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).

• 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

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

  breast early-stage diffuse dlbcl gene

• Effects of two common polymorphisms in the 3' untranslated regions of estrogen receptor beta on mRNA stability and translatability.

  PMID 19754929 · PMC2759954 · BMC genetics · 2009 · 8 claims · 4 setups

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  Breast tumor heterozygotes show a significant difference in relative mRNA levels between the two alleles of rs4986938

  breast hek293 erβ1 allelic luciferase stability

• HapMap-based study of the 17q21 ERBB2 amplicon in susceptibility to breast cancer.

  PMID 17117180 · PMC2360759 · British journal of cancer · 2006 · 6 claims · 5 setups

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  Common genetic variation (tSNPs and haplotypes) across the 400-kb 17q21 ERBB2 amplicon is not associated with breast cancer risk in British women.

  white same hapmap snp haplotype tagging

• Cognitive and emotional factors predicting decisional conflict among high-risk breast cancer survivors who receive uninformative BRCA1/2 results.

  PMID 19751083 · PMC3510002 · Health psychology : official journal of the Division of Health Psychology, American Psychological Association · 2009 · 8 claims · 8 setups

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  High-risk breast cancer survivors who receive uninformative BRCA1/2 results show four distinct patterns of decision making about breast cancer risk management, based on timing and stability of decision status across 1-, 6-, and 12-month post-disclosure assessments

  high-risk decisional single-item brief

• 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

• Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer.

  PMID 17868458 · PMC2375029 · Genome biology · 2007 · 8 claims · 8 setups

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  Co-culture of certain breast cancer cell lines with stromal fibroblasts induces interferon-response genes (IRGs) in a subset of cancer cells

  mda-mb231 epithelial breast early-stage cdna quantitative facs

• BRCA1 and BRCA2 missense variants of high and low clinical significance influence lymphoblastoid cell line post-irradiation gene expression.

  PMID 18497862 · PMC2375115 · PLoS genetics · 2008 · 8 claims · 6 setups

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  BRCA1 and BRCA2 pathogenic mutation carriers have similar post-irradiation LCL gene expression profiles to each other, more so than to BRCAX samples without an LCS variant

  lymphoblastoid lcl gene microarray unsupervised t-test

• GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data.

  PMID 31110304 · PMC6527554 · Scientific reports · 2019 · 8 claims · 7 setups

  Has reproduction · 73

  GREIN is a web application providing user-friendly interfaces to manipulate, visualize, and analyze GEO RNA-seq data.

  mcf10a nde&dt hypoxia bulk correlation pca

• Stemming cancer: functional genomics of cancer stem cells in solid tumors.

  PMID 18561035 · PMC2758383 · Stem cell reviews · 2008 · 8 claims · 8 setups

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  Cancer stem cells are a minority tumor subpopulation that alone can maintain indefinite tumor growth, as shown by serial transplantation experiments

  solid fetal cd133+ breast facs neurosphere genome-wide

• Contribution of oncoproteomics to cancer biomarker discovery.

  PMID 17407558 · PMC1852117 · Molecular cancer · 2007 · 6 claims · 8 setups

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  Oncoproteomic biomarker panels (2-DE/MS-based) show higher sensitivity and specificity than currently used single tumor markers across multiple cancer types (Table 1)

  serum bladder nipple colorectal 2-de isotope-coded immunoblotting

• The proteogenomic path towards biomarker discovery.

  PMID 18764911 · PMC2574627 · Pediatric transplantation · 2008 · 8 claims · 8 setups

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  Serum creatinine is a widely used but non-ideal biomarker for renal transplant monitoring because it lacks specificity and sensitivity for graft injury

  renal urine breast chronic microarray immunoassay gel

• Editing of hnRNP K protein mRNA in colorectal adenocarcinoma and surrounding mucosa.

  PMID 16404425 · PMC2361188 · British journal of cancer · 2006 · 7 claims · 8 setups

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  A G274A base substitution in hnRNP K mRNA is present in colorectal tumours and surrounding mucosa but absent from corresponding genomic DNA, indicating an RNA editing event rather than a germline polymorphism.

  colorectal cdna matched thyroid rt-pcr restriction genomic