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 25

System / cell line: patients ✕ Assay: proportional ✕ Clear

Computationally scalable regression modeling for ultrahigh-dimensional omics data with ParProx.

PMID 34254998 · PMC8575036 · Briefings in bioinformatics · 2021 · 6 claims · 4 setups

Has reproduction · 79

ParProx implements latent group lasso penalized regression (overlapping and non-overlapping groups) for survival (Cox) and classification (logistic) analysis of omics data.

tcga breast liver simulated cox logistic simulation
Predicting survival outcomes using subsets of significant genes in prognostic marker studies with microarrays.

PMID 16549007 · PMC1544357 · BMC bioinformatics · 2006 · 7 claims · 2 setups

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A methodology combining Cox proportional hazards models with a compound covariate, cross-validated log partial likelihood (ACVL) for predictive accuracy, and permutation-based significance testing can identify an optimal subset of significant genes for survival prediction

simulated diffuse simulation cdna
Comparative analysis of molecular signatures reveals a hybrid approach in breast cancer: Combining the Nottingham Prognostic Index with gene expressions into a hybrid signature.

PMID 35143511 · PMC8830616 · PloS one · 2022 · 8 claims · 6 setups

Has reproduction · 48

A Hybrid signature combining the NPI with 14 SIS-selected genes was constructed from METABRIC training data

metabric gse96058 test gene sure cox
B-RAF and N-RAS mutations are preserved during short time in vitro propagation and differentially impact prognosis.

PMID 17311103 · PMC1794595 · PloS one · 2007 · 5 claims · 4 setups

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B-RAF and N-RAS mutation status is well preserved (strongly concordant) between tumor tissue biopsies and corresponding short-term in vitro propagated cell lines.

tumor biopsy-derived metastatic pcr direct survival
Comparison of prognostic gene expression signatures for breast cancer.

PMID 18717985 · PMC2533026 · BMC genomics · 2008 · 8 claims · 5 setups

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The three prognostic signatures (70-gene, 76-gene, GGI) show similar prognostic performance for predicting DMFS despite differing gene identity and development approach

tbagd tbvdx gene clinical survival
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 · 8 setups

Has reproduction · 72

edgeR-based DEG selection is more appropriate for feature selection than Elastic Net when sample sizes are small.

ffpe same nanostring tnbc nanostring immunohistochemistry differential
Joint association of polymorphism of the FGFR4 gene and mutation TP53 gene with bladder cancer prognosis.

PMID 17088904 · PMC2360734 · British journal of cancer · 2006 · 8 claims · 5 setups

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No clear correlation was found between the FGFR4 Gly388Arg genotype and risk of developing bladder cancer.

blood bladder rflp manual genechip
Prognostic significance of p53 and ras gene abnormalities in lung adenocarcinoma patients with stage I disease after curative resection.

PMID 7852188 · PMC5919395 · Japanese journal of cancer research : Gann · 1994 · 6 claims · 5 setups

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Presence of p53 gene abnormalities is associated with shorter disease-free survival in stage I lung adenocarcinoma

formalin-fixed stage pcr-dgge immunohistochemistry pcr-rflp
A novel polymorphism in the 1A promoter region of the vitamin D receptor is associated with altered susceptibilty and prognosis in malignant melanoma.

PMID 15238985 · PMC2364794 · British journal of cancer · 2004 · 7 claims · 6 setups

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A novel A-1012G (adenine-guanine) polymorphism exists in the VDR exon 1a promoter region, identified by SSCP screening and sequencing

blood variant patients same sscp sanger pcr-rflp
MDM2 gene SNP309 T/G and p53 gene SNP72 G/C do not influence diffuse large B-cell non-Hodgkin lymphoma onset or survival in central European Caucasians.

PMID 18433491 · PMC2375899 · BMC cancer · 2008 · 6 claims · 4 setups

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MDM2 SNP309 T/G genotype is not associated with DLBCL or NHL onset, diagnosis, or age of onset in central European Caucasians, including in pre-menopausal women

genomic nhl pcr case-control survival
A urine extracellular vesicle lncRNA classifier for high-grade prostate cancer and increased risk of progression: A multi-center study.

PMID 37852185 · PMC10591064 · Cell reports. Medicine · 2023 · 8 claims · 8 setups

Has reproduction · 65

A 3-lncRNA urine extracellular vesicle classifier (Clnc: AC015987.1, CTD-2589M5.4, RP11-363E6.3) detects high-grade PCa with higher accuracy than PCA3, mpMRI, PCPT-RC 2.0, and ERSPC-RC

urinary tcga paired urine sequencing lncrna qrt-pcr
Association of p53 gene mutations with short survival in pancreatic adenocarcinoma.

PMID 7730141 · PMC5920762 · Japanese journal of cancer research : Gann · 1995 · 8 claims · 4 setups

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p53 gene mutations were detected in 16 of 37 (43%) pancreatic adenocarcinomas by SSCP and direct sequencing

pancreatic single-strand direct univariate
Multiple molecular marker testing (p53, C-Ki-ras, c-erbB-2) improves estimation of prognosis in potentially curative resected non-small cell lung cancer.

PMID 10945494 · PMC2374666 · British journal of cancer · 2000 · 6 claims · 4 setups

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Testing 3 molecular markers (c-Ki-ras, p53, c-erbB-2) together improves estimation of prognosis compared to single marker testing and defines low- and high-risk groups for treatment failure in R0-resected NSCLC.

paired frozen nsclc sscp immunohistochemistry clinical
Detection of BRAF mutations in the tumour and serum of patients enrolled in the AZD6244 (ARRY-142886) advanced melanoma phase II study.

PMID 19861964 · PMC2778539 · British journal of cancer · 2009 · 7 claims · 8 setups

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BRAF mutations can be detected in serum cfDNA of advanced melanoma patients using an ARMS allele-specific PCR assay

serum-derived tumour serum ht29 arms sanger topo
A genomic pathway approach to a complex disease: axon guidance and Parkinson disease.

PMID 17571925 · PMC1904362 · PLoS genetics · 2007 · 8 claims · 5 setups

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A genomic pathway approach using axon-guidance pathway SNPs strongly predicts PD susceptibility, survival free of PD, and age at onset of PD

cases patients postmortem whole-genome cox linear
Bayesian survival analysis in genetic association studies.

PMID 18617538 · PMC2530885 · Bioinformatics (Oxford, England) · 2008 · 7 claims · 5 setups

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A novel Bayesian method (BETA-Surv) extends prior case-control haplotype-clustering work to censored survival outcomes by clustering haplotypes via gene tree/perfect phylogeny topology and relative mutation age.

simulated same sanad bayesian univariate partial
Expression Patterns of Immune Genes Reveal Heterogeneous Subtypes of High-Risk Neuroblastoma.

PMID 32629858 · PMC7408437 · Cancers · 2020 · 8 claims · 8 setups

Has reproduction · 73

Unsupervised biclustering of 283 NB-specific immune genes stratifies HR-NB into two reproducible subtypes: ultra-high-risk (UHR-NB) and (revised) HR-NB.

pediatric target cohorts neuroblastoma bulk spectral kaplan-meier
Evaluating Distribution and Prognostic Value of New Tumor-Infiltrating Lymphocytes in HCC Based on a scRNA-Seq Study With CIBERSORTx.

PMID 33043022 · PMC7527443 · Frontiers in medicine · 2020 · 6 claims · 8 setups

Has reproduction · 78

CIBERSORTx can combine scRNA-seq-derived signature matrices with bulk RNA-seq data to estimate proportions of 11 TIL subsets in HCC tumor and normal tissue

tcga degs cd4-gzma prognostic scrna-seq cibersortx differential
Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients.

PMID 35012625 · PMC8743438 · Genome biology · 2022 · 8 claims · 9 setups

Has reproduction · 68

GENEVA (Gene Expression Variance Analysis) is a semi-automated framework that mines large-scale public RNA-seq datasets to identify conditions associated with a gene's expression variance

gtex genetic lncap heart rna-seq meta-analysis electronic
TP53 mutations in ovarian carcinomas from sporadic cases and carriers of two distinct BRCA1 founder mutations; relation to age at diagnosis and survival.

PMID 16229746 · PMC1276789 · BMC cancer · 2005 · 8 claims · 4 setups

Full-text index only

Survival for BRCA1-familial ovarian cancer cases with TP53 mutations was not significantly different from familial cases without TP53 mutations (p=0.25, RR=1.64)

ovarian sporadic paraffin-embedded mutation survival extraction

Experiments

Computationally scalable regression modeling for ultrahigh-dimensional omics data with ParProx.

Predicting survival outcomes using subsets of significant genes in prognostic marker studies with microarrays.

Comparative analysis of molecular signatures reveals a hybrid approach in breast cancer: Combining the Nottingham Prognostic Index with gene expressions into a hybrid signature.

B-RAF and N-RAS mutations are preserved during short time in vitro propagation and differentially impact prognosis.

Comparison of prognostic gene expression signatures for breast cancer.

Prediction of prognostic signatures in triple-negative breast cancer based on the differential expression analysis via NanoString nCounter immune panel.

Joint association of polymorphism of the FGFR4 gene and mutation TP53 gene with bladder cancer prognosis.

Prognostic significance of p53 and ras gene abnormalities in lung adenocarcinoma patients with stage I disease after curative resection.

A novel polymorphism in the 1A promoter region of the vitamin D receptor is associated with altered susceptibilty and prognosis in malignant melanoma.

MDM2 gene SNP309 T/G and p53 gene SNP72 G/C do not influence diffuse large B-cell non-Hodgkin lymphoma onset or survival in central European Caucasians.

A urine extracellular vesicle lncRNA classifier for high-grade prostate cancer and increased risk of progression: A multi-center study.

Association of p53 gene mutations with short survival in pancreatic adenocarcinoma.

Multiple molecular marker testing (p53, C-Ki-ras, c-erbB-2) improves estimation of prognosis in potentially curative resected non-small cell lung cancer.

Detection of BRAF mutations in the tumour and serum of patients enrolled in the AZD6244 (ARRY-142886) advanced melanoma phase II study.

A genomic pathway approach to a complex disease: axon guidance and Parkinson disease.

Bayesian survival analysis in genetic association studies.

Expression Patterns of Immune Genes Reveal Heterogeneous Subtypes of High-Risk Neuroblastoma.

Evaluating Distribution and Prognostic Value of New Tumor-Infiltrating Lymphocytes in HCC Based on a scRNA-Seq Study With CIBERSORTx.

Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients.

TP53 mutations in ovarian carcinomas from sporadic cases and carriers of two distinct BRCA1 founder mutations; relation to age at diagnosis and survival.