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).

Publications 1.3k Datasets 392.5k Experiments 20

System / cell line: er+ ✕ Assay: immunohistochemistry ✕ Clear

A metadata approach for clinical data management in translational genomics studies in breast cancer.

PMID 19948017 · PMC3225860 · BMC medical genomics · 2009 · 8 claims · 5 setups

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A metadata/CDE-based approach using CancerGrid's semantic web tools enables automatic integration of heterogeneous clinical datasets without loss of original detail

clinical breast metadata estrogen her2
Cell clusters overlying focally disrupted mammary myoepithelial cell layers and adjacent cells within the same duct display different immunohistochemical and genetic features: implications for tumor progression and invasion.

PMID 14580259 · PMC314413 · Breast cancer research : BCR · 2003 · 7 claims · 4 setups

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ER-negative cell clusters are far more likely than ER-positive clusters to overlie disrupted myoepithelial cell layers, both at the case level and the individual-disruption level

paraffin selected microdissected double immunohistochemistry loss
Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?

PMID 18036263 · PMC2246181 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups

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Revised multifactorial likelihood analysis incorporating ER, CK5/6, and CK14 tumor immunohistochemistry improves classification of BRCA1 unclassified variants

archival kconfab myriad lymphoblastoid immunohistochemistry multifactorial co-occurrence
Squamous morules are functionally inert elements of premalignant endometrial neoplasia.

PMID 19180120 · PMC2633489 · Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2009 · 8 claims · 5 setups

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Squamous morules are hormonally incompetent, lacking ER/PR expression and proliferative activity, unlike the glandular component

endometrial ein microdissected morule-bearing immunohistochemistry laser retrospective
Divide and conquer: progress in the molecular stratification of cancer.

PMID 19718393 · PMC2730607 · Yonsei medical journal · 2009 · 8 claims · 8 setups

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Cancers exhibit significant clinical, histopathologic, and molecular heterogeneity between individual patients

breast nsclc colon early-stage immunohistochemistry gene comparative
Germline truncating mutations in both MSH2 and BRCA2 in a single kindred.

PMID 14735197 · PMC2409581 · British journal of cancer · 2004 · 8 claims · 8 setups

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Kindred MON1080 carries germline truncating mutations in both MSH2 and BRCA2, with two family members being double heterozygotes

colonic astrocytoma breast microdissected immunohistochemistry microsatellite truncation
PIK3CA-activating mutations and chemotherapy sensitivity in stage II-III breast cancer.

PMID 18371219 · PMC2397526 · Breast cancer research : BCR · 2008 · 7 claims · 4 setups

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PIK3CA mutations are not associated with altered sensitivity to preoperative anthracycline-based or taxane-based chemotherapy in ER-positive and ER-negative breast tumors

tumor breast stage direct immunohistochemistry fluorescence
Basic and applied biology of the primate reproductive tract--a symposium in honor of the career of Dr Robert M Brenner: introduction and overview.

PMID 17118166 · PMC1775062 · Reproductive biology and endocrinology : RB&E · 2006 · 8 claims · 6 setups

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A critical ~36-hour window exists after progesterone withdrawal in macaques during which menstruation can still be blocked by progesterone add-back, after which it becomes inevitable

ovariectomized baboon endometrium macaque hormone laparoscopic immunohistochemistry
Alcohol consumption and breast tumor mitochondrial DNA mutations.

PMID 19847642 · PMC4403627 · Breast cancer research and treatment · 2010 · 8 claims · 6 setups

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Somatic mtDNA mutations are a frequent occurrence in breast tumors

breast paraffin-embedded blood study ttge sequencing immunohistochemistry
25th Annual San Antonio Breast Cancer Symposium, San Antonio, Texas, USA, 10-14 December 2002 Update on preclinical and translational research.

PMID 12631391 · PMC154153 · Breast cancer research : BCR · 2003 · 8 claims · 8 setups

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Growth factor signalling (EGF/HER-2/MAPK, AKT) phosphorylates the oestrogen receptor and drives development of endocrine-resistant breast cancer

xenograft serum frozen tumour xenograft mass cdna
COVID-19 lung disease shares driver AT2 cytopathic features with Idiopathic pulmonary fibrosis.

PMID 35870428 · PMC9297827 · EBioMedicine · 2022 · 8 claims · 8 setups

Has reproduction · 85

COVID-19 lung disease resembles IPF at a fundamental level, recapitulating ViP/IPF gene expression patterns, an IL15-centric cytokine storm, and AT2 cytopathic changes (injury, DNA damage, transient progenitor-state arrest, senescence/SASP).

lung covid-19 interaction pre-clinical composite single-cell kaplan-meier
TP53 mutation analyses on breast carcinomas: a study of paraffin-embedded archival material.

PMID 8761369 · PMC2074687 · British journal of cancer · 1996 · 8 claims · 8 setups

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CDGE can be used to successfully detect TP53 mutations (exons 5-8) in DNA extracted from archival paraffin-embedded breast carcinoma tissue

archival pcr breast tumour pcr-cdge direct restriction
Advances in breast cancer: pathways to personalized medicine.

PMID 19088015 · PMC4535810 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 8 setups

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Germline BRCA1/BRCA2 mutations are strong predictors of breast and ovarian cancer, conferring a 40-80% lifetime risk of breast cancer

population-based women breast high-risk germline genome-wide microarray
Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.

PMID 18510725 · PMC2481497 · Breast cancer research : BCR · 2008 · 7 claims · 7 setups

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Unsupervised hierarchical clustering of 130 SELDI-TOF peaks yielded six peak clusters and five distinct groups of breast cancer patients.

lysates breast microarrays imac-preseparated seldi-tof pilot immunohistochemistry
Two-dimensional electrophoretic comparison of metastatic and non-metastatic human breast tumors using in vitro cultured epithelial cells derived from the cancer tissues.

PMID 18416831 · PMC2377273 · BMC cancer · 2008 · 6 claims · 4 setups

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Three protein spots were significantly altered in abundance between metastase-positive and metastase-negative breast cancer patient groups

excised formalin-fixed log-normalized two-dimensional liquid immunohistochemistry
Tissue proteomics reveals differential and compartment-specific expression of the homologs transgelin and transgelin-2 in lung adenocarcinoma and its stroma.

PMID 19848416 · PMC2789179 · Journal of proteome research · 2009 · 6 claims · 6 setups

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Transgelin (TAGLN), transgelin-2 (TAGLN2), and cyclophilin A (PPIA) are overexpressed in lung adenocarcinoma tissue compared to matched normal lung

matched excised additional formalin-fixed 2-d lc-ms quantitative
IRSN-23 gene diagnosis enhances breast cancer subtype classification and predicts response to neoadjuvant chemotherapy: new validation analyses.

PMID 40128415 · PMC11993443 · Breast cancer (Tokyo, Japan) · 2025 · 8 claims · 8 setups

Has reproduction · 71

IRSN-23 Gp-R patients have significantly higher pCR rates than Gp-NR patients without anti-HER2 therapy, across the OUH cohort and multiple independent public datasets

breast microarray rna-seq exome
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
The motor neuron m6A repertoire governs neuronal homeostasis and FTO inhibition mitigates ALS symptom manifestation.

PMID 40307231 · PMC12043976 · Nature communications · 2025 · 8 claims · 8 setups

Has reproduction · 59

m6A hypomethylation (not hypermethylation) is consistently associated with ALS across patient iPSC-MNs, postmortem tissue, and independent transcriptomic datasets

familial wild-type hek293t motor transcriptomic m6a shrna
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

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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

Experiments

A metadata approach for clinical data management in translational genomics studies in breast cancer.

Cell clusters overlying focally disrupted mammary myoepithelial cell layers and adjacent cells within the same duct display different immunohistochemical and genetic features: implications for tumor progression and invasion.

Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?

Squamous morules are functionally inert elements of premalignant endometrial neoplasia.

Divide and conquer: progress in the molecular stratification of cancer.

Germline truncating mutations in both MSH2 and BRCA2 in a single kindred.

PIK3CA-activating mutations and chemotherapy sensitivity in stage II-III breast cancer.

Basic and applied biology of the primate reproductive tract--a symposium in honor of the career of Dr Robert M Brenner: introduction and overview.

Alcohol consumption and breast tumor mitochondrial DNA mutations.

25th Annual San Antonio Breast Cancer Symposium, San Antonio, Texas, USA, 10-14 December 2002 Update on preclinical and translational research.

COVID-19 lung disease shares driver AT2 cytopathic features with Idiopathic pulmonary fibrosis.

TP53 mutation analyses on breast carcinomas: a study of paraffin-embedded archival material.

Advances in breast cancer: pathways to personalized medicine.

Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.

Two-dimensional electrophoretic comparison of metastatic and non-metastatic human breast tumors using in vitro cultured epithelial cells derived from the cancer tissues.

Tissue proteomics reveals differential and compartment-specific expression of the homologs transgelin and transgelin-2 in lung adenocarcinoma and its stroma.

IRSN-23 gene diagnosis enhances breast cancer subtype classification and predicts response to neoadjuvant chemotherapy: new validation analyses.

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

The motor neuron m6A repertoire governs neuronal homeostasis and FTO inhibition mitigates ALS symptom manifestation.

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.