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 · 88
An engineered tumor organoid model reveals cellular identity and signaling trajectories underlying SFPQ-TFE3 driven translocation RCC.
PMID 40463960 · PMC12131257 · iScience · 2025 · 8 claims · 7 setups
SFPQ-TFE3 expression is sufficient to transform normal kidney epithelial tubuloids into tRCC
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Has reproduction · 73
Involvement of N4BP2L1, PLEKHA4, and BEGAIN genes in breast cancer and muscle cell development.
PMID 38859961 · PMC11163233 · Frontiers in cell and developmental biology · 2024 · 8 claims · 8 setups
N4BP2L1, PLEKHA4, and BEGAIN, normally highly expressed in breast myoepithelial and smooth muscle cells, are significantly downregulated in breast tumor tissue of a 50-patient cohort
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Has reproduction · 80
Decoding the tumor microenvironment and molecular mechanism: unraveling cervical cancer subpopulations and prognostic signatures through scRNA-Seq and bulk RNA-seq analyses.
PMID 38482016 · PMC10933018 · Frontiers in immunology · 2024 · 8 claims · 8 setups
C3 PLP2+ Tumor Epithelial Progenitor Cells are a noteworthy subpopulation exerting a pivotal influence on CC differentiation and progression
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Has reproduction · 76
Co-regulation and function of FOXM1/RHNO1 bidirectional genes in cancer.
PMID 33890574 · PMC8104967 · eLife · 2021 · 8 claims · 8 setups
FOXM1 and RHNO1 are head-to-head bidirectional genes regulated by a shared bidirectional promoter (F/R-BDP)
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Has reproduction · 64
Spatial-reprogramming derived GPNMB(+) macrophages interact with COL6A3(+) fibroblasts to enhance vascular fibrosis in glioblastoma.
PMID 41174767 · PMC12577258 · Genome medicine · 2025 · 8 claims · 8 setups
COL6A3+ TAFs are a distinct matrix-fibroblast subset significantly enriched in non-responders to neoadjuvant antiangiogenic+ICB combination therapy
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Has reproduction · 81
Deubiquitination enzyme USP35 negatively regulates MAVS signaling to inhibit anti-tumor immunity.
PMID 40016186 · PMC11868397 · Cell death & disease · 2025 · 8 claims · 8 setups
USP35 interacts with MAVS and removes its K63-linked polyubiquitin chains, inhibiting viral-induced MAVS-TBK1-IRF3 activation and downstream inflammatory gene expression
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Has reproduction · 67
Heterogeneity and Differentiation Trajectories of Infiltrating CD8+ T Cells in Lung Adenocarcinoma.
PMID 36358600 · PMC9658355 · Cancers · 2022 · 7 claims · 8 setups
Infiltrating CD8+ T cells in LUAD can be divided into ten transcriptionally distinct subsets: eight cytotoxic (CTL) subsets, one naive-like (NTL) subset, and one exhausted (ETL) subset.
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Has reproduction · 73
Expression of neurofibromin 1 in colorectal cancer and cetuximab resistance.
PMID 34779495 · PMC8611403 · Oncology reports · 2022 · 7 claims · 8 setups
NF1 is highly expressed in cetuximab-sensitive colorectal cancer cell lines (NCI-H508, Caco2) but weakly expressed in cetuximab-resistant lines (KM12C, SW480)
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Has reproduction · 59
Downregulation of Splicing Factor PTBP1 Curtails FBXO5 Expression to Promote Cellular Senescence in Lung Adenocarcinoma.
PMID 39057099 · PMC11276454 · Current issues in molecular biology · 2024 · 8 claims · 8 setups
PTBP1 is significantly upregulated across multiple cancer types including LUAD, and higher PTBP1 levels are associated with worse LUAD patient survival
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Identification of transformation-related pathways in a breast epithelial cell model using a ribonomics approach.
PMID 18829526 · PMC2692251 · Cancer research · 2008 · 7 claims · 6 setups
Global association of HuR and AUF1 with target mRNAs changes substantially and largely reciprocally between MCT-1-transformed and nontransformed MCF10A cells
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Has reproduction · 41
Unveiling the immunometabolic landscape of colorectal cancer through PANoptosis-related gene expression.
PMID 41601652 · PMC12832467 · Frontiers in immunology · 2025 · 8 claims · 8 setups
PANoptosis-related genes show significant expression heterogeneity across CRC samples, with apoptosis-related genes comprising the largest proportion (87.4%)
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Has reproduction · 85
PDGFRA defines the mesenchymal stem cell Kaposi's sarcoma progenitors by enabling KSHV oncogenesis in an angiogenic environment.
PMID 31881074 · PMC6980685 · PLoS pathogens · 2019 · 8 claims · 8 setups
Pα(+)S (PDGFRA-positive/SCA-1-positive) bone marrow-derived MSCs are KS spindle-cell progenitors
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Has reproduction · 71
Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.
PMID 37124622 · PMC10131083 · Frontiers in genetics · 2023 · 8 claims · 8 setups
Two distinct RNA modification patterns exist among BCa samples with radically varying clinical outcomes and biological characteristics
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Has reproduction · 61
Multi-omics analyses identify mannose phosphate isomerase-centered hypoxia-induced angiogenesis signature in colorectal cancer.
PMID 41204349 · PMC12595641 · Journal of translational medicine · 2025 · 8 claims · 8 setups
Twelve HIA-related genes were identified that are transcriptionally activated by HIF1A/HIF2A and functionally implicated in angiogenesis in CRC
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Identification of novel gene amplifications in breast cancer and coexistence of gene amplification with an activating mutation of PIK3CA.
PMID 19706770 · PMC2745517 · Cancer research · 2009 · 8 claims · 8 setups
Genome-wide DNA copy number analysis of 161 primary breast tumors identified six novel focally amplified genes: POLD3, IRAK4, IRX2, TBL1XR1, ASPH, and BRD4
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Has reproduction · 80
Comprehensive analysis of transcriptomics and radiomics revealed the potential of TEDC2 as a diagnostic marker for lung adenocarcinoma.
PMID 39553728 · PMC11569783 · PeerJ · 2024 · 8 claims · 8 setups
WGCNA identified 214 key genes in the blue module most correlated with LUAD
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Has reproduction · 49
Integrative transcriptomics and single-cell transcriptomics analyses reveal potential biomarkers and mechanisms of action in papillary thyroid carcinoma.
PMID 40520228 · PMC12162626 · Frontiers in genetics · 2025 · 8 claims · 8 setups
ENTPD1, SERPINA1, and TACSTD2 are potential transcriptomic biomarkers for PTC
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Has reproduction · 62
Specific Marker Gene Analysis for Primary Central Nervous System Lymphoma Based on Methylation Difference and Development of Detection Primers.
PMID 41097902 · PMC12528802 · Brain and behavior · 2025 · 7 claims · 5 setups
450K microarray analysis identified 26 overlapping differential methylation sites distinguishing PCNSL from CNS and non-CNS groups
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Has reproduction · 78
Identification of succinylation-related genes in bladder cancer: integration of single-cell and transcriptomic data.
PMID 42220482 · PMC13218921 · Frontiers in immunology · 2026 · 8 claims · 8 setups
KCTD16, CD3D, and GSDMB were identified as prognostic succinylation-related genes in BLCA
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Has reproduction · 55
Identification and verification of diagnostic biomarkers in recurrent pregnancy loss via machine learning algorithm and WGCNA.
PMID 37691920 · PMC10485775 · Frontiers in immunology · 2023 · 8 claims · 8 setups
352 DEGs (198 up-regulated, 154 down-regulated) were identified between RPL and control endometrial samples