cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11814234.v1
title: Additional file 2 of Comparison of brain connectomes by MRI and genomics and its implication in Alzheimer’s disease

description: Additional file 2: Table S1. Probability of tract reaching brain region (Reach probability). Table S2. Brain region mapping between Desikan-Killany atlas and post-mortem brain labels. Table S3. Number of Tissue-to-Tissue (TTC) correlated genes for each pair of Region-of-interests (ROIs). Table S4. Pathway list with annotated subtypes. Table S5. Pathway interactions in brain region pairs that are that are significantly different in tract-bound. Table S6. Pathway interactions in brain region pairs that are that are significantly different in AD-tract-bound. Table S7. Association between covariates and diffusion measures in each tract. Table S8. Effect sizes for associations in ADNI3 and ADNI2. Table S9. Pathway over-representation analysis between brain region pairs connected by white matter tracts and region pairs not connected by tracts. Table S10. Pathway interaction graph (degree). Table S11. Pathway over-representation analysis of symmetric gene synchronization in brain region pairs connected by white matter tracts. Table S12. Association between gene expression of Toll receptor signaling in the blood and diffusion measures in the brain. Table S13. Number of subjects in each study per site.
DOI: 10.6084/m9.figshare.11814234
title: Additional file 2 of Comparison of brain connectomes by MRI and genomics and its implication in Alzheimer’s disease

description: Additional file 2: Table S1. Probability of tract reaching brain region (Reach probability). Table S2. Brain region mapping between Desikan-Killany atlas and post-mortem brain labels. Table S3. Number of Tissue-to-Tissue (TTC) correlated genes for each pair of Region-of-interests (ROIs). Table S4. Pathway list with annotated subtypes. Table S5. Pathway interactions in brain region pairs that are that are significantly different in tract-bound. Table S6. Pathway interactions in brain region pairs that are that are significantly different in AD-tract-bound. Table S7. Association between covariates and diffusion measures in each tract. Table S8. Effect sizes for associations in ADNI3 and ADNI2. Table S9. Pathway over-representation analysis between brain region pairs connected by white matter tracts and region pairs not connected by tracts. Table S10. Pathway interaction graph (degree). Table S11. Pathway over-representation analysis of symmetric gene synchronization in brain region pairs connected by white matter tracts. Table S12. Association between gene expression of Toll receptor signaling in the blood and diffusion measures in the brain. Table S13. Number of subjects in each study per site.
DOI: 10.6084/m9.figshare.11814303
title: Additional file 10 of Network pharmacology-based study on the mechanism of Yiganling capsule in hepatitis B treatment

description: Additional file 10: Table S18. YGL capsule - Hepatitis B disease network only includes targets for disease. Table S19. Four topological feature values of YGL capsule - Hepatitis B disease network only includes targets for disease.
DOI: 10.6084/m9.figshare.11814315.v1
title: Additional file 14 of Network pharmacology-based study on the mechanism of Yiganling capsule in hepatitis B treatment

description: Additional file 14: Table S25. The direct action pathway targets of YGL capsule. Table S26. Four topological feature values of the pathways of direct action targets of YGL capsule.
DOI: 10.6084/m9.figshare.11814303.v1
title: Additional file 10 of Network pharmacology-based study on the mechanism of Yiganling capsule in hepatitis B treatment

description: Additional file 10: Table S18. YGL capsule - Hepatitis B disease network only includes targets for disease. Table S19. Four topological feature values of YGL capsule - Hepatitis B disease network only includes targets for disease.
DOI: 10.6084/m9.figshare.11814309
title: Additional file 12 of Network pharmacology-based study on the mechanism of Yiganling capsule in hepatitis B treatment

description: Additional file 12: Table S21. Pathway of YGL capsule- Hepatitis B Disease target. Table S22. Four topological feature values of Pathway of YGL capsule- Hepatitis B Disease target.
DOI: 10.6084/m9.figshare.11814309.v1
title: Additional file 12 of Network pharmacology-based study on the mechanism of Yiganling capsule in hepatitis B treatment

description: Additional file 12: Table S21. Pathway of YGL capsule- Hepatitis B Disease target. Table S22. Four topological feature values of Pathway of YGL capsule- Hepatitis B Disease target.
DOI: 10.6084/m9.figshare.11814330
title: Additional file 4 of Network pharmacology-based study on the mechanism of Yiganling capsule in hepatitis B treatment

description: Additional file 4: Table S9. The therapeutic target data for HB treatment from four resources, including Uniprot, OMIM, DIGSEE, and GADA.
DOI: 10.6084/m9.figshare.11814333
title: Additional file 5 of Network pharmacology-based study on the mechanism of Yiganling capsule in hepatitis B treatment

description: Additional file 5: Table S10. Detailed information on six existing protein-protein interaction databases.
DOI: 10.6084/m9.figshare.11814336
title: Additional file 6 of Network pharmacology-based study on the mechanism of Yiganling capsule in hepatitis B treatment

description: Additional file 6: Table S11. Hepatitis B disease protein- protein interaction network disease PPI Network. Table S12. Four topological feature values of Hepatitis B disease PPI network.
DOI: 10.5281/zenodo.10663935
title: Minichain v1.3 Benchmark Datasets

description: Benchmark datasets for Minichain v1.3 (https://github.com/at-cg/minichain)
DOI: 10.6084/m9.figshare.11814312.v1
title: Additional file 13 of Network pharmacology-based study on the mechanism of Yiganling capsule in hepatitis B treatment

description: Additional file 13: Table S23. Pathway for YGL capsule-HB-mechanism network only includes intersection targets network. Table S24. Four topological feature values of Pathway for YGL capsule-HB-mechanism network only include intersection targets network.
DOI: 10.6084/m9.figshare.11814333.v1
title: Additional file 5 of Network pharmacology-based study on the mechanism of Yiganling capsule in hepatitis B treatment

description: Additional file 5: Table S10. Detailed information on six existing protein-protein interaction databases.
DOI: 10.6084/m9.figshare.11814339
title: Additional file 7 of Network pharmacology-based study on the mechanism of Yiganling capsule in hepatitis B treatment

description: Additional file 7: Table S13. The enrichment analysis of the target cluster analysis of Hepatitis B disease PPI network.
DOI: 10.6084/m9.figshare.11814348.v1
title: Additional file 9 of Network pharmacology-based study on the mechanism of Yiganling capsule in hepatitis B treatment

description: Additional file 9: Table S16. YGL capsule- Hepatitis B Disease target. Table S17. Four topological feature values of YGL capsule- Hepatitis B Disease target.
DOI: 10.6084/m9.figshare.11814336.v1
title: Additional file 6 of Network pharmacology-based study on the mechanism of Yiganling capsule in hepatitis B treatment

description: Additional file 6: Table S11. Hepatitis B disease protein- protein interaction network disease PPI Network. Table S12. Four topological feature values of Hepatitis B disease PPI network.
DOI: 10.6084/m9.figshare.11814345.v1
title: Additional file 8 of Network pharmacology-based study on the mechanism of Yiganling capsule in hepatitis B treatment

description: Additional file 8: Table S14. Pathway of Hepatitis B. Table S15. Four topological feature values of Pathway with Hepatitis B target.
DOI: 10.6084/m9.figshare.11814315
title: Additional file 14 of Network pharmacology-based study on the mechanism of Yiganling capsule in hepatitis B treatment

description: Additional file 14: Table S25. The direct action pathway targets of YGL capsule. Table S26. Four topological feature values of the pathways of direct action targets of YGL capsule.
DOI: 10.6084/m9.figshare.11814321
title: Additional file 1 of Network pharmacology-based study on the mechanism of Yiganling capsule in hepatitis B treatment

description: Additional file 1: Table S1. Composite compounds of YGL capsule.
DOI: 10.6084/m9.figshare.11814306
title: Additional file 11 of Network pharmacology-based study on the mechanism of Yiganling capsule in hepatitis B treatment

description: Additional file 11: Table S20. The results of target enrichment analysis were obtained after cluster analysis of YGL capsule-hepatitis B disease PPI.
DOI: 10.6084/m9.figshare.11814321.v1
title: Additional file 1 of Network pharmacology-based study on the mechanism of Yiganling capsule in hepatitis B treatment

description: Additional file 1: Table S1. Composite compounds of YGL capsule.
DOI: 10.6084/m9.figshare.11814327
title: Additional file 3 of Network pharmacology-based study on the mechanism of Yiganling capsule in hepatitis B treatment

description: Additional file 3: Table S7. Prediction of putative targets for compositive compounds YGL capsule. Table S8. Four topological feature values of targets in target-compositive compounds network.
DOI: 10.6084/m9.figshare.11814330.v1
title: Additional file 4 of Network pharmacology-based study on the mechanism of Yiganling capsule in hepatitis B treatment

description: Additional file 4: Table S9. The therapeutic target data for HB treatment from four resources, including Uniprot, OMIM, DIGSEE, and GADA.
DOI: 10.6084/m9.figshare.11814324
title: Additional file 2 of Network pharmacology-based study on the mechanism of Yiganling capsule in hepatitis B treatment

description: Additional file 2: Table S2. Compounds with an oral bioavailability value greater than 30%. Table S3. Compounds with a Caco-2 value &gt; − 0.4. Table S4. Compounds with a drug-likeness value &gt; 0.18. Table S5. Compound with a half-life &gt; 3 h . Table S6. The potentially bioactive compounds of YGL capsule using the ADME in silico integrative model.
DOI: 10.6084/m9.figshare.11814324.v1
title: Additional file 2 of Network pharmacology-based study on the mechanism of Yiganling capsule in hepatitis B treatment

description: Additional file 2: Table S2. Compounds with an oral bioavailability value greater than 30%. Table S3. Compounds with a Caco-2 value &gt; − 0.4. Table S4. Compounds with a drug-likeness value &gt; 0.18. Table S5. Compound with a half-life &gt; 3 h . Table S6. The potentially bioactive compounds of YGL capsule using the ADME in silico integrative model.
DOI: 10.6084/m9.figshare.11814327.v1
title: Additional file 3 of Network pharmacology-based study on the mechanism of Yiganling capsule in hepatitis B treatment

description: Additional file 3: Table S7. Prediction of putative targets for compositive compounds YGL capsule. Table S8. Four topological feature values of targets in target-compositive compounds network.
DOI: 10.6084/m9.figshare.11814312
title: Additional file 13 of Network pharmacology-based study on the mechanism of Yiganling capsule in hepatitis B treatment

description: Additional file 13: Table S23. Pathway for YGL capsule-HB-mechanism network only includes intersection targets network. Table S24. Four topological feature values of Pathway for YGL capsule-HB-mechanism network only include intersection targets network.
DOI: 10.6084/m9.figshare.11814348
title: Additional file 9 of Network pharmacology-based study on the mechanism of Yiganling capsule in hepatitis B treatment

description: Additional file 9: Table S16. YGL capsule- Hepatitis B Disease target. Table S17. Four topological feature values of YGL capsule- Hepatitis B Disease target.
DOI: 10.6084/m9.figshare.11814345
title: Additional file 8 of Network pharmacology-based study on the mechanism of Yiganling capsule in hepatitis B treatment

description: Additional file 8: Table S14. Pathway of Hepatitis B. Table S15. Four topological feature values of Pathway with Hepatitis B target.
DOI: 10.6084/m9.figshare.8144363.v2
title: Table S2 from Evolutionary trade-offs between baseline and plastic gene expression in two congeneric oyster species.

description: General linear model of the effects of species, gene and time on basal expression under ambient conditions and relative expression under heat shock in two congeneric oyster species inhabiting northern (QD) and southern (XM) environments.
DOI: 10.6084/m9.figshare.21251584.v1
title: Additional file 10 of Small molecule modulation of microbiota: a systems pharmacology perspective

description: Additional file 10. Table S9. Background targets list used in target functional annotation analysis.
DOI: 10.6084/m9.figshare.21251590
title: Additional file 2 of Small molecule modulation of microbiota: a systems pharmacology perspective

description: Additional file 2. Table S1. Microbes with pathogenic effects on human health by manually literature review.
DOI: 10.6084/m9.figshare.21251590.v1
title: Additional file 2 of Small molecule modulation of microbiota: a systems pharmacology perspective

description: Additional file 2. Table S1. Microbes with pathogenic effects on human health by manually literature review.
DOI: 10.6084/m9.figshare.21251611.v1
title: Additional file 9 of Small molecule modulation of microbiota: a systems pharmacology perspective

description: Additional file 9. Table S8. Background drugs list used in drug overrepresentation analysis.
DOI: 10.6084/m9.figshare.21776258
title: A Pan-Cancer Analysis of the Role of small ArfGAP 1 in Human Tumors

description: This table shows the raw data in the study.<br>Supplementary Table 1: The expression data of SMAP1 gene in 34 tumors.Supplementary Table 2: Pan-cancer data and analysis results of the relationship between SMAP1 gene expression and prognosis.Supplementary Table 3: The SMAP1 clinical phenotype expression data in 37 cancer species.Supplementary Table 4-7: The results of correlation analysis between SMAP1 expression and clinical phenotype in various cancers.Supplementary Table 8: The expression data of SMAP1 genomic heterogeneity.Supplementary Table 9: The expression data of SMAP1 tumor stemness.Supplementary Table 10: Pan-cancer data and analysis results of the relationship between SMAP1 gene expression and tumor microenvironment.SMAP1,IHC DATA, LIHC, COAD, PAAD（Immunohistochemistry (IHC) analysis was performed to detect the expression of SMAP1 in three types of tumors: hepatocellular carcinoma (LIHC), colon adenocarcinoma (COAD), and pancreatic adenocarcinoma (PAAD)）
DOI: 10.6084/m9.figshare.22300657
title: Single Cell Pathway Enrichment

description: File “Single Cell Pathway Enrichment” provided enrichment scores of 50 hallmark pathways from MsigDB database evaluated for total cells using UCell R package.
DOI: 10.6084/m9.figshare.22300657.v1
title: Single Cell Pathway Enrichment

description: File “Single Cell Pathway Enrichment” provided enrichment scores of 50 hallmark pathways from MsigDB database evaluated for total cells using UCell R package.
DOI: 10.6084/m9.figshare.22300675
title: UMAP plots split by dataset and sample

description: File “UMAP plots split by dataset and sample” supplied the comparison of UMAP plots at dataset or sample level colored by major cell types.
DOI: 10.6084/m9.figshare.22300675.v1
title: UMAP plots split by dataset and sample

description: File “UMAP plots split by dataset and sample” supplied the comparison of UMAP plots at dataset or sample level colored by major cell types.
DOI: 10.6084/m9.figshare.21252306
title: iron-rich olivine grain growth

description: There are EBSD and electron microscopy data for olivine  samples with three iron contents (Fo30, Fo50, Fo70) annealed at different homologous temperatures for different times (0h, 3.2h, 10h, 32h, 100h)
FoMM_XXX_ebsd. The file named zip is the olivine sample data of MM forsterite ratio annealed at XXX absolute temperature obtained by EBSD.
Each file in the compressed folder is named "FoMM_XXX_Yh", where XXX is the absolute temperature of annealing and Y is the annealing time at that temperature. The files with the suffixes crc and cpr are the raw EBSD data of the samples, and the files with the suffix CTF are the raw data after noise reduction in the HKL Channel 5.
The file named FoMM_map.zip is the map of scanning area of olivine sample with magnesium content of M.
Each file in the compressed folder is named "FoMM_XXX_Yh. jpg". It is a map obtained by Mtex processing CTF data with the same file name.
DOI: 10.6084/m9.figshare.21776603
title: Supplementary dataset (Yamakawa et al., Early expression onset of tissue-specific effector genes during the specification process in sea urchin embryos)

description: The supplementary datasets of the paper entitled "Early expression onset of tissue-specific effector genes during the specification process in sea urchin embryos (Yamakawa et al.)". The datasets include the raw data such as the expression matrix and gene annotation lists, code/scripts for the analysis, and original figures/tables.
DOI: 10.6084/m9.figshare.21252408
title: Survival Data

description: Survival data for patients of 4 HCC cohorts and 2 ICC cohort were provided in this file.
DOI: 10.6084/m9.figshare.21252408.v1
title: Survival Data

description: Survival data for patients of 4 HCC cohorts and 2 ICC cohort were provided in this file.
DOI: 10.6084/m9.figshare.7096679
title: Additional file 1: of Comparative metabolomics reveals the metabolic variations between two endangered Taxus species (T. fuana and T. yunnanensis) in the Himalayas

description: Table S1. Detail information of all identified metabolites. (XLSX 2024 kb)
DOI: 10.6084/m9.figshare.24922623
title: Crop domestication

description: Here, we used keywords (crop, domestication, wild, cultivated, domesticated) to search in four websites (Google Scholar, Web of Science, CNKI, and Scopus). Only studies that encompass both wild and cultivated crops that cultivated in isolated individuals, monocultures or under identical conditions were selected to compile data. If plants were subjected to various treatments corresponding to fertilizer, light, CO2, temperature, and vapor pressure deficit levels, only the trait values of plants grown under normal conditions were incorporated into the study. We compiled a comprehensive multi-crop dataset comprised 54 wild and cultivated crops species including 29 functional traits.
DOI: 10.5281/zenodo.10663934
title: Minichain v1.3 Benchmark Datasets

description: Benchmark datasets for Minichain v1.3 (https://github.com/at-cg/minichain)

These datasets accompany the manuscript "Haplotype-aware sequence alignment to pangenome graphs", G Chandra, D Gibney, and C.Jain, 2024 (under review)

File descriptions:



MHC-CHM13.0.gfa.gz : Haplotype-aware MHC Pangenome graph constructed from 60 MHC haplotypes from HPRC, hosted at Zenodo.

MHC_CHM13_ONT_filt.part_001.fq.gz, MHC_CHM13_ONT_filt.part_002.fq.gz : Oxford Nanopore (SRR2336508) reads from MHC region of CHM13 human genome.

MHC_CHM13_PacBio_filt.part_001.fq.gz, MHC_CHM13_PacBio_filt.part_002.fq.gz : PacBio HiFi (SRX5633451) reads from MHC region of CHM13 human genome.

MHC_CHM13_PacBio_filt.fq.gz : PacBio HiFi (SRR11292121) reads from MHC region of CHM13 human genome.

Query_0.1.tar.gz, Query_1.tar.gz, Query_5.tar.gz : Simulated MHC haplotypes with 0.1%, 1% and 5% substitution rates, respectively.
DOI: 10.5281/zenodo.10665350
title: Minichain v1.3 Benchmark Datasets

description: Benchmark datasets for Minichain v1.3 (https://github.com/at-cg/minichain)

These datasets accompany the manuscript "Haplotype-aware sequence alignment to pangenome graphs", G Chandra, D Gibney, and C.Jain, 2024 (under review)

File descriptions:



MHC-CHM13.0.gfa.gz : Haplotype-aware MHC Pangenome graph constructed from 60 MHC haplotypes from HPRC, hosted at Zenodo.

MHC_CHM13_ONT_filt.part_001.fq.gz, MHC_CHM13_ONT_filt.part_002.fq.gz : Oxford Nanopore (SRR2336508) reads from MHC region of CHM13 human genome.

MHC_CHM13_PacBio_filt.part_001.fq.gz, MHC_CHM13_PacBio_filt.part_002.fq.gz : PacBio HiFi (SRX5633451) reads from MHC region of CHM13 human genome.

MHC_CHM13_PacBio_filt.fq.gz : PacBio HiFi (SRR11292121) reads from MHC region of CHM13 human genome.

Query_0.1.tar.gz, Query_1.tar.gz, Query_5.tar.gz : Simulated MHC haplotypes with 0.1%, 1% and 5% substitution rates, respectively.
DOI: 10.6084/m9.figshare.7097075.v1
title: Additional file 1: of Novel antibodies against GPIbÎą inhibit pulmonary metastasis by affecting vWF-GPIbÎą interaction

description: Table S1. The screening of hybridoma cell clones. (A) Rat anti-mouse platelet clones and (B) mouse anti-human platelet clones. Binding of clones to GPIb-IX complex was detected in ELISA. GPIb-IX complex was captured by anti-GPIX antibody, which was immobilized in microtiter plates. Supernatant of hybridoma cells were added to the coated wells. The bound clone was detected with HRP-conjugated rabbit anti-rat IgG or rabbit anti-mouse IgG. Effect of clones on BCECF-labeled platelets adherence to tumor cells was recorded by fluorescence plate reader. BCECF-labeled platelets pretreated with supernatant of different hybridoma cells were added into tumor cells coated plates. The adherence between platelets and tumor cells was detected by fluorescence plate reader. (XLSX 36 kb)
DOI: 10.6084/m9.figshare.7097099.v1
title: Additional file 3: of Novel antibodies against GPIbα inhibit pulmonary metastasis by affecting vWF-GPIbα interaction

description: Table S2. Mouse (B) and human (A) GPIbα peptides fragment sequences. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.21251443
title: Additional file 2 of Rapid and sensitive single-cell RNA sequencing with SHERRY2

description: Additional file 2: Table S1. Coverage uniformity across gene body and gene number detected by SHERRY2 when testing different conditions on bulk RNA. (data values of Additional file 1: Fig. S1).
DOI: 10.6084/m9.figshare.21251452.v1
title: Additional file 5 of Rapid and sensitive single-cell RNA sequencing with SHERRY2

description: Additional file 5: Table S4.Normalized abundance of marker genes in each GC cell type. (recording data values of Additional file 1: Fig. S7D).
DOI: 10.6084/m9.figshare.21251443.v1
title: Additional file 2 of Rapid and sensitive single-cell RNA sequencing with SHERRY2

description: Additional file 2: Table S1. Coverage uniformity across gene body and gene number detected by SHERRY2 when testing different conditions on bulk RNA. (data values of Additional file 1: Fig. S1).
DOI: 10.25505/fiz.icsd.cc2df8qv
title: CSD 2217297: Experimental Crystal Structure Determination

description: Related Article: V.V.Sharutin, I.V.Egorova, T.K.Ivanenko, A.V.Gerasimenko|2003|Koord.Khim.|29|163|
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.21155419.v2
title: Dataset of freshwater macroinvertebrate occurrences from Cuba

description: Dataset of georeferenced occurrence records of freshwater flatworms (Platyhelminthes: Tricladida), insects (Ephemeroptera, Odonata, Hemiptera, Trichoptera, Coleoptera, Diptera), crabs and shrimps (Crustacea: Decapoda), and mollusks (Mollusca) of Cuba. The information was collated from scientific literature, unpublished field records, museum collections and online databases. The dataset is organized in 31 fields that contains information about the taxonomic classification of each recorded species; sex, and life stage of individuals; location, author and date of the record and a reference to the original data source.
DOI: 10.34740/kaggle/dsv/4454062
title: Mahanagar Yatayat Dataset
DOI: 10.6084/m9.figshare.21302184
title: Table 6-Plagiarism Scoring Rubric

description: Table 6 resulted from "Developing a Comprehensive Plagiarism Scoring Rubric" published by Education and Information Technologies at https://doi.org/10.1007/s10639-022-11365-1.