior temporal lobe; BDPC, brain dorsolateral prefrontal cortex; BRSN, brain substantia nigra.
DOI: 10.6084/m9.figshare.22609684
title: Additional file 16 of Methylation in MAD1L1 is associated with the severity of suicide attempt and phenotypes of depression

description: Additional file 16: Table S8. Coefficients for candidate CpGs in the transcriptome–methylation association analysis in GSE49065. The expression of MAD1L1 was regressed against a candidate CpG site and age. Each row shows coefficients and estimates with statistics obtained from individual linear models. The models were implemented in R, using the standard implementation of linear regression. Confidence intervals were calculated with the R package stats.
DOI: 10.6084/m9.figshare.22609684.v1
title: Additional file 16 of Methylation in MAD1L1 is associated with the severity of suicide attempt and phenotypes of depression

description: Additional file 16: Table S8. Coefficients for candidate CpGs in the transcriptome–methylation association analysis in GSE49065. The expression of MAD1L1 was regressed against a candidate CpG site and age. Each row shows coefficients and estimates with statistics obtained from individual linear models. The models were implemented in R, using the standard implementation of linear regression. Confidence intervals were calculated with the R package stats.
DOI: 10.6084/m9.figshare.22609687.v1
title: Additional file 17 of Methylation in MAD1L1 is associated with the severity of suicide attempt and phenotypes of depression

description: Additional file 17: Table S9. 9.1 The source publications of stress-related CpG sites. 9.2 CpG–CpG associations in the SKI. The models were calculated, using the standard implementation of linear regression. The covariates are specific for every cohort (see methods). The p values were adjusted with the false discovery rate method. The Stress CpG genes were obtained from Illumina annotation files for HumanMethylation450 and MethylationEPIC arrays. 9.3 CpG–CpG associations in the Grady sample. 9.4 CpG–CpG associations in the E-GEOD-41826 (glia) sample. 9.5 CpG–CpG associations in the GSE88890 (BA11) sample. 9.6 CpG–CpG associations in the GSE88890 (BA25) sample. 9.7 Pooled CpG–CpG associations that were nominally significant and detected more than once. 9.8 Pooled CpG–CpG associations that were nominally significant, were detected more than once, and had matching directions for beta coefficients.
DOI: 10.6084/m9.figshare.22609690
title: Additional file 18 of Methylation in MAD1L1 is associated with the severity of suicide attempt and phenotypes of depression

description: Additional file 18: Table S10.Color codes for chromatin states tracks in Fig. 5.
DOI: 10.15156/bio/sh1138067.09fu
title: SH1138067.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.6084/m9.figshare.22609687
title: Additional file 17 of Methylation in MAD1L1 is associated with the severity of suicide attempt and phenotypes of depression

description: Additional file 17: Table S9. 9.1 The source publications of stress-related CpG sites. 9.2 CpG–CpG associations in the SKI. The models were calculated, using the standard implementation of linear regression. The covariates are specific for every cohort (see methods). The p values were adjusted with the false discovery rate method. The Stress CpG genes were obtained from Illumina annotation files for HumanMethylation450 and MethylationEPIC arrays. 9.3 CpG–CpG associations in the Grady sample. 9.4 CpG–CpG associations in the E-GEOD-41826 (glia) sample. 9.5 CpG–CpG associations in the GSE88890 (BA11) sample. 9.6 CpG–CpG associations in the GSE88890 (BA25) sample. 9.7 Pooled CpG–CpG associations that were nominally significant and detected more than once. 9.8 Pooled CpG–CpG associations that were nominally significant, were detected more than once, and had matching directions for beta coefficients.
DOI: 10.6084/m9.figshare.22609690.v1
title: Additional file 18 of Methylation in MAD1L1 is associated with the severity of suicide attempt and phenotypes of depression

description: Additional file 18: Table S10.Color codes for chromatin states tracks in Fig. 5.
DOI: 10.15156/bio/sh1138068.09fu
title: SH1138068.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1138069.09fu
title: SH1138069.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1138070.09fu
title: SH1138070.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1138071.09fu
title: SH1138071.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1138072.09fu
title: SH1138072.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.6084/m9.figshare.22609702
title: Additional file 1 of Application of probabilistic methods to address variability and uncertainty in estimating risks for non-cancer health effects

description: Additional file 1. Dataset supporting analytical conclusion.
DOI: 10.6084/m9.figshare.22609702.v1
title: Additional file 1 of Application of probabilistic methods to address variability and uncertainty in estimating risks for non-cancer health effects

description: Additional file 1. Dataset supporting analytical conclusion.
DOI: 10.15156/bio/sh1138073.09fu
title: SH1138073.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1138074.09fu
title: SH1138074.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.