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).

• Specific signature biomarkers highlight the potential mechanisms of circulating neutrophils in aneurysmal subarachnoid hemorrhage.

  PMID 36438795 · PMC9685413 · Frontiers in pharmacology · 2022 · 8 claims · 8 setups

  Has reproduction · 80

  A neutrophil-related co-expression gene module (blue module) is significantly associated with aSAH occurrence

  peripheral genes overlapping neutrophil-related microarray weighted kegg

• Evaluating Distribution and Prognostic Value of New Tumor-Infiltrating Lymphocytes in HCC Based on a scRNA-Seq Study With CIBERSORTx.

  PMID 33043022 · PMC7527443 · Frontiers in medicine · 2020 · 6 claims · 8 setups

  Has reproduction · 78

  CIBERSORTx can combine scRNA-seq-derived signature matrices with bulk RNA-seq data to estimate proportions of 11 TIL subsets in HCC tumor and normal tissue

  tcga degs cd4-gzma prognostic scrna-seq cibersortx differential

• 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

  Has reproduction · 55

  352 DEGs (198 up-regulated, 154 down-regulated) were identified between RPL and control endometrial samples

  endometrial degs hub decidua microarray wgcna machine

• Prediction of prognostic signatures in triple-negative breast cancer based on the differential expression analysis via NanoString nCounter immune panel.

  PMID 33138797 · PMC7607642 · BMC cancer · 2020 · 8 claims · 8 setups

  Has reproduction · 72

  edgeR-based DEG selection is more appropriate for feature selection than Elastic Net when sample sizes are small.

  ffpe same nanostring tnbc nanostring immunohistochemistry differential

• Identification of a novel 10 immune-related genes signature as a prognostic biomarker panel for gastric cancer.

  PMID 34382341 · PMC8446556 · Cancer medicine · 2021 · 8 claims · 8 setups

  Has reproduction

  A 10-IRG prognostic signature (BMPR1B, GHR, IL11RA, INHBB, NPR3, OBP2A, PTN, R3HDML, TAC1, TPM2) predicts overall survival in gastric cancer.

  gastric tcga-stad overlapping candidate microarray gene rna-seq

• Integrative analysis reveals chemokines CCL2 and CXCL5 mediated shear stress-induced aortic dissection formation.

  PMID 38163105 · PMC10757018 · Heliyon · 2024 · 8 claims · 8 setups

  Has reproduction · 75

  Integration of three AD RNA-seq datasets identifies 150 common DEGs (100 down-regulated, 50 up-regulated) enriched for blood vessel morphogenesis, muscle structure/tissue development, and chemotaxis.

  aortic gene computational normalized bulk ppi connectivity

• 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

  Has reproduction · 71

  AML cases can be categorized into two distinct PANRG (PANoptosis-related gene) clusters with differentially expressed prognostic genes (PRDEGs)

  aml hovon cancer tcga bulk consensus machine

• Identification of Key Genes in Atherosclerosis by Combined DNA Methylation and miRNA Expression Analyses.

  PMID 35949126 · PMC9682560 · Anatolian journal of cardiology · 2022 · 7 claims · 7 setups

  Full-text index only

  10 key genes (TCF7L2, CACNA1C, NRP1, GABBR2, FANCC, DCK, CCDC88C, TCF12, ABLIM1, PBX1) are regulated by both aberrant DNA methylation and miRNA activity in atherosclerosis

  aorta cardiovascular peripheral blood methylation mirna expression

• Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis.

  PMID 20003344 · PMC2801700 · BMC genomics · 2009 · 7 claims · 8 setups

  Full-text index only

  Meta-analysis of 16 microarray datasets across human, mouse, rat and yeast identifies 164 genes (MDEGs) consistently differentially expressed in response to high fat diet or PPAR signaling perturbation.

  liver saccharomyces mdeg independent microarray transcription chromosomal

• Cancer-wide in silico analyses using differentially expressed genes demonstrate the functions and clinical relevance of JAG, DLL, and NOTCH.

  PMID 39074091 · PMC11285958 · PloS one · 2024 · 7 claims · 8 setups

  Full-text index only

  JAG, DLL, and NOTCH family gene/protein expression varies diversely across 15 cancer types relative to normal tissue, sometimes discordant between mRNA and protein levels.

  tumor degs cancer jag bulk proteomics gene

• Assessing personalized molecular portraits underlying endothelial-to-mesenchymal transition within pulmonary arterial hypertension.

  PMID 39462326 · PMC11513636 · Molecular medicine (Cambridge, Mass.) · 2024 · 8 claims · 8 setups

  Has reproduction · 81

  scRNA-seq of PAH and control lung tissue identifies nine distinct cell populations with high heterogeneity in composition, function, distribution, and communication

  lung pah scrna-seq-derived endothelial scrna-seq bulk cell-cell

• Migratory Tumor Cells Cooperate with Cancer Associated Fibroblasts in Hormone Receptor-Positive and HER2-Negative Breast Cancer.

  PMID 38892065 · PMC11172245 · International journal of molecular sciences · 2024 · 8 claims · 8 setups

  Full-text index only

  HR+/HER2-BC tumor epithelial cells comprise four single-cell-defined functional (SC-f) subtypes: migratory, secretory, proliferating, and dysfunctional.

  hr+ epcam-sorted tumor tcga-brca droplet sidr-seq bulk

• Artificial Intelligence Meets Whole Slide Images: Deep Learning Model Shapes an Immune-Hot Tumor and Guides Precision Therapy in Bladder Cancer.

  PMID 36245985 · PMC9553530 · Journal of oncology · 2022 · 8 claims · 8 setups

  Has reproduction

  A three-class WSI cluster (C0/C1/C2) derived via mini batch K-means clustering on Inception V3-extracted image features is significantly associated with overall survival and is an independent prognostic predictor in BLCA.

  tcga-blca gse32894 deep transfer machine

• High DNA methylation age deceleration defines an aggressive phenotype with immunoexclusion environments in endometrial carcinoma.

  PMID 37388735 · PMC10303802 · Frontiers in immunology · 2023 · 8 claims · 8 setups

  Has reproduction · 76

  Almost 90% of TCGA EC tumors exhibit DNA methylation age deceleration (DNAmad) relative to patient chronological age as assessed by the Horvath clock

  tumors metastatic methylation bulk kegg

• 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

  Has reproduction · 73

  Consensus clustering on 32 disulfidptosis-associated genes stratifies GBM patients into two subtypes, DRGcluster A and B, with distinct survival outcomes.

  fresh tcga gbm bulk rna-seq consensus