Datasets:

OTAR3088
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CeLLaTe-benchMark-set-fulltext

PMCID stringclasses 49 values	Title stringclasses 49 values	Sentence_ID int64 0 775	Sentence stringlengths 5 6.13k	Source stringclasses 1 value
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	0	Ulcerative colitis (UC) patients carry a 2.5-fold increased risk of colorectal cancer (CRC), yet the shared multi-scale genetic architecture remains poorly understood.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	1	We constructed an integrative framework across tissue, cellular, and variant levels to systematically dissect the pathogenic evolution of this comorbidity across spatiotemporal dimensions.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	2	We integrated GWAS data from 100,204 CRC cases and 12,160 UC patients with tissue-specific MAGMA enrichment, embryonic spatial mapping (gsMap), and multidimensional single-cell prioritization (ECLIPSER, CELLECT, scDRS).	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	3	We further resolved cell-specific co-expression patterns using hdWGCNA and identified high-confidence causal variants and genes through Bayesian fine-mapping (eCAVIAR, fastenloc) and Open4Gene analysis.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	4	Genetic susceptibility for both diseases was significantly enriched in the terminal ileum and transverse colon, anchored to E16.5 embryonic gut programs.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	5	CD4 + T cells emerged as the core immune hub in UC, exhibiting profound immunometabolic polarization (Th17/IL-17 axis and Warburg effect), while progenitors were identified as the primary cellular origin for CRC malignancy.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	6	Pathological progression was characterized by a transition from chronic inflammatory stress toward p53-mediated genomic instability, epithelial-mesenchymal transition (EMT), and vascular remodeling.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	7	We prioritized Tier 1 candidate genes—ARPC5, PTGER4, CIB1, PREX1, and S100A10—as key mediators of the comorbidity association between inflammation and cancer.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	8	These findings partially support a “genetic programming-microenvironment triggering” hypothesis, where regional vulnerabilities established by embryonic developmental programs are activated by postnatal insults, though its broad applicability warrants caution.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	9	This study provides a comprehensive multi-scale molecular framework for understanding UC-CRC comorbidity, offering potential targets for risk stratification and therapeutic intervention.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	10	The comorbidity mechanisms between ulcerative colitis (UC) and colorectal cancer (CRC) are far more complex than traditionally recognized.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	11	Although UC patients exhibit significantly elevated CRC risk (standardized incidence ratio [SIR] of 2.48, with 30-year cumulative risk of 4.6%–6.5%) , genomic evidence reveals that the pathogenesis of UC-associated CRC involves complex genetic and epigenetic events rather than simple inflammation-to-cancer transformati...	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	12	Previous approaches including Mendelian randomization (MR) and colocalization analyses have failed to identify significant causal relationships or shared causal variants between the two diseases , necessitating novel methodologies that transcend single genetic loci to systematically dissect their shared biological unde...	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	13	Recent advances in multi-omics technologies have provided unprecedented opportunities to address this challenge.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	14	Expression quantitative trait locus (eQTL) analysis can link GWAS (Genome-Wide Association Study) signals to gene expression regulatory mechanisms, identifying functional risk variants and their target genes , while splicing quantitative trait locus (sQTL) analysis further elucidates how genetic variants modulate disea...	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	15	Single-cell RNA sequencing has revealed 101 cellular states and morphogenic programs during human gut development, and identified remarkable heterogeneity of macrophages/neutrophils in UC as well as the spatial organization of multiple immunosuppressive mechanisms within the CRC tumor microenvironment [8, 9].	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	16	Spatial transcriptomics enables preservation of tissue spatial information, mapping gene expression patterns to specific anatomical regions .	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	17	More importantly, embryonic spatial transcriptomic studies have revealed reactivation of embryonic-like gene expression profiles during intestinal injury repair and enrichment of disease-associated genes in fetal-like cellular subpopulations within inflamed tissues , suggesting that spatial programming during embryonic...	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	18	However, existing studies predominantly focus on single diseases or single technological platforms, lacking a multi-scale analytical framework that integrates GWAS-QTL-single cell-spatial transcriptomics-developmental biology, to systematically dissect the shared and distinct mechanisms between UC and CRC across geneti...	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	19	Fernandez-Rozadilla et al. integrated 100,204 colorectal cancer cases and 154,587 controls from European and East Asian populations, measuring genome-wide single nucleotide polymorphism (SNP) data.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	20	The study employed logistic regression analysis for each analytical unit and utilized a fixed-effects inverse-variance weighted model for meta-analysis.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	21	Quality control procedures included filtering variants with imputation quality scores (info/R2) > 0.4 and minor allele frequency (MAF) > 0.005, ultimately incorporating 8,782,440 variants in the meta-analysis.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	22	Heterogeneity across studies was assessed using the I2 statistic, yielding GWAS summary statistics for colorectal cancer.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	23	Our analysis was restricted to the European ancestry cohort from this dataset.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	24	De Lange et al. enrolled individuals of European ancestry, including 12,160 inflammatory bowel disease patients and 13,145 controls, with genome-wide SNP genotyping.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	25	The study implemented stringent quality control measures, excluding variants with missingness > 5%, loci deviating from Hardy–Weinberg equilibrium (P < 1 × 10−5), and variants affected by batch effects.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	26	Association analysis was performed on 9.7 million variants, and meta-analysis was conducted to integrate newly generated data with previously published summary statistics, producing GWAS summary statistics for ulcerative colitis.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	27	Khaliq et al. enrolled 16 treatment-naïve patients with resectable colorectal cancer (comprising 9 Caucasians, 6 African Americans, and 1 Asian) along with 8 adjacent normal tissue samples, performing single-cell RNA sequencing using the 10 × Genomics single-cell 5′ platform.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	28	Stringent quality control measures were implemented, including removal of cells with mitochondrial gene expression > 25% and doublet detection, ultimately yielding 49,859 high-quality single cells for analysis.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	29	Consensus Molecular Subtype (CMS) classification was performed for each tumor using bulk RNA sequencing data, and pseudo-bulk differential expression analysis coupled with pathway analysis revealed the complexity of the tumor microenvironment.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	30	Integration of multiple independent external cohort datasets enabled analysis of a total of 487,829 single cells, providing high-resolution characterization of cellular diversity in colorectal cancer and its microenvironment.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	31	Boland et al. enrolled 9 healthy individuals and 7 patients with active ulcerative colitis, all of European ancestry, collecting rectal mucosal biopsies and peripheral blood samples.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	32	The study employed the 10 × Genomics single-cell 5′ platform for single-cell RNA sequencing (scRNA-seq), T cell receptor sequencing (scTCR-seq), and B cell receptor sequencing (scBCR-seq).	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	33	Quality control procedures included removal of cells with mitochondrial gene expression > 25% and low-quality cells, ultimately retaining genes with mean expression of at least 1 UPM (unique molecular identifiers per million reads).	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	34	Clustering analysis using t-SNE and UMAP generated a dataset comprising 10,160 genes, with FACS (Fluorescence-Activated Cell Sorting) purification based on CD45 + immune cell sorting, ultimately obtaining high-quality single-cell data that revealed the heterogeneity and clonal relationships of adaptive immune cells in ...	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	35	Single-cell multiomics analysis was performed on PBMCs from a 25-year-old healthy female donor using the 10 × Genomics Chromium platform.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	36	Following enrichment of mononuclear cells via fluorescence-activated cell sorting, nuclei were isolated according to the standard protocol (CG000365 Rev A), capturing a total of 11,909 high-quality single cells.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	37	ATAC (Assay for Transposase-Accessible Chromatin) and transcriptome sequencing libraries were simultaneously constructed following the Chromium Next GEM Multiome workflow (CG000338 Rev A), with paired-end sequencing completed on the Illumina NovaSeq 6000 sequencer.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	38	The data demonstrated excellent quality: gene expression profiling revealed median values of 1826 genes and 3776 UMIs (Unique Molecular Identifiers) per cell; chromatin accessibility analysis showed a median of 13,486 fragments per cell, identifying 108,377 open chromatin regions and 15,494 expressed genes, and establi...	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	39	This dataset provides a solid foundation for investigating immune cell heterogeneity and epigenetic regulation.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	40	This study implemented a systematic quality control workflow to ensure data reliability.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	41	For GWAS data, a minor allele frequency (MAF) threshold of 0.01 was initially applied to exclude low-frequency variants, thereby reducing uncertainty and false-positive risks.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	42	Considering that the MHC (major histocompatibility complex) region on chromosome 6 exhibits extensive linkage disequilibrium that can confound analytical accuracy, SNPs within this region were excluded.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	43	Following filtering, genome build versions were uniformly converted to ensure data standardization.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	44	For single-cell transcriptome data processing, the Seurat package was employed to load data and calculate the expression proportions of mitochondrial genes (MT-prefixed) and hemoglobin genes (HBA/HBB/HBD, etc.)	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	45	as quality assessment metrics.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	46	Filtering criteria were set as follows: cells with UMI counts ≥ 500, detected gene numbers between 200–6000, mitochondrial gene proportion ≤ 15%, and hemoglobin gene proportion ≤ 5%.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	47	Dimensionality reduction analysis integrated principal component analysis (PCA) and t-distributed stochastic neighbor embedding (t-SNE), with elbow plots employed to validate dimensionality reduction performance.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	48	Finally, the Harmony algorithm (theta = 2, lambda = 1) was applied to remove batch effects, achieving inter-sample data integration and correction.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	49	This study employed the GeneEnrich toolkit to perform gene set enrichment analysis on genetic variants and expression profile data from ulcerative colitis and colorectal cancer.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	50	Through a combined strategy of hypergeometric distribution testing and random permutation validation, we systematically evaluated the enrichment of target gene clusters within intestinal tissue-specific functional phenotypes.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	51	To ensure result reliability, we selected intestinal tissue genes as the reference background set and utilized permutation algorithms to obtain empirical P-values.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	52	Additionally, to avoid confounding effects such as linkage disequilibrium, genetic loci within the MHC region were excluded.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	53	Functional annotation data were integrated from multiple authoritative biological databases including Gene Ontology, Reactome, KEGG, MSigDB, and MGI, with a Bonferroni-corrected P-value < 0.05 established as the statistical significance threshold.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	54	This study employed the MAGMA (Multi-marker Analysis of GenoMic Annotation) gene-set enrichment analysis method to systematically assess the genomic characteristics of ulcerative colitis and colorectal cancer.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	55	Following conversion of disease-associated genetic data into MAGMA-compatible format, gene-level association enrichment analysis was performed, with Bonferroni-corrected P < 0.05 established as the significance threshold for tissue expression.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	56	Furthermore, we applied a genetically informed spatial mapping of cells for complex traits (gsMap) algorithm to dissect the spatial distribution characteristics of ulcerative colitis and colorectal cancer at single-cell resolution by integrating single-cell spatial transcriptomic (sc-ST) data with genome-wide associati...	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	57	This approach leverages spatial transcriptomic atlases of 25 organs during mouse embryonic development (E16.5), combined with cross-species datasets (including mouse embryonic), to map GWAS-identified disease-associated gene expression patterns onto spatially resolved cellular populations.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	58	This establishes cellular-level associations between diseases and specific anatomical regions, ultimately constructing spatial pathogenic mechanism networks at single-cell resolution.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	59	This study conducted a systematic analysis based on single-cell transcriptomic data corrected using the Harmony algorithm .	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	60	Dimensionality reduction results were visualized via t-SNE, while the distribution characteristics of cell types within the samples were quantitatively evaluated.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	61	To dissect the molecular signatures of each cell population, the FindAllMarkers function (expression proportion ≥ 25%, logFC ≥ 0.25) was applied to identify cluster-specific highly expressed genes, and expression heatmaps were constructed.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	62	Finally, automated cell type annotation was performed using the SingleR algorithm .	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	63	The ECLIPSER method identifies cell type-specific signals based on Bayesian Fisher's exact test .	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	64	This approach uses a background GWAS locus set as a reference baseline and, for each trait-tissue-cell type three-dimensional combination, quantitatively calculates cell type-specific enrichment fold changes and their statistical significance.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	65	The cell type specificity threshold was set at the 95th percentile of background locus scores.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	66	Through Bayesian statistical inference, 95% confidence interval estimates for enrichment fold changes can be obtained, making this method particularly suitable for trait analyses with limited locus numbers or traits that fail to reach enrichment thresholds.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	67	During the data preparation phase, significant genetic loci for the target trait were first extracted based on GWAS results, followed by expansion of the original signals using linkage disequilibrium relationships (r2 > 0.8) to capture additional potential functional variants.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	68	In the differential expression analysis component, Wilcoxon rank-sum tests were employed for inter-group comparisons within each cell type, with parameters set as follows: minimum of 3 cells per group, minimum gene expression proportion of 10%, and log2 fold change (log2FC) threshold of 0.5.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	69	Finally, statistically significant enriched cell populations were determined through Benjamini–Hochberg multiple testing correction (BH ≤ 0.05).	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	70	This study employed the CELLECT (CELLtype-specific Expression Integration and Complex Traits) framework, integrating two complementary analytical strategies to dissect the impact of cell type specificity on disease heritability .	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	71	The first strategy utilized the stratified linkage disequilibrium score regression (S-LDSC) method based on heritability to perform in-depth analysis of GWAS summary statistics for ulcerative colitis and colorectal cancer.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	72	Cell type definition data were derived from the tabula_muris-test and mousebrain-test databases, and LD scores were calculated based on the 1000 Genomes Project Phase 3 European population reference panel.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	73	The second strategy utilized the gene-set analysis module of MAGMA software to identify characteristic association signals independent of other cell types by testing the correlation between gene-level association statistics and the mean expression profiles of specific cell types.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	74	The statistical significance criteria for both methods were consistent, with Bonferroni-adjusted P < 0.05 established as the threshold for significant enrichment.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	75	scDRS integrates polygenic GWAS signals with single-cell transcriptomics to evaluate disease relevance at single-cell resolution, bypassing the constraints of traditional marker-based annotations.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	76	By constructing disease-associated gene sets (e.g., top 1000 MAGMA genes) and employing dual weighting—balancing GWAS association strength with single-cell technical noise—complemented by 1000 Monte Carlo simulations, the method ensures robust statistical inference.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	77	Its primary advantage lies in capturing fine-grained intra-cluster heterogeneity and identifying cryptic pathogenic subpopulations that conventional methods often overlook.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	78	By mapping macro-scale genetic susceptibility onto micro-scale cellular states, scDRS provides a refined lens into the mechanisms of complex diseases.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	79	For instance, in inflammatory bowel disease (IBD), scDRS successfully identified diverse associated subpopulations, including CD4 + regulatory T cells, Th2-like, Th17-like, and effector CD8 + T cells, highlighting their distinct functional states ranging from immunosuppressive to pro-inflammatory .	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	80	To ensure statistical robustness across cell populations, significance was defined as FDR-corrected P < 0.05.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	81	To systematically identify key pathogenic cell types in ulcerative colitis and colorectal cancer, this study constructed an integrated assessment framework based on multidimensional evidence.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	82	This framework synthesized evidence chains from four complementary analytical methods: single-cell transcriptomic annotation atlas, ECLIPSER cellular signature identification, CELLECT heritability contribution analysis, and scDRS cellular association analysis .	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	83	In the scoring mechanism design, an equal weighting strategy was adopted, where each independent line of evidence was assigned 1 point for nominal significance and 2 points for significance after multiple testing correction.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	84	The final cumulative score for each cell type was obtained through simple summation of all evidence categories, with higher scores indicating greater likelihood that the cell type plays a central role in disease pathogenesis.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	85	This study employed the hdWGCNA method to perform systematic network analysis on key cell types.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	86	At the initial stage, annotated Seurat objects were loaded and target populations specified.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	87	Following initialization, genes expressed in at least 5% of cells were selected.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	88	To overcome single-cell sparsity, the MetacellsByGroups function constructed metacells (k = 25) based on cell type and sample origin.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	89	After normalization and Harmony-based batch correction, the TestSoftPowers function determined optimal soft-thresholding parameters for constructing a signed topological overlap matrix.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	90	Gene modules were identified using the dynamic tree-cutting algorithm, and module eigengenes (MEs) were calculated.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	91	To delineate module relationships and cell-type specificity, we performed inter-module Pearson correlation analysis and visualized MEs expression across clusters via DotPlots.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	92	Core regulatory components were identified by calculating gene module membership (kME), with the top 10 genes designated as hub genes for network visualization.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	93	Finally, comprehensive functional enrichment analysis was performed using multiple databases (GO, KEGG, Reactome, etc.)	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	94	via the Enrich framework.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	95	This study employed the FUMA (Functional Mapping and Annotation) bioinformatics platform (https://fuma.ctglab.nl/snp2gene) for systematic identification and functional annotation of genomic risk loci .	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	96	The input data for analysis consisted of genome-wide association study result files for ulcerative colitis and colorectal cancer, containing SNP identifiers and their corresponding genomic linkage disequilibrium reference information.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	97	The FUMA platform first implemented a stringent quality control pipeline on uploaded GWAS data, automatically removing SNP loci with missing values or substandard quality.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	98	We set the genome-wide significance threshold at P < 5 × 10−8.	FullText
PMC13160972	Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis	99	To comprehensively dissect the functional regulatory mechanisms underlying risk loci for ulcerative colitis and colorectal cancer, this study employed the eCAVIAR colocalization analysis method based on a Bayesian statistical framework, aimed at identifying high-confidence functional genes and regulatory elements (eQTL...	FullText

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Dataset Card for CeLLaTe FullText Benchmark Dataset

Dataset summary

The CeLLaTe FullText Benchmark Dataset is a curated collection of biomedical fulltext created as a benchmark set for evaluating CeLLaTe named entity recognition (NER) models. It was extracted from Europe PMC article XML sources, with a focus on open-access articles. The dataset is intended to support model development and testing by providing an independent evaluation set for demo production runs and for rigorously assessing the tagging capacity of the models.

The dataset is unannotated and therefore not suitable for supervised training or quantitative metric-based evaluation. Instead, it is designed for qualitative inspection of model outputs, including entity boundary behaviour, consistency, and error analysis.

Dataset variants

CeLLaTe Abstract Benchmark Dataset (separate release available here) Contains article abstracts extracted from Europe PMC XML sources and prepared as a standalone benchmark set.
CeLLaTe Full-Text Benchmark Dataset(this release) Contains fulltext articles extracted from Europe PMC XML sources and prepared as a standalone benchmark set.

Dataset Sources [optional]

Curated from : Europe PMC
Repository: [More Information Needed]
Paper [optional]: [More Information Needed]
Demo [optional]: [More Information Needed]

Intended Uses

This dataset can be used for:

qualitative benchmarking of NER model outputs
manual inspection of tagging performance
exploratory analysis of entity coverage and boundary consistency
analysing entity coverage in fulltext scientific writing
unsupervised or semi-supervised use cases such as pretraining and representation learning
sentence-level processing tasks such as sentence segmentation or sentence-based downstream analysis

Direct Use

Qualitative performance analysis of Biomedical NER models
Several Unsupervised NLP tasks such as Topic modelling, pretraining/domain-specific contuined pretraning, sentence-based downstream analysis etc

Out-of-Scope Use

This dataset cannot be used as:

supervised training data for NER/NLP models
validation data for metric reporting (e.g. F1, precision, recall)
quantitative benchmarking against annotated gold labels
a source of ground-truth entity spans

Data characteristics

Domain: Biomedical literature Source type: Europe PMC XML-derived article text Text type: Article FullText Annotation status: Unannotated Primary purpose: Qualitative NER evaluation

Dataset Structure

The dataset is organised at the sentence level. Each record corresponds to a sentence extracted from an article fulltext and includes the following fields:

Sentence: the sentence-level text extracted from the fulltext articles
PMCID: the PMCID of the source article from which the sentence was generated
Title: the title of the source article
Sentence_ID: a sequential identifier for the sentence within the article

Dataset Creation

Curation Rationale

The dataset was curated to provide a representative fulltext-level benchmark for qualitative evaluation of CeLLaTe NER models. Its purpose is to support:

independent testing on unseen biomedical text
demo-style production evaluation
inspection of entity boundary behaviour
assessment of tagging consistency across models
comparison of model behaviour on fulltext scientific writing

Evaluation notes

Because the dataset is unannotated, its primary value lies in qualitative analysis rather than formal supervised evaluation. Therefore, evaluation should focus on:

qualitative error inspection
entity boundary behaviour
false positive and false negative patterns
consistency across models and samples
robustness of the tagging pipeline

Data Collection and Processing

The fulltexts were collected from Europe PMC XML records for open-access biomedical articles. The source XML was parsed to extract article metadata and fulltext text, including the article title and PMCID.

During preprocessing:

irrelevant or non-informative XML sections were removed e.g acknowledgements, references etc
whitespace and formatting artefacts were normalised
fulltext texts was split into sentence-level units
each sentence was linked back to its source article using the PMCID and Title fields

Versioning

Dataset name: CeLLaTe FullText Benchmark Dataset Release type: FullText benchmark set Current state: Unannotated Use case: Qualitative NER evaluation and demo testing

Limitations

No gold-standard labels are available.
Quantitative scores cannot be interpreted as absolute model performance on this dataset.
Results depend on manual review and qualitative comparison rather than formal metric computation.

Citation and attribution

If this dataset is used in reports or publications, it should be described as a CeLLaTe benchmark dataset derived from Europe PMC article text and clearly identified as an unannotated qualitative evaluation set.

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Curated by:

Amina Mardiyyah Rufai

Funded by [optional]:

[OTAR3088]

Shared by [optional]:

Amina Mardiyyah Rufai