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).

• Tissue microarrays characterise the clinical significance of a VEGF-A protein expression signature in gastrointestinal stromal tumours.

  PMID 17299397 · PMC2360083 · British journal of cancer · 2007 · 8 claims · 5 setups

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  A combined VEGF-A ligand and flt-1 receptor protein expression signature discriminates malignant from benign GIST

  archival tma genomic pcr immunohistochemistry unsupervised pcr-dhplc

• High resolution melting analysis for rapid and sensitive EGFR and KRAS mutation detection in formalin fixed paraffin embedded biopsies.

  PMID 18495026 · PMC2408599 · BMC cancer · 2008 · 8 claims · 4 setups

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  HRM correctly identified all 73 EGFR-mutation-positive FFPE samples previously found by sequencing, giving 100% sensitivity and 90% specificity

  ffpe single high direct hrm

• Generative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material.

  PMID 41029822 · PMC12486589 · Journal of translational medicine · 2025 · 8 claims · 5 setups

  Has reproduction · 67

  fRNA-seq transcript counts are best fit by the negative binomial distribution, with little evidence supporting zero-inflated extensions

  compendium frna-seq nb-generated breast ffpe distribution synthetic

• Expression and mutational analysis of c-kit in ovarian surface epithelial tumors.

  PMID 16479070 · PMC2733984 · Journal of Korean medical science · 2006 · 8 claims · 3 setups

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  KIT protein expression by immunohistochemistry is more frequent in mucinous ovarian tumors (borderline and malignant) than in serous tumors

  ovarian genomic immunohistochemistry pcr-sscp

• 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 · 7 setups

  Has reproduction · 72

  edgeR identifies 9 DEGs associated with pCR and 13 DEGs associated with relapse from 579 immune genes in a small TNBC sample set (n=55)

  ffpe same nanostring training nanostring immunohistochemistry differential

• STAT3-dependent analysis reveals PDK4 as independent predictor of recurrence in prostate cancer.

  PMID 32323921 · PMC7178451 · Molecular systems biology · 2020 · 6 claims · 4 setups

  Has reproduction · 66

  Low STAT3 expression in primary prostate cancer is associated with up-regulated OXPHOS and ribosomal biosynthesis at the transcriptomic level.

  prostate pca bulk reverse ssgsea

• nm23-H1 protein expression and gene mutation in 150 patients with non-Hodgkin's lymphomas.

  PMID 16891807 · PMC2729885 · Journal of Korean medical science · 2006 · 8 claims · 4 setups

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  High nm23-H1 protein expression is associated with high IPI score in non-Hodgkin's lymphomas

  non-hodgkin's immunohistochemistry pcr-sscp sequencing

• Epidermal growth factor receptor structural alterations in gastric cancer.

  PMID 18199332 · PMC2244615 · BMC cancer · 2008 · 8 claims · 4 setups

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  EGFR structural alterations are rare in gastric carcinoma

  gastric genomic direct fluorescence pcr

• Multimodal data integration for biologically-relevant artificial intelligence to guide adjuvant chemotherapy in stage II colorectal cancer.

  PMID 40472802 · PMC12171563 · EBioMedicine · 2025 · 6 claims · 7 setups

  Has reproduction · 83

  AI-derived radiological clustering identifies stage II CRC patients with significantly different survival benefit from adjuvant chemotherapy

  stage patients tumour whole-tumour radiomics bulk cellular

• Association between cyclo-oxygenase-2 overexpression and missense p53 mutations in gastric cancer.

  PMID 11161397 · PMC2363738 · British journal of cancer · 2001 · 8 claims · 4 setups

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  p53 missense mutation is associated with COX-2 overexpression in gastric cancer

  gastric sscp-shifted immunohistochemistry pcr-sscp direct

• Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling.

  PMID 24888378 · PMC4070569 · BMC genomics · 2014 · 8 claims · 8 setups

  Has reproduction · 77

  Ribo-Zero-Seq removes rRNA with efficiency comparable to poly(A)-based mRNA-Seq in both FF and FFPE RNA, whereas DSN-Seq leaves significantly more rRNA and shows greater variation.

  fresh-frozen ffpe breast unc microarray mrna-seq ribo-zero-seq

• Spatial-reprogramming derived GPNMB(+) macrophages interact with COL6A3(+) fibroblasts to enhance vascular fibrosis in glioblastoma.

  PMID 41174767 · PMC12577258 · Genome medicine · 2025 · 7 claims · 8 setups

  Has reproduction · 64

  A distinct subset of COL6A3+ tumor-associated fibroblasts (TAFs) with matrix-fibroblast characteristics exists in GBM and is significantly enriched in non-responders to neoadjuvant combination therapy.

  newly glioma ffpe tafs single-cell spatial bulk

• FRMD8 inhibits tumor metastasis in BRCA1-associated TNBC by negatively regulating tmTNF-α.

  PMID 40619383 · PMC12229025 · Cellular & molecular biology letters · 2025 · 8 claims · 8 setups

  Has reproduction · 73

  Low FRMD8 expression in BRCA1-mutant breast cancer cells significantly enhances metastatic potential to various organs

  tnbc geo breast frmd8 bulk meta-analysis single-cell

• Correlation between KIT expression and KIT mutation in melanoma: a study of 173 cases with emphasis on the acral-lentiginous/mucosal type.

  PMID 19718013 · PMC4120323 · Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2009 · 8 claims · 2 setups

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  Immunohistochemical KIT expression is significantly associated with KIT mutation status in acral lentiginous/mucosal melanoma

  melanoma immunohistochemistry pcr

• Association between cigarette smoking, APC mutations and the risk of developing sporadic colorectal adenomas and carcinomas.

  PMID 16545110 · PMC1475604 · BMC cancer · 2006 · 8 claims · 4 setups

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  Smoking is associated with adenoma and CRC development, with the association strongest in tumors lacking APC truncation mutations

  formalin-fixed ffpe paired study direct pcr restriction

• Unique clinicopathologic features characterize ALK-rearranged lung adenocarcinoma in the western population.

  PMID 19671850 · PMC2865649 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 6 setups

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  20 of 358 (5.6%) lung adenocarcinomas from Western institutions harbored ALK rearrangements

  formalin-fixed lung sections poorly fluorescent immunohistochemistry mutational

• Somatic mutations of KIT in familial testicular germ cell tumours.

  PMID 15150569 · PMC2410291 · British journal of cancer · 2004 · 6 claims · 3 setups

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  No germline KIT mutations were found in constitutional DNA from 240 familial TGCT pedigrees

  blood ffpe familial csge direct contingency

• PD-1 blockade potentiates neoadjuvant chemotherapy in NSCLC via increasing CD127(+) and KLRG1(+) CD8 T cells.

  PMID 37231145 · PMC10213055 · NPJ precision oncology · 2023 · 8 claims · 4 setups

  Has reproduction · 40

  Adding PD-1 blockade to neoadjuvant chemotherapy (NAPC) increases tumor infiltration of CD20+ B cells, CD4+ T cells, CD4+CD127+ T cells, CD8+ T cells, CD8+CD127+ and CD8+KLRG1+ T cells, whereas NAC alone increases only CD20+ B cells.

  cd45+ ffpe nsclc scrna-seq single-cell multiplex geo

• AI-assisted discovery of an ethnicity-influenced driver of cell transformation in esophageal and gastroesophageal junction adenocarcinomas.

  PMID 36134663 · PMC9675486 · JCI insight · 2022 · 8 claims · 8 setups

  Has reproduction · 84

  An AI-guided Boolean network approach (BoNE) models transcriptomic continuum states of normal esophagus, BE, and EAC to derive classifier gene signatures

  gene keratinocyte-derived ffpe spt6-depleted boolean rna-seq immunohistochemistry

• Elucidating the Prognostic and Therapeutic Implications of Insulin Resistance Genes in Breast Cancer: A Machine Learning-Powered Analysis.

  PMID 40427728 · PMC12109394 · Biology · 2025 · 8 claims · 8 setups

  Has reproduction · 84

  A seven-gene IRG prognostic signature (LIFR, EZR, TBC1D4, NSF, RPL5, SAA1, PGK1) predicts overall survival in breast cancer across training and four validation cohorts

  tcga-brca triple-negative ffpe bulk univariate kaplan-meier