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).

• Specific signature biomarkers highlight the potential mechanisms of circulating neutrophils in aneurysmal subarachnoid hemorrhage.

  PMID 36438795 · PMC9685413 · Frontiers in pharmacology · 2022 · 7 claims · 8 setups

  Has reproduction · 80

  Six genes (CST7, HSP90AB1, PADI4, PLBD1, RAB32, SLAMF6) are signature diagnostic biomarkers for aSAH identified by LASSO and SVM-RFE.

  peripheral overlapping asah drug-treatment microarray wgcna ppi

• T Cells With Activated STAT4 Drive the High-Risk Rejection State to Renal Allograft Failure After Kidney Transplantation.

  PMID 35844542 · PMC9283858 · Frontiers in immunology · 2022 · 8 claims · 8 setups

  Has reproduction · 78

  Unsupervised UMAP/Leiden clustering of 2,611 microarray datasets reveals 6 rejection states that diverge from traditional Banff clinical classification

  kidney scrna-seq microarray meblack microarray single-cell scissor

• Reverse Engineering of the Pediatric Sepsis Regulatory Network and Identification of Master Regulators.

  PMID 34680414 · PMC8533457 · Biomedicines · 2021 · 7 claims · 8 setups

  Has reproduction · 67

  A set of 15 TFs was identified as sepsis-specific master regulators of pediatric sepsis, dividing into two non-overlapping clusters.

  blood cd4+ pbmc regulons microarray differential master

• A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

  PMID 19923232 · PMC2817484 · Nucleic acids research · 2010 · 8 claims · 7 setups

  Full-text index only

  A Perl-based pipeline that BLASTs/BLATs Illumina probe sequences against genomes and transcript databases (RefSeq, UCSC Known Genes, UniGene/GenBank, Ensembl) can classify probes by quality grade (Perfect/Good/Bad/No match) and is applicable across 8 BeadArray platforms and other array types

  maqc hepatocytes japanese illeum microarray dasl sequence

• Whither genomics?

  PMID 11104516 · PMC138820 · Genome biology · 2000 · 8 claims · 8 setups

  Full-text index only

  Genomics is both a science (understanding genome structure/evolution) and a tool (learning gene function) that collects comprehensive data on all genes, in contrast to genetics which studies a few genes controlling a phenotype

  mammalian budding yeast general expression genome-wide synthetic

• First step toward gene expression data integration: transcriptomic data acquisition with COMMAND>_.

  PMID 30691411 · PMC6348648 · BMC bioinformatics · 2019 · 7 claims · 3 setups

  Has reproduction · 30

  COMMAND>_ is a flexible multi-user web application that searches, downloads, parses, re-annotates, and imports gene expression experiments into a coherent data model.

  small user-defined microarray affymetrix rna-seq probe-to-gene

• Gene-expression patterns in peripheral blood classify familial breast cancer susceptibility.

  PMID 26538066 · PMC4634735 · BMC medical genomics · 2015 · 8 claims · 5 setups

  Has reproduction · 83

  A multigene peripheral-blood gene-expression biomarker accurately classifies which women from high-risk families develop familial breast cancer.

  peripheral pbmcs blood normal gene-expression lymphocyte gene

• Identification of TYR, TYRP1, DCT and LARP7 as related biomarkers and immune infiltration characteristics of vitiligo via comprehensive strategies.

  PMID 34107850 · PMC8806433 · Bioengineered · 2021 · 6 claims · 6 setups

  Has reproduction · 55

  TYR, TYRP1, DCT and LARP7 are biomarkers associated with vitiligo

  vitiligo merged robust gse90880 gene robust kegg

• 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 Nottingham Prognostic Index with SIS-selected gene expressions can be built in a data-driven fashion (NPI treated as a gene expression during feature selection).

  metabric scan-b gene rna-seq feature

• An OMICs-based meta-analysis to support infection state stratification.

  PMID 33560295 · PMC8388022 · Bioinformatics (Oxford, England) · 2021 · 7 claims · 6 setups

  Has reproduction · 44

  Multi-class machine learning models built from cross-platform microarray meta-analysis can distinguish bacterial, viral and no-infection states with high accuracy (best model: 93% bacterial, 89% viral correct).

  blood merged affymetrix-optimized gene feature out-of-sample

• The molecular landscape of sepsis severity in infants: enhanced coagulation, innate immunity, and T cell repression.

  PMID 38817614 · PMC11137207 · Frontiers in immunology · 2024 · 7 claims · 7 setups

  Has reproduction · 50

  Most published adult/other-cohort sepsis gene signatures have limited utility for infant sepsis; only 2 of 7 achieved >80% accuracy in infants

  infant merged individual pairwise whole-blood coconut gene-signature

• Digital sorting of complex tissues for cell type-specific gene expression profiles.

  PMID 23497278 · PMC3626856 · BMC bioinformatics · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  The Digital Sorting Algorithm (DSA) deconvolves mixed tissue expression into cell type-specific profiles using only marker genes, without requiring prior knowledge of cell type frequencies or in vitro pure-cell profiles.

  liver im-9 immune deconvolved microarray simulation roc

• Expanding the vision of environmental health at UNC-CH.

  PMID 15248304 · PMC1247395 · Environmental health perspectives · 2004 · 8 claims · 8 setups

  Full-text index only

  Human breast tumors arise from at least two distinct cell types, basal and luminal epithelial, with different clinical behavior

  breast chinese carolina rodent microarray functional genetic

• Integrative analysis of RUNX1 downstream pathways and target genes.

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

  Full-text index only

  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

• A genomic approach to improve prognosis and predict therapeutic response in chronic lymphocytic leukemia.

  PMID 19861443 · PMC2783430 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 8 setups

  Full-text index only

  A genomic signature derived from CLL patient leukemic cells significantly differentiates stable from progressive disease

  duke nci-60 mayo spanish gene cdna igvh

• Survival analysis with high-dimensional covariates.

  PMID 19654171 · PMC4806549 · Statistical methods in medical research · 2010 · 8 claims · 1 setups

  Full-text index only

  The classical Cox proportional hazards model cannot be fit when p >> n because the partial likelihood maximizer is not unique and the matrix X^T A X is singular in the IRLS procedure

  renal gene

• Newborn sex-specific transcriptome signatures and gestational exposure to fine particles: findings from the ENVIRONAGE birth cohort.

  PMID 28583124 · PMC5458481 · Environmental health : a global access science source · 2017 · 7 claims · 6 setups

  Has reproduction · 71

  Gestational PM2.5 exposure is associated with sex-specific gene expression changes in newborn cord blood, with major differences between boys and girls.

  cord maternal genes significant genome pm2.5 isolation

• PulmonDB: a curated lung disease gene expression database.

  PMID 31949184 · PMC6965635 · Scientific reports · 2020 · 6 claims · 6 setups

  Has reproduction · 53

  PulmonDB is a curated, web-based gene expression database and R package integrating microarray and RNA-seq data for COPD and IPF with manually curated controlled-vocabulary annotation.

  lung ipf copd curated hierarchical differential

• Predicting Bone Metastasis Using Gene Expression-Based Machine Learning Models.

  PMID 34858485 · PMC8631472 · Frontiers in genetics · 2021 · 7 claims · 5 setups

  Has reproduction · 62

  A DNN model using the top 34 betweenness-centrality-ranked hub genes predicts bone metastasis with AUC of 92.11% on the GEO validation data.

  breast degs geo tcga gene protein-protein machine

• Interpretation of genomic data: questions and answers.

  PMID 18582627 · PMC2528831 · Seminars in hematology · 2008 · 8 claims · 6 setups

  Full-text index only

  The main challenge in using genomic technology in cancer research is not managing the volume of data but the proper design, analysis, and reporting of studies.

  genetically wound tumor breast gene expression comparative