cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3908473_d1
title: Additional file 10: Table S7. of The dynamics of smoking-related disturbed methylation: a two time-point study of methylation change in smokers, non-smokers and former smokers

description: All results of the analysis of longitudinal effect of continued smoking. The longitudinal regression coefficients represent the rate of change of methylation M-value per year from baseline to follow-up for continued smokers relative to never smokers. The cross-sectional coefficients represent the methylation M-value difference to never smokers at baseline. Also presented are the results for the time coefficient from the model. “Chromosome” is the chromosome of the CpG site and “Gene or region” is based on the annotation file provided by Illumina (HumanMethylation450 v1.2 Manifest File). (XLS 179 kb)
DOI: 10.6084/m9.figshare.c.3908443_d4.v1
title: Additional file 4: Table S3. of Genome sequencing of 39 Akkermansia muciniphila isolates reveals its population structure, genomic and functional diverisity, and global distribution in mammalian gut microbiotas

description: Candidate horizontal gene transfer events identified from A. muciniphila genomes. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3908443_d4
title: Additional file 4: Table S3. of Genome sequencing of 39 Akkermansia muciniphila isolates reveals its population structure, genomic and functional diverisity, and global distribution in mammalian gut microbiotas

description: Candidate horizontal gene transfer events identified from A. muciniphila genomes. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3908443_d3
title: Additional file 3: Table S2. of Genome sequencing of 39 Akkermansia muciniphila isolates reveals its population structure, genomic and functional diverisity, and global distribution in mammalian gut microbiotas

description: Genome information of the 106 constructed A. muciniphila MAGs which are assembled from human and other mammalian gut microbiotas. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3908443_d3.v1
title: Additional file 3: Table S2. of Genome sequencing of 39 Akkermansia muciniphila isolates reveals its population structure, genomic and functional diverisity, and global distribution in mammalian gut microbiotas

description: Genome information of the 106 constructed A. muciniphila MAGs which are assembled from human and other mammalian gut microbiotas. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3908443_d2.v1
title: Additional file 2: Figure S1. of Genome sequencing of 39 Akkermansia muciniphila isolates reveals its population structure, genomic and functional diverisity, and global distribution in mammalian gut microbiotas

description: Pangenome â  opennessâ   of A. muciniphila. Figure S2. Principal components analysis shows the clustering of A. muciniphila isolates. Figure S3. Functional composition of the A. muciniphila pangenome. Figure S4. Principal components analysis on CAZymes profiles of A. muciniphila isolates. Figure S5. Relative abundance of A. muciniphila phylogroups in 368 Chinese gut microbiome samples. Figure S6. Gene flow and recombination events in A. muciniphila phylogroups. Figure S7. Loss and gain of orthologous groups during A. muciniphila evolution. (DOCX 682 kb)
DOI: 10.6084/m9.figshare.c.3908443_d2
title: Additional file 2: Figure S1. of Genome sequencing of 39 Akkermansia muciniphila isolates reveals its population structure, genomic and functional diverisity, and global distribution in mammalian gut microbiotas

description: Pangenome â  opennessâ   of A. muciniphila. Figure S2. Principal components analysis shows the clustering of A. muciniphila isolates. Figure S3. Functional composition of the A. muciniphila pangenome. Figure S4. Principal components analysis on CAZymes profiles of A. muciniphila isolates. Figure S5. Relative abundance of A. muciniphila phylogroups in 368 Chinese gut microbiome samples. Figure S6. Gene flow and recombination events in A. muciniphila phylogroups. Figure S7. Loss and gain of orthologous groups during A. muciniphila evolution. (DOCX 682 kb)
DOI: 10.6084/m9.figshare.c.3907213_d8
title: Additional file 8: Table S7. of Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS

description: Phenotypes analyzed in this study. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.c.3907213_d8.v1
title: Additional file 8: Table S7. of Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS

description: Phenotypes analyzed in this study. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.c.3907213_d7.v1
title: Additional file 7: Table S6. of Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS

description: Comparison of eQTL analyses for 13 traits and eRD genes with different GWAS results. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.c.3907213_d6.v1
title: Additional file 6: Table S5. of Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS

description: Characterization of five genes associated with DTA identified via eRD-GWAS with highest model frequencies. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.c.3907213_d7
title: Additional file 7: Table S6. of Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS

description: Comparison of eQTL analyses for 13 traits and eRD genes with different GWAS results. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.c.3907213_d6
title: Additional file 6: Table S5. of Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS

description: Characterization of five genes associated with DTA identified via eRD-GWAS with highest model frequencies. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.c.3907213_d5
title: Additional file 5: Table S4. of Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS

description: Accuracy of associations from SNP-BayesB and eRD-GWAS as estimated via tenfold cross-validation. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.c.3907213_d5.v1
title: Additional file 5: Table S4. of Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS

description: Accuracy of associations from SNP-BayesB and eRD-GWAS as estimated via tenfold cross-validation. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.c.3907213_d4.v1
title: Additional file 4: Table S3 of Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS

description: Enrichment test for TFs among nine different gene categories. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.c.3907213_d3.v1
title: Additional file 3: Table S2. of Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS

description: Functional enrichment and GO term enrichment tests. a Functional enrichment tests of genes that exhibit extreme expression variation across genotypes. b GO term enrichment tests of genes that exhibit extreme expression variation across genotypes. c Functional enrichment tests of genes that exhibit extreme expression variation across tissues. d GO term enrichment tests of genes that exhibit extreme expression variation across tissues. e Functional enrichment tests of genes that exhibit extreme expression variation across genotypes and tissues. f GO term enrichment tests of genes that exhibit extreme expression variation across genotypes and tissues. (XLSX 61 kb)
DOI: 10.6084/m9.figshare.c.3907213_d4
title: Additional file 4: Table S3 of Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS

description: Enrichment test for TFs among nine different gene categories. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.c.3907213_d3
title: Additional file 3: Table S2. of Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS

description: Functional enrichment and GO term enrichment tests. a Functional enrichment tests of genes that exhibit extreme expression variation across genotypes. b GO term enrichment tests of genes that exhibit extreme expression variation across genotypes. c Functional enrichment tests of genes that exhibit extreme expression variation across tissues. d GO term enrichment tests of genes that exhibit extreme expression variation across tissues. e Functional enrichment tests of genes that exhibit extreme expression variation across genotypes and tissues. f GO term enrichment tests of genes that exhibit extreme expression variation across genotypes and tissues. (XLSX 61 kb)
DOI: 10.6084/m9.figshare.c.3907213_d1.v1
title: Additional file 1: Table S1. of Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS

description: Summary of RNA-seq processing. (XLSX 64 kb)
DOI: 10.6084/m9.figshare.c.3907213_d1
title: Additional file 1: Table S1. of Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS

description: Summary of RNA-seq processing. (XLSX 64 kb)
DOI: 10.6084/m9.figshare.c.3907117_d2.v1
title: Additional file 1: Table S1. of Reprogramming of stromal fibroblasts by SNAI2 contributes to tumor desmoplasia and ovarian cancer progression

description: Listing of the Genes included in the signatures used from MSigDB or published literatures. Listing of the detailed genes included in the aforementioned signatures, all of which used for gene set enrichment analysis (GSEA) or single sample GSEA (ssGSEA) analysis were extracted either from MSigDB ( http://software.broadinstitute.org/gsea/msigdb/index.jsp ) or published literatures. Table S2. Clinicopathological characteristics of our enrolled ovarian cancer patients analysed by immunohistochemistry dichotomised by SNAI2 protein expression levels in carcinoma cells or tumor stromal fibroblasts. The associations between SNAI2 expression level and variant clinicopathological characteristics of ovarian cancer patients were analysed with χ2 test (Fisher’s exact test). Table S3. Univariate and multivariate Cox regression analysis of SNAI2 expression level and overall survival of ovarian cancer patients. The prognostic significance of SNAI2 expression and other clinicopathological variables was first assessed by univariate Cox, followed by multivariate Cox regression analysis regarding to the overall survival time in a cohort of 160 ovarian cancer patients. Table S4. Genes significantly positively correlated with SNAI2 expression in the ‘mesenchymal’ subtype of ovarian TCGA dataset. List of the 111 genes that were calculated significantly positively related with SNAI2 expression in the ‘mesenchymal’ subtype of ovarian TCGA profile, using the R2 Genomic Analysis and Visualization Platform ( http://r2.amc.nl ). Genes with a Pearson correlation greater than or equal to 0.35 and a p value less than 1% were selected from each cohort. Table S5. Genes significantly positively correlated with Snai2 expression in the ‘C1’ subtype of Tothill’s dataset (GSE9891). List of the 288 genes that were calculated strongly positively correlated with SNAI2 expression in the ‘C1’ subtype of Tothill’s dataset (GSE9891), using the R2 Genomic Analysis and Visualization Platform ( http://r2.amc.nl ). Genes with a Pearson correlation greater than or equal to 0.4 and a p value less than 1% were selected from each cohort. Table S6. Listing of the 77 Genes included in the calculated ‘Snai2 mesenchymal signature’ of ovarian cancer. Designation of our defined ‘Snai2 mesenchymal signature’ and listing of the 77 genes included in the signature, through Overlapping analysis of the gene set that were calculated positively correlated with SNAI2 expression in the ‘mesenchymal’ subtype of ovarian TCGA profile and the ‘C1’ subtype of Tothill’s dataset (GSE9891). (XLSX 120 kb)
DOI: 10.6084/m9.figshare.c.3907117_d2
title: Additional file 1: Table S1. of Reprogramming of stromal fibroblasts by SNAI2 contributes to tumor desmoplasia and ovarian cancer progression

description: Listing of the Genes included in the signatures used from MSigDB or published literatures. Listing of the detailed genes included in the aforementioned signatures, all of which used for gene set enrichment analysis (GSEA) or single sample GSEA (ssGSEA) analysis were extracted either from MSigDB ( http://software.broadinstitute.org/gsea/msigdb/index.jsp ) or published literatures. Table S2. Clinicopathological characteristics of our enrolled ovarian cancer patients analysed by immunohistochemistry dichotomised by SNAI2 protein expression levels in carcinoma cells or tumor stromal fibroblasts. The associations between SNAI2 expression level and variant clinicopathological characteristics of ovarian cancer patients were analysed with χ2 test (Fisher’s exact test). Table S3. Univariate and multivariate Cox regression analysis of SNAI2 expression level and overall survival of ovarian cancer patients. The prognostic significance of SNAI2 expression and other clinicopathological variables was first assessed by univariate Cox, followed by multivariate Cox regression analysis regarding to the overall survival time in a cohort of 160 ovarian cancer patients. Table S4. Genes significantly positively correlated with SNAI2 expression in the ‘mesenchymal’ subtype of ovarian TCGA dataset. List of the 111 genes that were calculated significantly positively related with SNAI2 expression in the ‘mesenchymal’ subtype of ovarian TCGA profile, using the R2 Genomic Analysis and Visualization Platform ( http://r2.amc.nl ). Genes with a Pearson correlation greater than or equal to 0.35 and a p value less than 1% were selected from each cohort. Table S5. Genes significantly positively correlated with Snai2 expression in the ‘C1’ subtype of Tothill’s dataset (GSE9891). List of the 288 genes that were calculated strongly positively correlated with SNAI2 expression in the ‘C1’ subtype of Tothill’s dataset (GSE9891), using the R2 Genomic Analysis and Visualization Platform ( http://r2.amc.nl ). Genes with a Pearson correlation greater than or equal to 0.4 and a p value less than 1% were selected from each cohort. Table S6. Listing of the 77 Genes included in the calculated ‘Snai2 mesenchymal signature’ of ovarian cancer. Designation of our defined ‘Snai2 mesenchymal signature’ and listing of the 77 genes included in the signature, through Overlapping analysis of the gene set that were calculated positively correlated with SNAI2 expression in the ‘mesenchymal’ subtype of ovarian TCGA profile and the ‘C1’ subtype of Tothill’s dataset (GSE9891). (XLSX 120 kb)
DOI: 10.6084/m9.figshare.c.3906022_d1
title: MOESM1 of Molecular and virulence characterization of highly prevalent Streptococcus agalactiae circulated in bovine dairy herds

description: Additional file 1. S. agalactiae strains used in this study.
DOI: 10.6084/m9.figshare.c.3906022_d1.v1
title: MOESM1 of Molecular and virulence characterization of highly prevalent Streptococcus agalactiae circulated in bovine dairy herds

description: Additional file 1. S. agalactiae strains used in this study.
DOI: 10.6084/m9.figshare.c.3905956_d4.v1
title: Additional file 4: of An uncertain model-based approach for identifying dynamic protein complexes in uncertain protein-protein interaction networks

description: STRING PPI data. (TXT 3624Â kb)
DOI: 10.6084/m9.figshare.c.3905956_d4
title: Additional file 4: of An uncertain model-based approach for identifying dynamic protein complexes in uncertain protein-protein interaction networks

description: STRING PPI data. (TXT 3624Â kb)
DOI: 10.6084/m9.figshare.c.3905956_d3.v1
title: Additional file 3: of An uncertain model-based approach for identifying dynamic protein complexes in uncertain protein-protein interaction networks

description: MIPS PPI data. (TXT 184Â kb)
DOI: 10.6084/m9.figshare.c.3905971_d1.v1
title: MOESM1 of Prediction of microbeâ  disease association from the integration of neighbor and graph with collaborative recommendation model

description: Additional file 1: Table S1. We publicly released the predicted of microbes for each disease, which may offer valuable information and clues for biological experiments.
DOI: 10.6084/m9.figshare.c.3905956_d3
title: Additional file 3: of An uncertain model-based approach for identifying dynamic protein complexes in uncertain protein-protein interaction networks

description: MIPS PPI data. (TXT 184Â kb)
DOI: 10.6084/m9.figshare.c.3905857_d11.v1
title: Additional file 6: Table S4. of Genome-wide trait-trait dynamics correlation study dissects the gene regulation pattern in maize kernels

description: Annotations of the top 50 triplets with the highest LA scores. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.c.3905857_d10.v1
title: Additional file 5: Table S3. of Genome-wide trait-trait dynamics correlation study dissects the gene regulation pattern in maize kernels

description: Quantile-based permutation thresholds for P values, LA scores and FDRs. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3905857_d11
title: Additional file 6: Table S4. of Genome-wide trait-trait dynamics correlation study dissects the gene regulation pattern in maize kernels

description: Annotations of the top 50 triplets with the highest LA scores. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.c.3905857_d10
title: Additional file 5: Table S3. of Genome-wide trait-trait dynamics correlation study dissects the gene regulation pattern in maize kernels

description: Quantile-based permutation thresholds for P values, LA scores and FDRs. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3905857_d8.v1
title: Additional file 3: Table S2. of Genome-wide trait-trait dynamics correlation study dissects the gene regulation pattern in maize kernels

description: The number of LAPs with expression mediated by the LA-scouting leaders (P values &lt;1.00 × 10−5). (XLSX 844 kb)
DOI: 10.6084/m9.figshare.c.3905857_d8
title: Additional file 3: Table S2. of Genome-wide trait-trait dynamics correlation study dissects the gene regulation pattern in maize kernels

description: The number of LAPs with expression mediated by the LA-scouting leaders (P values &lt;1.00 × 10−5). (XLSX 844 kb)
DOI: 10.6084/m9.figshare.c.3905857_d6.v1
title: Additional file 1: Table S1. of Genome-wide trait-trait dynamics correlation study dissects the gene regulation pattern in maize kernels

description: The permutation test for positive and negative LA thresholds. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3905857_d5.v1
title: Additional file 14: Table S7. of Genome-wide trait-trait dynamics correlation study dissects the gene regulation pattern in maize kernels

description: The LA results for PSY1, lcyE, and crtRB1 in the carotene biosynthetic pathway. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3905857_d6
title: Additional file 1: Table S1. of Genome-wide trait-trait dynamics correlation study dissects the gene regulation pattern in maize kernels

description: The permutation test for positive and negative LA thresholds. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3905857_d5
title: Additional file 14: Table S7. of Genome-wide trait-trait dynamics correlation study dissects the gene regulation pattern in maize kernels

description: The LA results for PSY1, lcyE, and crtRB1 in the carotene biosynthetic pathway. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3905857_d4.v1
title: Additional file 13: Table S6. of Genome-wide trait-trait dynamics correlation study dissects the gene regulation pattern in maize kernels

description: The LA results for ZÂ =Â GRMZM5G858880 with significant LA scores in the oil biosynthetic pathway. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3905857_d4
title: Additional file 13: Table S6. of Genome-wide trait-trait dynamics correlation study dissects the gene regulation pattern in maize kernels

description: The LA results for ZÂ =Â GRMZM5G858880 with significant LA scores in the oil biosynthetic pathway. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3905857_d2
title: Additional file 11: Table S5. of Genome-wide trait-trait dynamics correlation study dissects the gene regulation pattern in maize kernels

description: The LA results for XÂ =Â GRMZM2G122767 with significant LA scores in oil biosynthesis. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3905857_d2.v1
title: Additional file 11: Table S5. of Genome-wide trait-trait dynamics correlation study dissects the gene regulation pattern in maize kernels

description: The LA results for XÂ =Â GRMZM2G122767 with significant LA scores in oil biosynthesis. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3904507_d17.v1
title: Additional file 4: of miRNAs involved in the development and differentiation of fertile and sterile flowers in Viburnum macrocephalum f. keteleeri

description: Non-coding RNAs among the sRNAs. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3904507_d16.v1
title: Additional file 3: of miRNAs involved in the development and differentiation of fertile and sterile flowers in Viburnum macrocephalum f. keteleeri

description: Summary of mapped sRNAs. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3904507_d17
title: Additional file 4: of miRNAs involved in the development and differentiation of fertile and sterile flowers in Viburnum macrocephalum f. keteleeri

description: Non-coding RNAs among the sRNAs. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3904507_d16
title: Additional file 3: of miRNAs involved in the development and differentiation of fertile and sterile flowers in Viburnum macrocephalum f. keteleeri

description: Summary of mapped sRNAs. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3904537_d1
title: Additional file 1: of Infection by and genotype characteristics of Enterocytozoon bieneusi in HIV/AIDS patients from Guangxi Zhuang autonomous region, China

description: The data of unique nucleotide sequences. (TXT 1 kb)
DOI: 10.6084/m9.figshare.c.3904507_d15.v1
title: Additional file 2: of miRNAs involved in the development and differentiation of fertile and sterile flowers in Viburnum macrocephalum f. keteleeri

description: Summary of clean 18â  30Â nt sRNAs. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3904537_d1.v1
title: Additional file 1: of Infection by and genotype characteristics of Enterocytozoon bieneusi in HIV/AIDS patients from Guangxi Zhuang autonomous region, China

description: The data of unique nucleotide sequences. (TXT 1 kb)
DOI: 10.6084/m9.figshare.c.3904507_d15
title: Additional file 2: of miRNAs involved in the development and differentiation of fertile and sterile flowers in Viburnum macrocephalum f. keteleeri

description: Summary of clean 18â  30Â nt sRNAs. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3904507_d11
title: Additional file 1: of miRNAs involved in the development and differentiation of fertile and sterile flowers in Viburnum macrocephalum f. keteleeri

description: All the primers used in this study, including 29 pairs of primers for precursor sequences,10 pairs of primers for quantitative real-time PCR of precursor sequences, and 6 pairs of primers for quantitative real-time PCR of target genes. (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.c.3904507_d10.v1
title: Additional file 19: of miRNAs involved in the development and differentiation of fertile and sterile flowers in Viburnum macrocephalum f. keteleeri

description: Differentially expressed genes with gene description. (XLSX 606Â kb)
DOI: 10.6084/m9.figshare.c.3904507_d9.v1
title: Additional file 18: of miRNAs involved in the development and differentiation of fertile and sterile flowers in Viburnum macrocephalum f. keteleeri

description: Down-regulated miRNAs in VMS and related mRNA. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3904507_d10
title: Additional file 19: of miRNAs involved in the development and differentiation of fertile and sterile flowers in Viburnum macrocephalum f. keteleeri

description: Differentially expressed genes with gene description. (XLSX 606Â kb)