cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6131672.v1
title: Additional file 1: of iSeg: an efficient algorithm for segmentation of genomic and epigenomic data

description: The zipped supplementary file submitted with this manuscript contains Coriell (Snijders et al.) profiles, BACarray profiles, and simulated data files. (ZIP 1970kb)
DOI: 10.6084/m9.figshare.6131675
title: Additional file 2: of Comparative transcriptome analysis of hypothalamus-regulated feed intake induced by exogenous visfatin in chicks

description: Table S2. DEGs in the three comparisons. (XLSX 102Â kb)
DOI: 10.6084/m9.figshare.6131675.v1
title: Additional file 2: of Comparative transcriptome analysis of hypothalamus-regulated feed intake induced by exogenous visfatin in chicks

description: Table S2. DEGs in the three comparisons. (XLSX 102Â kb)
DOI: 10.6084/m9.figshare.6131678
title: Additional file 1: of A comparative genomics study of carbohydrate/glucose metabolic genes: from fish to mammals

description: Table S1. Carbohydrate/glucose metabolic genes in 5 vertebrate organisms. All genes IDs were standardized as Ensembl gene IDs. Respectively, 791, 593, 523, 666 and 698 carbohydrate/glucose metabolic genes were present in the zebrafish, frog, chicken, mouse and human genomes. All gene descriptions were from Ensembl BioMart. (XLS 2875Â kb)
DOI: 10.6084/m9.figshare.6131699
title: Additional file 3: of Comparative transcriptome analysis of hypothalamus-regulated feed intake induced by exogenous visfatin in chicks

description: Table S3. GO analyses of DEGs in the three comparisons. (XLSX 328Â kb)
DOI: 10.6084/m9.figshare.6131699.v1
title: Additional file 3: of Comparative transcriptome analysis of hypothalamus-regulated feed intake induced by exogenous visfatin in chicks

description: Table S3. GO analyses of DEGs in the three comparisons. (XLSX 328Â kb)
DOI: 10.6084/m9.figshare.6131708
title: Additional file 3: of A comparative genomics study of carbohydrate/glucose metabolic genes: from fish to mammals

description: Table S2. KEGG pathway annotations of zebrafish carbohydrate/glucose metabolic genes by DAVID. We found 791 carbohydrate/glucose metabolic genes in zebrafish that were not only involved in distinct carbohydrate metabolic processes but also played multiple roles in response to lipid metabolism, amino acid metabolism, drug metabolism, apoptosis and other biological processes. (XLS 58Â kb)
DOI: 10.6084/m9.figshare.6131708.v1
title: Additional file 3: of A comparative genomics study of carbohydrate/glucose metabolic genes: from fish to mammals

description: Table S2. KEGG pathway annotations of zebrafish carbohydrate/glucose metabolic genes by DAVID. We found 791 carbohydrate/glucose metabolic genes in zebrafish that were not only involved in distinct carbohydrate metabolic processes but also played multiple roles in response to lipid metabolism, amino acid metabolism, drug metabolism, apoptosis and other biological processes. (XLS 58Â kb)
DOI: 10.6084/m9.figshare.6131726
title: Additional file 4: of A comparative genomics study of carbohydrate/glucose metabolic genes: from fish to mammals

description: Table S3. OMIM disease annotations of human carbohydrate/glucose metabolic genes by DAVID. Some genes are involved in noninsulin-dependent diabetes mellitus, thyroid carcinoma, paraganglioma and gastric stromal sarcoma, glycine encephalopathy, breast cancer and colorectal cancer. (XLS 25Â kb)
DOI: 10.6084/m9.figshare.6131726.v1
title: Additional file 4: of A comparative genomics study of carbohydrate/glucose metabolic genes: from fish to mammals

description: Table S3. OMIM disease annotations of human carbohydrate/glucose metabolic genes by DAVID. Some genes are involved in noninsulin-dependent diabetes mellitus, thyroid carcinoma, paraganglioma and gastric stromal sarcoma, glycine encephalopathy, breast cancer and colorectal cancer. (XLS 25Â kb)
DOI: 10.6084/m9.figshare.6131738
title: Additional file 5 of A comparative genomics study of carbohydrate/glucose metabolic genes: from fish to mammals

description: Table S4. Human T2D-related gene database and their corresponding orthologues in mouse, chicken, frog and zebrafish. To integrate existing knowledge about T2D, 2620 human T2D genes were identified in our database. Correspondingly, 2395, 1843, 2040, and 2573 orthologues of human T2D genes could be found among mouse, chicken, frog, and zebrafish, respectively. All genes IDs were standardized as Ensembl gene IDs. (XLS 464Â kb)
DOI: 10.6084/m9.figshare.6131738.v1
title: Additional file 5 of A comparative genomics study of carbohydrate/glucose metabolic genes: from fish to mammals

description: Table S4. Human T2D-related gene database and their corresponding orthologues in mouse, chicken, frog and zebrafish. To integrate existing knowledge about T2D, 2620 human T2D genes were identified in our database. Correspondingly, 2395, 1843, 2040, and 2573 orthologues of human T2D genes could be found among mouse, chicken, frog, and zebrafish, respectively. All genes IDs were standardized as Ensembl gene IDs. (XLS 464Â kb)
DOI: 10.6084/m9.figshare.6131759
title: Additional file 6: of A comparative genomics study of carbohydrate/glucose metabolic genes: from fish to mammals

description: Table S5. The list of overlapping genes between carbohydrate/glucose metabolic genes and type 2 diabetes-associated genes. Respectively, 400, 388, 313, 336 and 464 human, mouse, chicken, frog and zebrafish carbohydrate/glucose metabolic genes are associated with T2D. (XLSX 30Â kb)
DOI: 10.6084/m9.figshare.6131759.v1
title: Additional file 6: of A comparative genomics study of carbohydrate/glucose metabolic genes: from fish to mammals

description: Table S5. The list of overlapping genes between carbohydrate/glucose metabolic genes and type 2 diabetes-associated genes. Respectively, 400, 388, 313, 336 and 464 human, mouse, chicken, frog and zebrafish carbohydrate/glucose metabolic genes are associated with T2D. (XLSX 30Â kb)
DOI: 10.6084/m9.figshare.6131774
title: Additional file 7: of A comparative genomics study of carbohydrate/glucose metabolic genes: from fish to mammals

description: Table S6. Five species orthologues. Information including orthologue gene ID, gene name, % identity target species, identical genes to the query gene, orthology confidence and homology type are listed in the table. (XLSX 4387Â kb)
DOI: 10.6084/m9.figshare.6131774.v1
title: Additional file 7: of A comparative genomics study of carbohydrate/glucose metabolic genes: from fish to mammals

description: Table S6. Five species orthologues. Information including orthologue gene ID, gene name, % identity target species, identical genes to the query gene, orthology confidence and homology type are listed in the table. (XLSX 4387Â kb)
DOI: 10.6084/m9.figshare.6131777
title: Additional file 6: of Comparative transcriptome analysis of hypothalamus-regulated feed intake induced by exogenous visfatin in chicks

description: Table S4. KEGG analyses of DEGs in the three comparisons. (XLSX 31Â kb)
DOI: 10.6084/m9.figshare.6131777.v1
title: Additional file 6: of Comparative transcriptome analysis of hypothalamus-regulated feed intake induced by exogenous visfatin in chicks

description: Table S4. KEGG analyses of DEGs in the three comparisons. (XLSX 31Â kb)
DOI: 10.6084/m9.figshare.6131789
title: Additional file 8: of A comparative genomics study of carbohydrate/glucose metabolic genes: from fish to mammals

description: Table S7. Organism-specific genes by Ensemble Compara. Each gene was manually verified and annotated by HomoloGene, TreeFam, OrthoDB, ZFIN, MGI, Xenbase, and HCOP (Methods). (XLS 71Â kb)
DOI: 10.6084/m9.figshare.6131789.v1
title: Additional file 8: of A comparative genomics study of carbohydrate/glucose metabolic genes: from fish to mammals

description: Table S7. Organism-specific genes by Ensemble Compara. Each gene was manually verified and annotated by HomoloGene, TreeFam, OrthoDB, ZFIN, MGI, Xenbase, and HCOP (Methods). (XLS 71Â kb)
DOI: 10.6084/m9.figshare.6131801
title: Additional file 7: of Comparative transcriptome analysis of hypothalamus-regulated feed intake induced by exogenous visfatin in chicks

description: Table S5. The correlation coefficient between receptor genes expression and ligand genes expression in the neuroactive-ligand receptor interaction pathway. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.6131801.v1
title: Additional file 7: of Comparative transcriptome analysis of hypothalamus-regulated feed intake induced by exogenous visfatin in chicks

description: Table S5. The correlation coefficient between receptor genes expression and ligand genes expression in the neuroactive-ligand receptor interaction pathway. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.6131891
title: Additional file 1: of SP1-induced upregulation of lncRNA SPRY4-IT1 exerts oncogenic properties by scaffolding EZH2/LSD1/DNMT1 and sponging miR-101-3p in cholangiocarcinoma

description: Table S1. Primer sequences and siRNAs/shRNA oligonucleotides information. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.6131891.v1
title: Additional file 1: of SP1-induced upregulation of lncRNA SPRY4-IT1 exerts oncogenic properties by scaffolding EZH2/LSD1/DNMT1 and sponging miR-101-3p in cholangiocarcinoma

description: Table S1. Primer sequences and siRNAs/shRNA oligonucleotides information. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.6131900
title: Additional file 1: of Structure and transcriptional regulation of the major intrinsic protein gene family in grapevine

description: Supplementary Tables. (XLSX 748 kb)
DOI: 10.6084/m9.figshare.6131900.v1
title: Additional file 1: of Structure and transcriptional regulation of the major intrinsic protein gene family in grapevine

description: Supplementary Tables. (XLSX 748 kb)
DOI: 10.6084/m9.figshare.6132143
title: Additional file 10: of Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

description: Table S5. Correlated methylation siteâ mRNA expression pairs. (XLS 24 kb)
DOI: 10.6084/m9.figshare.6132143.v1
title: Additional file 10: of Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

description: Table S5. Correlated methylation siteâ mRNA expression pairs. (XLS 24 kb)
DOI: 10.6084/m9.figshare.6132164
title: Additional file 11: of Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

description: Table S6. Survival prognostis related genes from cox regression. (XLS 22 kb)
DOI: 10.6084/m9.figshare.6132164.v1
title: Additional file 11: of Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

description: Table S6. Survival prognostis related genes from cox regression. (XLS 22 kb)
DOI: 10.6084/m9.figshare.6132170
title: Additional file 10: of Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers

description: Table S13. (XLSX 46Â kb)
DOI: 10.6084/m9.figshare.6132170.v1
title: Additional file 10: of Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers

description: Table S13. (XLSX 46Â kb)
DOI: 10.6084/m9.figshare.6132182
title: Additional file 12: of Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

description: Table S7. Clinic and gene factor information for model. (XLS 62 kb)
DOI: 10.6084/m9.figshare.6132182.v1
title: Additional file 12: of Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

description: Table S7. Clinic and gene factor information for model. (XLS 62 kb)
DOI: 10.6084/m9.figshare.6132185
title: Additional file 11: of Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers

description: Table S15. Markers selected by leave-one-cohort-out. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.6132185.v1
title: Additional file 11: of Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers

description: Table S15. Markers selected by leave-one-cohort-out. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.6132188
title: Additional file 1: of Prevalence of latent tuberculosis infection among coal workersâ pneumoconiosis patients in China: a cross-sectional study

description: The results of QFT among 244 CWP patients. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.6132188.v1
title: Additional file 1: of Prevalence of latent tuberculosis infection among coal workersâ pneumoconiosis patients in China: a cross-sectional study

description: The results of QFT among 244 CWP patients. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.6132203
title: Additional file 13: of Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

description: Table S8. Model gene factor expression in Low and High risk samples. (XLS 52 kb)
DOI: 10.6084/m9.figshare.6132203.v1
title: Additional file 13: of Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

description: Table S8. Model gene factor expression in Low and High risk samples. (XLS 52 kb)
DOI: 10.6084/m9.figshare.6132215
title: Additional file 14: of Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

description: Table S9. Model gene factor expression in Normal and Cancer samples. (XLS 57 kb)
DOI: 10.6084/m9.figshare.6132215.v1
title: Additional file 14: of Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

description: Table S9. Model gene factor expression in Normal and Cancer samples. (XLS 57 kb)
DOI: 10.6084/m9.figshare.6132230
title: Additional file 15: of Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

description: Table S10. Clinic and gene expression information for testing dataset GSE22226. (XLS 32 kb)
DOI: 10.6084/m9.figshare.6132230.v1
title: Additional file 15: of Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

description: Table S10. Clinic and gene expression information for testing dataset GSE22226. (XLS 32 kb)
DOI: 10.6084/m9.figshare.6132242
title: Additional file 16: of Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

description: Table S11. Clinic information for samples in this study. (XLS 56 kb)
DOI: 10.6084/m9.figshare.6132242.v1
title: Additional file 16: of Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

description: Table S11. Clinic information for samples in this study. (XLS 56 kb)
DOI: 10.6084/m9.figshare.6132245
title: Additional file 15: of Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers

description: Table S2. Correlation between differentially abundant bacteria in Control. (XLSX 22Â kb)
DOI: 10.6084/m9.figshare.6132245.v1
title: Additional file 15: of Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers

description: Table S2. Correlation between differentially abundant bacteria in Control. (XLSX 22Â kb)
DOI: 10.6084/m9.figshare.6132260
title: Additional file 17: of Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

description: Table S12. DEGs screened from High and low risk groups. (XLS 31 kb)
DOI: 10.6084/m9.figshare.6132260.v1
title: Additional file 17: of Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

description: Table S12. DEGs screened from High and low risk groups. (XLS 31 kb)
DOI: 10.6084/m9.figshare.6132272
title: Additional file 18: of Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

description: Table S13â 1. Biology process annotations for DEGs negatively correlated to High and Low risk. Table S13â 2. Biology process annotations for DEGs positively correlated to High and Low risk. (XLS 23 kb)
DOI: 10.6084/m9.figshare.6132272.v1
title: Additional file 18: of Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

description: Table S13â 1. Biology process annotations for DEGs negatively correlated to High and Low risk. Table S13â 2. Biology process annotations for DEGs positively correlated to High and Low risk. (XLS 23 kb)
DOI: 10.6084/m9.figshare.6132284
title: Additional file 17: of Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers

description: Table S6. Differentially Abundant GO categories. (XLSX 17Â kb)
DOI: 10.6084/m9.figshare.6132284.v1
title: Additional file 17: of Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers

description: Table S6. Differentially Abundant GO categories. (XLSX 17Â kb)
DOI: 10.6084/m9.figshare.6132287
title: Additional file 19: of Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

description: Table S14. KEGG pathways annotations for DEGs from High and Low risk. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.6132287.v1
title: Additional file 19: of Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

description: Table S14. KEGG pathways annotations for DEGs from High and Low risk. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.6132302
title: Additional file 18: of Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers

description: Table S7. Differentially Abundant KO categories. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.6132302.v1
title: Additional file 18: of Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers

description: Table S7. Differentially Abundant KO categories. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.6132320
title: Additional file 19: of Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers

description: Table S10. Correlation between bacteria correlated-CRC-enriched KO categories. (XLSX 22Â kb)
DOI: 10.6084/m9.figshare.6132320.v1
title: Additional file 19: of Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers

description: Table S10. Correlation between bacteria correlated-CRC-enriched KO categories. (XLSX 22Â kb)
DOI: 10.6084/m9.figshare.6132374
title: Additional file 6: of Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

description: Table S1. Clinical information of 210 luminal breast cancer samples. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.6132374.v1
title: Additional file 6: of Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

description: Table S1. Clinical information of 210 luminal breast cancer samples. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.6132386
title: Additional file 7: of Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

description: Table S2. List of DEmethylated sites. (XLS 105 kb)
DOI: 10.6084/m9.figshare.6132386.v1
title: Additional file 7: of Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

description: Table S2. List of DEmethylated sites. (XLS 105 kb)
DOI: 10.6084/m9.figshare.6132398
title: Additional file 1 of Composite mathematical modeling of calcium signaling behind neuronal cell death in Alzheimerâ s disease

description: This file contains the parameters, initial conditions and equations used to generate the results in this paper. It can be run using XPP [19]. (ODE 8.18 kb)
DOI: 10.6084/m9.figshare.6132398.v1
title: Additional file 1 of Composite mathematical modeling of calcium signaling behind neuronal cell death in Alzheimerâ s disease

description: This file contains the parameters, initial conditions and equations used to generate the results in this paper. It can be run using XPP [19]. (ODE 8.18 kb)
DOI: 10.6084/m9.figshare.6132401
title: Additional file 8: of Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

description: Table S3. Intersection of DEGs in hypo and hyper methylated groups. (XLS 96 kb)
DOI: 10.6084/m9.figshare.6132401.v1
title: Additional file 8: of Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

description: Table S3. Intersection of DEGs in hypo and hyper methylated groups. (XLS 96 kb)
DOI: 10.6084/m9.figshare.6132410
title: Additional file 24: of Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers

description: Table S5. Correlation between differentially abundant bacteria in late CRC. (XLSX 21Â kb)
DOI: 10.6084/m9.figshare.6132410.v1
title: Additional file 24: of Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers

description: Table S5. Correlation between differentially abundant bacteria in late CRC. (XLSX 21Â kb)
DOI: 10.6084/m9.figshare.6132416
title: Additional file 9: of Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

description: Table S4. Methylation sites that significantly associated with breast cancer prognosis. (XLS 38 kb)
DOI: 10.6084/m9.figshare.6132416.v1
title: Additional file 9: of Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

description: Table S4. Methylation sites that significantly associated with breast cancer prognosis. (XLS 38 kb)
DOI: 10.6084/m9.figshare.6132419
title: Additional file 25: of Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers

description: Table S9. Node attributes of the correlation network between CRC-enriched bacteria and GO categories. (XLSX 171Â kb)
DOI: 10.6084/m9.figshare.6132419.v1
title: Additional file 25: of Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers

description: Table S9. Node attributes of the correlation network between CRC-enriched bacteria and GO categories. (XLSX 171Â kb)
DOI: 10.6084/m9.figshare.6132425
title: Additional file 26: of Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers

description: Table S11. Correlation network between the CRC-depleted bacteria and KO categories. (XLSX 81Â kb)
DOI: 10.6084/m9.figshare.6132425.v1
title: Additional file 26: of Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers

description: Table S11. Correlation network between the CRC-depleted bacteria and KO categories. (XLSX 81Â kb)
DOI: 10.6084/m9.figshare.6132440
title: Additional file 27: of Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers

description: Table S12. Correlation network between the CRC depleted bacteria and GO categories. (XLSX 29Â kb)
DOI: 10.6084/m9.figshare.6132440.v1
title: Additional file 27: of Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers

description: Table S12. Correlation network between the CRC depleted bacteria and GO categories. (XLSX 29Â kb)