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 27

System / cell line: cancer ✕ Assay: sirna ✕ Clear

Solute exchange through gap junctions lessens the adverse effects of inactivating mutations in metabolite-handling genes.

PMID 36107487 · PMC9534548 · eLife · 2022 · 8 claims · 8 setups

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Colorectal cancer (CRC) cells are coupled by gap junctions assembled predominantly from Cx26 (GJB2)

colorectal normal crc microarray tcga single-cell
Proteomic analysis of differential proteins in pancreatic carcinomas: Effects of MBD1 knock-down by stable RNA interference.

PMID 18445260 · PMC2386481 · BMC cancer · 2008 · 8 claims · 5 setups

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Stable RNAi-mediated MBD1 knock-down was successfully established in the BxPC-3 pancreatic cancer cell line using a recombinant siRNA plasmid

bxpc-3 2-d maldi-tof-ms western
Functional restoration of BRCA2 protein by secondary BRCA2 mutations in BRCA2-mutated ovarian carcinoma.

PMID 19654294 · PMC2754824 · Cancer research · 2009 · 8 claims · 7 setups

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Secondary BRCA2 mutations restore BRCA2 protein/reading frame and thereby cause acquired platinum and PARP inhibitor resistance in BRCA2-mutated ovarian carcinoma

ovarian peo1 v-c8-dr-gfp western brca2 crystal
A Double-Negative Prostate Cancer Subtype Is Vulnerable to SWI/SNF-Targeting Degrader Molecules.

PMID 41534092 · PMC13044530 · Cancer research · 2026 · 8 claims · 8 setups

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SWI/SNF-targeting PROTAC treatment reduces viability of CRPC-WNT (AR-negative) cell lines and organoids, not just AR-dependent CRPC

prostate nsg formalin-fixed patient-derived viability western xenograft
Discovering cancer genes by integrating network and functional properties.

PMID 19765316 · PMC2758898 · BMC medical genomics · 2009 · 8 claims · 6 setups

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Cancer genes have distinct PPI network topology (higher connectivity, higher clustering coefficient, shorter path length to known cancer genes) compared to non-cancer genes

genes gene colon ppi pfam term
Epigenome screening highlights that JMJD6 confers an epigenetic vulnerability and mediates sunitinib sensitivity in renal cell carcinoma.

PMID 33634984 · PMC7882098 · Clinical and translational medicine · 2021 · 8 claims · 8 setups

Has reproduction · 85

JMJD6 is identified as a potent epigenetic vulnerability/fitness gene in RCC by integrating GeCK CRISPR screening data with TCGA-KIRC epigenetic regulator survival analysis

pan-cancer tcga-kirc rcc balb crispr rna-seq mtt
A platelet-related signature for predicting the prognosis and immunotherapy benefit in bladder cancer based on machine learning combinations.

PMID 39280688 · PMC11399026 · Translational andrology and urology · 2024 · 8 claims · 8 setups

Has reproduction · 51

An Enet (alpha=0.4) machine-learning algorithm built from 10 platelet-related genes yields the optimal platelet-related signature (PRS) for bladder cancer prognosis, with average C-index 0.73

bladder tcga bulk univariate integrative
Dicer, Drosha, and outcomes in patients with ovarian cancer.

PMID 19092150 · PMC2710981 · The New England journal of medicine · 2008 · 8 claims · 6 setups

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Dicer and Drosha mRNA levels correlate with corresponding protein levels and are decreased in 60% and 51% of ovarian-cancer specimens, respectively

invasive ovarian subgroup cohorts quantitative western immunohistochemistry
Somatic mutations of the Parkinson's disease-associated gene PARK2 in glioblastoma and other human malignancies.

PMID 19946270 · PMC4002225 · Nature genetics · 2010 · 8 claims · 8 setups

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PARK2 is a frequently and specifically targeted gene within recurrent 6q25.2-q27 copy number losses in glioblastoma and colon cancer

colon gbm cancer dbtrg array pcr colony
Prevalence and functional analysis of sequence variants in the ATR checkpoint mediator Claspin.

PMID 19737971 · PMC2994259 · Molecular cancer research : MCR · 2009 · 8 claims · 8 setups

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CLSPN is a mediator protein essential for the ATR- and CHK1-dependent checkpoint response to replicative stress or single-stranded DNA

ebv-immortalized sporadic same caucasian genomic denaturing genotyping
Crunching the bio-numbers.

PMID 14664241 · PMC1316909 · Environmental health perspectives · 2003 · 8 claims · 6 setups

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The eTag Assay System rapidly identifies genes and related proteins without complex sample preparation or follow-up bioinformatics, unlike microarrays

blood model brain lung etag sirna addl
Understanding the function of Pax5 in development of docetaxel-resistant neuroendocrine-like prostate cancers.

PMID 39183332 · PMC11345443 · Cell death & disease · 2024 · 7 claims · 8 setups

Has reproduction · 69

Pax5 is an important transcription factor driving neuronal gene expression and is specific to t-NEPC

ne-like prostate lucap mcrpc atac-seq acetylated-histone rna-seq
Comprehensive analysis of peroxisome proliferator-activated receptors to predict the drug resistance, immune microenvironment, and prognosis in stomach adenocarcinomas.

PMID 38529307 · PMC10962337 · PeerJ · 2024 · 8 claims · 8 setups

Has reproduction · 58

PPARA, PPARD and PPARG are more abnormally expressed in STAD samples and cell lines compared to most of 32 cancer types in TCGA

cancer tcga-stad stomach ges1 rna-seq pearson gsva
Functional role of the KLF6 tumour suppressor gene in gastric cancer.

PMID 19101139 · PMC2970616 · European journal of cancer (Oxford, England : 1990) · 2009 · 7 claims · 8 setups

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The KLF6 locus undergoes loss of heterozygosity (LOH) in a majority of gastric cancer samples and is associated with advanced tumour stage

gastric ags hs746t fluorescent direct quantitative
The dietary bioflavonoid, quercetin, selectively induces apoptosis of prostate cancer cells by down-regulating the expression of heat shock protein 90.

PMID 18726985 · PMC2826114 · The Prostate · 2008 · 7 claims · 8 setups

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Quercetin treatment of prostate cancer cells decreases cell proliferation and viability in a dose-dependent manner

pc-3 excised prostate viability difference nano
Human CRAMP1 specifically promotes the expression of histone H1 genes.

PMID 41663757 · PMC12979687 · EMBO reports · 2026 · 8 claims · 8 setups

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CRAMP1 is a selective regulator of histone H1 gene expression that does not significantly affect core histone gene expression

cancer hek293t rpe1 genome-wide immunoprecipitation-mass western
Constructing an APOBEC-related gene signature with predictive value in the overall survival and therapeutic sensitivity in lung adenocarcinoma.

PMID 37954334 · PMC10637964 · Heliyon · 2023 · 8 claims · 8 setups

Has reproduction · 88

APOBEC family genes are differentially expressed across cancer types and tissues, with APOBEC3B being the most aberrantly upregulated gene in most cancers including LUAD

tcga tcga-luad beas-2b rna-seq somatic gene
Merger of ayurveda and tissue culture-based functional genomics: inspirations from systems biology.

PMID 18348714 · PMC2311278 · Journal of translational medicine · 2008 · 8 claims · 8 setups

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Crude LASH extract and its purified components (withanone, withaferin A) act through distinct but partially overlapping molecular gene-regulatory networks

tumor-derived tumor lash gene cytotoxicity sirna ribozyme
Decoding the tumor microenvironment and molecular mechanism: unraveling cervical cancer subpopulations and prognostic signatures through scRNA-Seq and bulk RNA-seq analyses.

PMID 38482016 · PMC10933018 · Frontiers in immunology · 2024 · 8 claims · 8 setups

Has reproduction · 80

C3 PLP2+ Tumor Epithelial Progenitor Cells are a noteworthy subpopulation exerting a pivotal influence on CC differentiation and progression

cervical tcga siha scrna-seq bulk rt-qpcr
Unveiling the NEFH+ malignant cell subtype: Insights from single-cell RNA sequencing in prostate cancer progression and tumor microenvironment interactions.

PMID 39759507 · PMC11695424 · Frontiers in immunology · 2024 · 8 claims · 8 setups

Full-text index only

A malignant cell subtype in PCa with high expression of NEFH was identified, located at the differentiation terminal, showing higher malignancy and association with advanced tumor lesions.

pca malignant tcga mda single-cell infercnv pseudotime

Experiments

Solute exchange through gap junctions lessens the adverse effects of inactivating mutations in metabolite-handling genes.

Proteomic analysis of differential proteins in pancreatic carcinomas: Effects of MBD1 knock-down by stable RNA interference.

Functional restoration of BRCA2 protein by secondary BRCA2 mutations in BRCA2-mutated ovarian carcinoma.

A Double-Negative Prostate Cancer Subtype Is Vulnerable to SWI/SNF-Targeting Degrader Molecules.

Discovering cancer genes by integrating network and functional properties.

Epigenome screening highlights that JMJD6 confers an epigenetic vulnerability and mediates sunitinib sensitivity in renal cell carcinoma.

A platelet-related signature for predicting the prognosis and immunotherapy benefit in bladder cancer based on machine learning combinations.

Dicer, Drosha, and outcomes in patients with ovarian cancer.

Somatic mutations of the Parkinson's disease-associated gene PARK2 in glioblastoma and other human malignancies.

Prevalence and functional analysis of sequence variants in the ATR checkpoint mediator Claspin.

Crunching the bio-numbers.

Understanding the function of Pax5 in development of docetaxel-resistant neuroendocrine-like prostate cancers.

Comprehensive analysis of peroxisome proliferator-activated receptors to predict the drug resistance, immune microenvironment, and prognosis in stomach adenocarcinomas.

Functional role of the KLF6 tumour suppressor gene in gastric cancer.

The dietary bioflavonoid, quercetin, selectively induces apoptosis of prostate cancer cells by down-regulating the expression of heat shock protein 90.

Human CRAMP1 specifically promotes the expression of histone H1 genes.

Constructing an APOBEC-related gene signature with predictive value in the overall survival and therapeutic sensitivity in lung adenocarcinoma.

Merger of ayurveda and tissue culture-based functional genomics: inspirations from systems biology.

Decoding the tumor microenvironment and molecular mechanism: unraveling cervical cancer subpopulations and prognostic signatures through scRNA-Seq and bulk RNA-seq analyses.

Unveiling the NEFH+ malignant cell subtype: Insights from single-cell RNA sequencing in prostate cancer progression and tumor microenvironment interactions.