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).

• SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data.

  PMID 18208605 · PMC2265264 · BMC bioinformatics · 2008 · 8 claims · 1 setups

  Full-text index only

  SignS is a web-based tool and R package implementing four gene-selection/signature-building methods for survival data (Dave et al., Gui and Li, random forests with conditional inference trees, and boosting with component-wise Cox models).

  microarray gene-by-gene

• 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

• 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

• Alternative polyadenylation of cyclooxygenase-2.

  PMID 15872218 · PMC1088970 · Nucleic acids research · 2005 · 8 claims · 5 setups

  Full-text index only

  The human COX-2 gene undergoes alternative polyadenylation using proximal and distal polyadenylation signals

  cox-2 ht29 hela bioinformatics western rnase

• Integrated drug resistance and leukemic stemness gene-expression scores predict outcomes in large cohort of over 3500 AML patients from 10 trials.

  PMID 39090192 · PMC11294346 · NPJ precision oncology · 2024 · 7 claims · 6 setups

  Has reproduction · 50

  A 5-gene ADE-Resistance Score (ADE-RS5), derived via LASSO regression from 67 pharmacologically relevant genes, predicts MRD positivity, EFS and OS in pediatric AML.

  pediatric combined lasso gene-expression-based integrated

• Construction and Validation of an Immune Infiltration-Related Gene Signature for the Prediction of Prognosis and Therapeutic Response in Breast Cancer.

  PMID 33986754 · PMC8110914 · Frontiers in immunology · 2021 · 7 claims · 8 setups

  Has reproduction · 51

  A higher immune infiltration-related risk score (IRS) indicates worse prognosis and lower sensitivity to immunotherapy in breast cancer patients

  tcga candidate cancer univariate weighted lasso

• Bayesian survival analysis in genetic association studies.

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

  Full-text index only

  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

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

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

  Full-text index only

  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

• 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

• Holliday junction recognition protein (HJURP) could reflect the clinical outcomes of lung adenocarcinoma patients, and impact the choice of precision therapy.

  PMID 39649097 · PMC11621083 · Frontiers in genetics · 2024 · 7 claims · 8 setups

  Full-text index only

  HJURP is a significant prognostic biomarker in LUAD, with high expression associated with increased risk of overall survival death across four independent cohorts

  tcga-luad best brain advanced bulk kaplan-meier pearson

• The relationship between PLOD1 expression level and glioma prognosis investigated using public databases.

  PMID 34040895 · PMC8127981 · PeerJ · 2021 · 8 claims · 8 setups

  Has reproduction · 79

  PLOD1 mRNA expression is significantly higher in glioma tissue than in normal brain tissue

  glioma gbm cancer gene online genomic

• Identification of a novel 10 immune-related genes signature as a prognostic biomarker panel for gastric cancer.

  PMID 34382341 · PMC8446556 · Cancer medicine · 2021 · 8 claims · 8 setups

  Has reproduction

  A 10-IRG prognostic signature (BMPR1B, GHR, IL11RA, INHBB, NPR3, OBP2A, PTN, R3HDML, TAC1, TPM2) predicts overall survival in gastric cancer.

  gastric tcga-stad overlapping candidate microarray gene rna-seq

• 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

• The genomic analysis of lactic acidosis and acidosis response in human cancers.

  PMID 19057672 · PMC2585811 · PLoS genetics · 2008 · 8 claims · 8 setups

  Full-text index only

  Lactic acidosis and hypoxia induce largely distinct gene expression programs in HMECs, with lactic acidosis producing a much larger and more dramatic response

  mammary hmec gene breast gene real-time bayesian

• Comparison of prognostic gene expression signatures for breast cancer.

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

  Full-text index only

  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

• Molecular and Clinical Relevance of ZBTB38 Expression Levels in Prostate Cancer.

  PMID 32365491 · PMC7281456 · Cancers · 2020 · 8 claims · 8 setups

  Has reproduction · 35

  ZBTB38 mRNA expression is significantly lower in prostate cancer than in normal/benign prostate tissue, and further reduced in metastatic versus localised tumours

  localised tcga taylor metastatic microarray rna-sequencing clinico-pathological

• 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

• Proneural-mesenchymal antagonism dominates the patterns of phenotypic heterogeneity in glioblastoma.

  PMID 38433919 · PMC10905000 · iScience · 2024 · 8 claims · 8 setups

  Has reproduction · 100

  The four proposed GBM molecular subtypes (Proneural, Neural, Classical, Mesenchymal / NPC-like, OPC-like, AC-like, MES-like) are not mutually exclusive or independent of one another

  scrna-seq tcga-gbm gse131928 tumor gene pairwise principal

• Enhancing chemotherapy response prediction via matched colorectal tumor-organoid gene expression analysis and network-based biomarker selection.

  PMID 39754813 · PMC11754497 · Translational oncology · 2025 · 6 claims · 8 setups

  Has reproduction · 78

  A consensus WGCNA approach combining matched tumor-organoid and independent organoid drug-response expression data identifies gene modules and hub genes predictive of 5-FU chemotherapy response

  colorectal matched combined expression microarray rna-seq consensus

• 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