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).

• Comprehensive analyses of telomerase component DKC1 and its association with clinical, molecular and immune landscapes in uterine corpus endometrial carcinoma.

  PMID 40458122 · PMC12127311 · Frontiers in cell and developmental biology · 2025 · 8 claims · 8 setups

  Has reproduction · 71

  DKC1 mRNA and protein expression are significantly upregulated in UCEC tumors compared with non-tumorous endometrial tissue

  ucec ishikawa rna-seq proteomics immunohistochemistry

• Single-Cell Transcriptomic Landscape of Right-Sided Colon Cancer Reveals Cellular and Molecular Features of Metastatic Potential.

  PMID 41898210 · PMC13024220 · Biomedicines · 2026 · 8 claims · 6 setups

  Has reproduction · 71

  RCC_LM tumors exhibit higher genomic instability (CNV score) than RCC_noM tumors

  right-sided malignant epithelial types scrna-seq copy trajectory

• Stage-stratified molecular profiling of non-muscle-invasive bladder cancer enhances biological, clinical, and therapeutic insight.

  PMID 35028613 · PMC8714941 · Cell reports. Medicine · 2021 · 8 claims · 8 setups

  Has reproduction · 75

  Stage-stratified molecular subclassification (analyzing Ta and T1 separately) is more biologically and clinically informative than subtypes derived from all NMIBC combined, especially for T1 tumors.

  stage combined patients copy genome-wide targeted

• 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

• Rapid detection of SMARCB1 sequence variation using high resolution melting.

  PMID 20003390 · PMC2801682 · BMC cancer · 2009 · 8 claims · 6 setups

  Full-text index only

  HRM screening of SMARCB1 amplicons has a zero false negative rate compared to direct sequencing

  genomic same tumor rhabdoid high direct hrm

• Machine learning-based identification of biomarkers and drugs in immunologically cold and hot pancreatic adenocarcinomas.

  PMID 39152432 · PMC11328457 · Journal of translational medicine · 2024 · 7 claims · 8 setups

  Has reproduction · 42

  PAAD tumors can be consensus-clustered into immunologically hot and cold subtypes based on CIBERSORT-derived immune cell fractions, with significantly different survival outcomes.

  paad degs bulk consensus tumor

• Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma.

  PMID 31784732 · PMC6886578 · Nature genetics · 2019 · 8 claims · 8 setups

  Has reproduction · 58

  SOX8 is a previously unrecognized core regulatory TF in FP-RMS, co-localizing with other CR TFs at SEs and essential for tumor cell growth

  rms rh4 h3k27ac pooled chip-seq

• Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes.

  PMID 37190091 · PMC10137100 · Cells · 2023 · 8 claims · 8 setups

  Has reproduction · 54

  Single-cell transcriptomic analysis of EPCAM+Lin- epithelial cells identified unique gene signatures/markers that distinguish ER+, HER2+, ER+HER2+, and TNBC molecular subtypes

  breast epcam+cd45-cd8a-cd4-cd19-cd3e cancer identified single-cell differential crispr-cas9

• Expression genomics in breast cancer research: microarrays at the crossroads of biology and medicine.

  PMID 17397520 · PMC1868923 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups

  Full-text index only

  Genome-wide expression microarray studies reveal transcriptional networks/signatures that explain breast cancer biological and clinical heterogeneity

  breast early-stage diffuse dlbcl gene

• Transcriptomic-Based Quantification of the Epithelial-Hybrid-Mesenchymal Spectrum across Biological Contexts.

  PMID 35053177 · PMC8773604 · Biomolecules · 2021 · 8 claims · 8 setups

  Has reproduction · 100

  The 76GS, KS, and MLR EMT scoring metrics show concordant trends in quantifying EMP across bulk RNA-seq datasets spanning multiple cancer types

  bulk py2t mcf10a airway transcriptomic rna-seq single-cell

• ATBF1 and NQO1 as candidate targets for allelic loss at chromosome arm 16q in breast cancer: absence of somatic ATBF1 mutations and no role for the C609T NQO1 polymorphism.

  PMID 18416817 · PMC2377272 · BMC cancer · 2008 · 8 claims · 7 setups

  Full-text index only

  Five genes (NQO1, ATBF1, DBNDD1, HSBP1, CGI-38) at 16q show significantly lower mRNA expression in breast tumors with LOH at 16q compared to tumors without LOH

  ductal same sporadic paired cdna quantitative genotyping

• Canine tumor cross-species genomics uncovers targets linked to osteosarcoma progression.

  PMID 20028558 · PMC2803201 · BMC genomics · 2009 · 8 claims · 7 setups

  Full-text index only

  High expression of IL-8 and SLC1A3, identified via cross-species mining, is associated with poor outcome in an independent population of human osteosarcoma patients

  canine osteosarcoma independent third oligonucleotide cross-species quantitative

• Indoleamine 2, 3-Dioxygenase 1 and CD8 Expression Profiling Revealed an Immunological Subtype of Colon Cancer With a Poor Prognosis.

  PMID 33425745 · PMC7793995 · Frontiers in oncology · 2020 · 8 claims · 8 setups

  Has reproduction · 48

  A colon cancer subtype with CD8Ahigh IDO1high tumors shows the worst survival despite high CD8 T cell infiltrates

  tcga-coad ncbi-geo tisidb gepia rna-seq tumor-infiltrating gene

• Using random walks to identify cancer-associated modules in expression data.

  PMID 24128261 · PMC4015830 · BioData mining · 2013 · 8 claims · 8 setups

  Has reproduction

  Walktrap-GM, a random-walk community detection algorithm adapted with stopping criteria (maximum modularity, maximum size, maximum module score), identifies modules significantly enriched with cancer genes in expression-weighted interaction networks.

  hepatocellular breast sporadic geo gene differential interaction

• miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes.

  PMID 18029362 · PMC2238982 · Nucleic acids research · 2008 · 8 claims · 6 setups

  Full-text index only

  miRNAMap 2.0 is a resource collecting experimentally verified miRNAs and experimentally verified miRNA target genes in human, mouse, rat and other metazoan genomes

  major tissues conserved predicted quantitative bead-based microarray

• A novel oxidative stress-related gene signature as an indicator of prognosis and immunotherapy responses in HNSCC.

  PMID 38157249 · PMC10781479 · Aging · 2023 · 7 claims · 8 setups

  Has reproduction · 85

  Consensus clustering of 74 oxidative stress-related genes identifies three distinct HNSCC molecular subgroups (Cluster1-3) with significantly different overall survival and tumor stage distribution

  tcga-hnscc gse41613 gse103322 prjeb23709 bulk single-cell immunohistochemistry

• In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs.

  PMID 33636127 · PMC7871767 · Cell · 2021 · 8 claims · 8 setups

  Has reproduction · 95

  icSHAPE was used to determine the in vivo and in vitro structural landscape of the SARS-CoV-2 RNA genome in infected Huh7.5.1 cells, plus UTR structures of six other coronaviruses

  huh7.5.1 sars-cov-2 utrs 18s icshape structure deep-learning

• APC promoter methylation and protein expression in hepatocellular carcinoma.

  PMID 17973119 · PMC2757596 · Journal of cancer research and clinical oncology · 2008 · 6 claims · 7 setups

  Full-text index only

  APC promoter methylation is significantly higher in HCC compared to non-cancerous liver tissue

  hcc liver cholangiocellular benign methylight truncation western

• PD-1 and TIGIT coexpression identifies a circulating CD8 T cell subset predictive of response to anti-PD-1 therapy.

  PMID 33188038 · PMC7668369 · Journal for immunotherapy of cancer · 2020 · 7 claims · 6 setups

  Has reproduction · 75

  The frequency of circulating PD-1+TIGIT+ (DPOS) CD8+ T cells after 1 month of anti-PD-1 therapy is associated with clinical response and overall survival

  pbmcs sorted expanded cancer multiparameter receptor targeted

• Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity.

  PMID 23326238 · PMC3542081 · PLoS genetics · 2013 · 8 claims · 8 setups

  Has reproduction · 49

  B-cell non-Hodgkin lymphomas display striking intra-tumor (intra-sample) and inter-patient (inter-sample) cytosine methylation heterogeneity that increases progressively with disease aggressiveness (NBC<NGC<FL<GCB<ABC).

  dlbcl normal same lymphoma help errbs massarray