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 272

System / cell line: lines ✕ Assay: gene ✕ Clear

Chipping away at 'stemness'.

PMID 15287966 · PMC507869 · Genome biology · 2004 · 8 claims · 6 setups

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Global gene-expression analyses across five independent studies identify known and new candidate regulators of human ES-cell growth, self-renewal, and pluripotency.

microarray sage custom
Integrative analysis of RUNX1 downstream pathways and target genes.

PMID 18671852 · PMC2529319 · BMC genomics · 2008 · 7 claims · 8 setups

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Integrating gene expression profiles from three independent RUNX1 perturbation platforms (FPD-AML patient cell lines, RUNX1/CBFβ overexpression in HeLa cells, Runx1 knockout mouse embryos) identifies RUNX1-regulated genes and downstream pathways

lymphoblastic hela runx1 aml cdna microarray affymetrix
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
Integrating complex genomic datasets and tumour cell sensitivity profiles to address a 'simple' question: which patients should get this drug?

PMID 20003409 · PMC2799438 · BMC medicine · 2009 · 8 claims · 5 setups

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A panel of 48 genomically characterized breast cancer cell lines can model patient tumour heterogeneity to identify biomarkers predicting response to PG-11047

panel breast 250-gene candidate genome growth pathway
Exploiting convergent phenotypes to derive a pan-cancer cisplatin response gene expression signature.

PMID 37076665 · PMC10115855 · NPJ precision oncology · 2023 · 8 claims · 8 setups

Has reproduction · 50

A convergent-phenotype-based seed gene/co-expression method can extract consensus gene expression signatures predictive of response to chemotherapeutic drugs in the GDSC database

epithelial-based tcga gdsc muscle-invasive differential co-expression signature
The human homologue of unc-93 maps to chromosome 6q27 - characterisation and analysis in sporadic epithelial ovarian cancer.

PMID 12381271 · PMC134458 · BMC genetics · 2002 · 7 claims · 8 setups

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UNC93A maps within the minimal region of allele loss on 6q27 between D6S264 and D6S149, centromeric to D6S149

panel 293-t malignant same rt-pcr northern fluorescence
Towards precise classification of cancers based on robust gene functional expression profiles.

PMID 15774002 · PMC1274255 · BMC bioinformatics · 2005 · 6 claims · 7 setups

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Functional expression profiles (FEPs) achieve comparable or better classification performance than conventional gene expression profiles (GEPs) across four public microarray datasets

nci60 lymphoma fep go-annotated cdna recursive hypergeometric
Does tumorigenesis select for or against mutations of the DNA repair-associated genes BRCA2 and MRE11?: considerations from somatic mutations in microsatellite unstable (MSI) gastrointestinal cancers.

PMID 16417627 · PMC1382246 · BMC genetics · 2006 · 8 claims · 7 setups

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Heterozygous truncating BRCA2 mutations occur in 47% (7/15) of gastrointestinal MSI cancer cell lines/xenografts, a higher rate than previously reported

gastrointestinal ls174t pl3 msi gene rt-pcr rad51
Population genomics of human gene expression.

PMID 17873874 · PMC2683249 · Nature genetics · 2007 · 8 claims · 8 setups

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Gene expression levels in lymphoblastoid cell lines are a heritable trait

ebv-transformed ceu lymphoblastoid unrelated genome-wide custom cis-eqtl
Cis sequence effects on gene expression.

PMID 17727713 · PMC2077339 · BMC genomics · 2007 · 6 claims · 4 setups

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Approximately one in four genes (8 of 30, 26.7%) exhibit statistically significant cis sequence effects on gene expression in this study, consistent with a literature-wide weighted average of 26.2%

lymphoblastoid genomic oligonucleotide gene candidate snp
Relative impact of nucleotide and copy number variation on gene expression phenotypes.

PMID 17289997 · PMC2665772 · Science (New York, N.Y.) · 2007 · 8 claims · 5 setups

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SNPs and CNVs capture largely non-overlapping signals of genetic variation affecting gene expression

lymphoblastoid same computational subset gene snp array
Allelic imbalance in gene expression as a guide to cis-acting regulatory single nucleotide polymorphisms in cancer cells.

PMID 17267408 · PMC1865061 · Nucleic acids research · 2007 · 6 claims · 6 setups

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Measuring allelic imbalance (AI) of two SNP alleles within the same sample is an effective approach for identifying cis-acting rSNPs, since each allele serves as an internal control for the other.

tumor promoter hela cdna bead tag-microarray
A simple and robust method for connecting small-molecule drugs using gene-expression signatures.

PMID 18518950 · PMC2464610 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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A new method for building reference gene-expression profiles and scoring/testing connections improves on the original Connectivity Map by enabling statistical significance testing of connections.

lines random gene-expression connectivity
Functional epigenomics approach to identify methylated candidate tumour suppressor genes in renal cell carcinoma.

PMID 18195710 · PMC2361461 · British journal of cancer · 2008 · 8 claims · 4 setups

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HAI-2/SPINT2 was previously identified as a novel epigenetically inactivated candidate RCC tumour suppressor gene

rcc skrc39 gene rt-pcr bisulphite
Scapuloperoneal spinal muscular atrophy and CMT2C are allelic disorders caused by alterations in TRPV4.

PMID 20037587 · PMC3786192 · Nature genetics · 2010 · 8 claims · 6 setups

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SPSMA and CMT2C are allelic disorders caused by mutations in TRPV4

spsma spsma-affected hek293 candidate histopathology confocal
Identification of phenotype-specific networks from paired gene expression-cell shape imaging data.

PMID 35197309 · PMC8997347 · Genome research · 2022 · 8 claims · 5 setups

Has reproduction · 100

A network-based approach integrating RNA-seq and cell-shape imaging data identifies data-derived signaling networks specific to cell-shape regulation in breast cancer.

breast representative kinases bulk high-throughput immunofluorescence
Mutually exclusive teams-like patterns of gene regulation characterize phenotypic heterogeneity along the noradrenergic-mesenchymal axis in neuroblastoma.

PMID 38230570 · PMC10795782 · Cancer biology & therapy · 2024 · 8 claims · 6 setups

Has reproduction · 87

NOR-specific and MES-specific gene expression patterns are largely mutually exclusive, exhibiting a teams-like behavior across multiple bulk NB transcriptomic datasets

lines bulk single-cell housekeeping bulk pca single-sample
Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.

PMID 38974967 · PMC11225361 · iScience · 2024 · 7 claims · 7 setups

Has reproduction · 95

Luminal breast cancer gene expression signature is closely/positively associated with an epithelial signature

breast-cancer-specific tcga ccle four single-sample survival genome-wide
Molecular analysis of tumor suppressor genes, Rb, p53, p16INK4A, p15INK4B and p14ARF in natural killer cell neoplasms.

PMID 11676855 · PMC5926606 · Japanese journal of cancer research : Gann · 2001 · 8 claims · 5 setups

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Gene amplification of p53 was detected in one nasal NK cell lymphoma

same shifted neoplasm cases southern pcr-sscp direct
Frequent loss of the AXIN1 locus but absence of AXIN1 gene mutations in adenocarcinomas of the gastro-oesophageal junction with nuclear beta-catenin expression.

PMID 14970870 · PMC3215949 · British journal of cancer · 2004 · 8 claims · 7 setups

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Nuclear β-catenin expression in GEJ adenocarcinoma cell lines correlates with enhanced TCF-mediated reporter gene transcription

gej paired showing tumours tcf pcr-sscp bidirectional

Experiments

Chipping away at 'stemness'.

Integrative analysis of RUNX1 downstream pathways and target genes.

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

Integrating complex genomic datasets and tumour cell sensitivity profiles to address a 'simple' question: which patients should get this drug?

Exploiting convergent phenotypes to derive a pan-cancer cisplatin response gene expression signature.

The human homologue of unc-93 maps to chromosome 6q27 - characterisation and analysis in sporadic epithelial ovarian cancer.

Towards precise classification of cancers based on robust gene functional expression profiles.

Does tumorigenesis select for or against mutations of the DNA repair-associated genes BRCA2 and MRE11?: considerations from somatic mutations in microsatellite unstable (MSI) gastrointestinal cancers.

Population genomics of human gene expression.

Cis sequence effects on gene expression.

Relative impact of nucleotide and copy number variation on gene expression phenotypes.

Allelic imbalance in gene expression as a guide to cis-acting regulatory single nucleotide polymorphisms in cancer cells.

A simple and robust method for connecting small-molecule drugs using gene-expression signatures.

Functional epigenomics approach to identify methylated candidate tumour suppressor genes in renal cell carcinoma.

Scapuloperoneal spinal muscular atrophy and CMT2C are allelic disorders caused by alterations in TRPV4.

Identification of phenotype-specific networks from paired gene expression-cell shape imaging data.

Mutually exclusive teams-like patterns of gene regulation characterize phenotypic heterogeneity along the noradrenergic-mesenchymal axis in neuroblastoma.

Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.

Molecular analysis of tumor suppressor genes, Rb, p53, p16INK4A, p15INK4B and p14ARF in natural killer cell neoplasms.

Frequent loss of the AXIN1 locus but absence of AXIN1 gene mutations in adenocarcinomas of the gastro-oesophageal junction with nuclear beta-catenin expression.