Experiments
Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).
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Has reproduction · 45
NUSAP1 Could be a Potential Target for Preventing NAFLD Progression to Liver Cancer.
PMID 35431924 · PMC9010788 · Frontiers in pharmacology · 2022 · 7 claims · 8 setups
NUSAP1 is a hub gene linking NAFLD fibrosis progression and NAFLD-associated HCC
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Has reproduction · 63
Creation of a Single Cell RNASeq Meta-Atlas to Define Human Liver Immune Homeostasis.
PMID 34335581 · PMC8322955 · Frontiers in immunology · 2021 · 7 claims · 8 setups
Three independently generated human liver CD45+ scRNA-seq datasets (LACEe, Lnb, LCD45e) can be co-clustered and integrated despite differing sequencing platforms and processing protocols.
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Has reproduction
Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data.
PMID 35473573 · PMC9044877 · Genome biology · 2022 · 8 claims · 8 setups
Combining multiple enhancer-definition and enhancer-gene link data sources yields 1860 genome-wide EnTDefs covering >500 cell types
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Has reproduction · 100
Identification of phenotype-specific networks from paired gene expression-cell shape imaging data.
PMID 35197309 · PMC8997347 · Genome research · 2022 · 8 claims · 8 setups
WGCNA-derived gene coexpression modules from breast cancer cell line RNA-seq data correlate significantly with specific cell-shape features
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Has reproduction · 63
RummaGEO: Automatic mining of human and mouse gene sets from GEO.
PMID 39569206 · PMC11573963 · Patterns (New York, N.Y.) · 2024 · 8 claims · 7 setups
RummaGEO is a gene expression signature search engine built from automatically mined human and mouse RNA-seq perturbation studies in GEO
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Has reproduction · 67
Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites.
PMID 37847658 · PMC10628388 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 6 setups
PSPred-ALE outperforms state-of-the-art SARS-CoV-2 phosphorylation site predictors (e.g. DeepIPs) and handcrafted feature-based methods in benchmarking comparisons
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Has reproduction
Systematic analysis of CNGCs in cotton and the positive role of GhCNGC32 and GhCNGC35 in salt tolerance.
PMID 35931984 · PMC9356423 · BMC genomics · 2022 · 8 claims · 8 setups
114 CNGC genes were identified across the genomes of four cotton species (G. arboreum, G. raimondii, G. barbadense, G. hirsutum)
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Has reproduction · 71
Machine Learning-Based Integrated Analysis of PANoptosis Patterns in Acute Myeloid Leukemia Reveals a Signature Predicting Survival and Immunotherapy.
PMID 38322112 · PMC10846924 · International journal of clinical practice · 2024 · 8 claims · 8 setups
AML cases can be categorized into two distinct PANRG (PANoptosis-related gene) clusters with differentially expressed prognostic genes (PRDEGs)
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Has reproduction · 62
A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference.
PMID 32019526 · PMC7001327 · BMC plant biology · 2020 · 8 claims · 6 setups
Inter-specific differences in vertical distribution/microhabitat preference are associated with distinct dynamics of gene expression during dehydration and rehydration phases
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Has reproduction · 91
Exploring the key genetic association between chronic pancreatitis and pancreatic ductal adenocarcinoma through integrated bioinformatics.
PMID 37501719 · PMC10369079 · Frontiers in genetics · 2023 · 8 claims · 8 setups
CP and PDAC share a co-expression gene network identifiable via WGCNA on independent GEO datasets
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Has reproduction · 67
Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data.
PMID 37994351 · PMC10663991 · F1000Research · 2023 · 8 claims · 6 setups
A comprehensive open-source R workflow combining trajectory inference (monocle3) and pseudo-bulk time course analysis (edgeR) can be applied to multi-sample scRNA-seq data of the mouse mammary gland.
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Has reproduction · 78
Emergent dynamics of underlying regulatory network links EMT and androgen receptor-dependent resistance in prostate cancer.
PMID 36851919 · PMC9957767 · Computational and structural biotechnology journal · 2023 · 8 claims · 7 setups
Simulations of the EMT-AR crosstalk network reveal four possible phenotypes: epithelial-sensitive (ES), epithelial-resistant (ER), mesenchymal-resistant (MR), and mesenchymal-sensitive (MS), with MS occurring rarely
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Has reproduction · 50
Inflammatory Bone Marrow Mesenchymal Stem Cells in Multiple Myeloma: Transcriptional Signature and In Vitro Modeling.
PMID 37958322 · PMC10650304 · Cancers · 2023 · 8 claims · 8 setups
A 279-gene 'iMSC signature' is upregulated in BM MSCs from MM patients compared to healthy donors, identified by reanalysis of single-cell RNA-seq data.
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Has reproduction · 92
Similarities and Differences in Gene Expression Networks Between the Breast Cancer Cell Line Michigan Cancer Foundation-7 and Invasive Human Breast Cancer Tissues.
PMID 34056582 · PMC8155268 · Frontiers in artificial intelligence · 2021 · 8 claims · 6 setups
MCF-7 cell lines and human breast cancer tissues show only minimal similarity in biological processes, though some fundamental functions like cell cycle are conserved.
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Has reproduction · 83
A temporal classifier predicts histopathology state and parses acute-chronic phasing in inflammatory bowel disease patients.
PMID 36694043 · PMC9873918 · Communications biology · 2023 · 8 claims · 8 setups
Disease-specific temporal (dynamic) gene expression and splicing signatures, distinct from fixed timepoint differential expression, can be derived from DSS and adoptive transfer colitis models to capture acute-chronic disease dynamics
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Has reproduction · 78
SPRR1B+ keratinocytes prime oral mucosa for rapid wound healing via STAT3 activation.
PMID 39300285 · PMC11413210 · Communications biology · 2024 · 8 claims · 8 setups
A shared wound healing gene set (P2-WHGs, 146 genes) is constitutively expressed in uninjured oral mucosa but not in uninjured skin
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Has reproduction · 71
Comprehensive comparison of gene expression diversity among a variety of human stem cells.
PMID 36458020 · PMC9706419 · NAR genomics and bioinformatics · 2022 · 8 claims · 8 setups
Tissue origin has a stronger influence on gene expression in iPSCs than in other stem cell types
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Has reproduction · 73
Integrated multiomic analysis reveals disulfidptosis subtypes in glioblastoma: implications for immunotherapy, targeted therapy, and chemotherapy.
PMID 38504986 · PMC10950096 · Frontiers in immunology · 2024 · 8 claims · 8 setups
Consensus clustering on 32 disulfidptosis-associated genes stratifies GBM patients into two subtypes, DRGcluster A and B, with distinct survival outcomes.
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Has reproduction · 100
Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs.
PMID 38594607 · PMC11003151 · Genetics, selection, evolution : GSE · 2024 · 8 claims · 8 setups
H3K27ac ChIP-seq and RNA-seq were used to construct eRNA expression profiles across multiple tissues in Enshi Black (ES) and Duroc pigs, revealing tissue-level eRNA regulatory landscapes
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Has reproduction · 87
Mutually exclusive teams-like patterns of gene regulation characterize phenotypic heterogeneity along the noradrenergic-mesenchymal axis in neuroblastoma.
PMID 38230570 · PMC10795782 · Cancer biology & therapy · 2024 · 8 claims · 6 setups
NOR-specific and MES-specific gene expression patterns are largely mutually exclusive, exhibiting a teams-like behavior across multiple bulk NB transcriptomic datasets