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 370

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

Critical care: applying genomics to inflammation outcomes.

PMID 16330338 · PMC1314943 · Environmental health perspectives · 2005 · 8 claims · 6 setups

Full-text index only

Genetic factors drive key aspects of an individual's inflammatory outcome after trauma, burns, or sepsis

leukocytes whole-blood healthy peripheral genomewide whole-genome microarray
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
Systems biology approaches for the study of multiple sclerosis.

PMID 18505469 · PMC3865652 · Journal of cellular and molecular medicine · 2008 · 8 claims · 8 setups

Full-text index only

The MHC locus on chromosome 6p21 is the strongest genetic region linked to MS susceptibility.

patients lesion osteopontin monocyte-depleted genetic large-scale gene
Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.

PMID 38254989 · PMC10815467 · Genes · 2024 · 8 claims · 8 setups

Has reproduction · 85

Combining scRNA-seq and spatial transcriptomics enables inference of malignant cells at the invasive front of the ER+ breast cancer TME and dissection of events at the tumor infiltration forefront

normal er+ epithelial malignant single-cell spatial copy
Distinct lncRNA transcriptional fingerprints characterize progressive stages of multiple myeloma.

PMID 26895470 · PMC4924754 · Oncotarget · 2016 · 8 claims · 4 setups

Has reproduction · 36

31 lncRNAs are deregulated in plasma cell dyscrasia tumor samples compared to normal plasma cell controls (19 upregulated, 12 downregulated)

plasma gene patients proprietary lncrna custom gene
Application of proteomics in the study of tumor metastasis.

PMID 15862116 · PMC5172469 · Genomics, proteomics & bioinformatics · 2004 · 8 claims · 8 setups

Full-text index only

Cell function is directly regulated through proteins, not genes or mRNA, so metastasis-related gene findings need protein-level validation via proteomics.

young metastatic hepatocellular lines microarray 2de cdna
Integrated weighted gene co-expression network analysis with an application to chronic fatigue syndrome.

PMID 18986552 · PMC2625353 · BMC systems biology · 2008 · 8 claims · 6 setups

Full-text index only

Integrated WGCNA (IWGCNA), which adds genetic marker-based causality testing to standard WGCNA, can identify a disease-related module and its causal drivers

cfs most candidate second microarray snp weighted
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
Indirect genomic effects on survival from gene expression data.

PMID 18358079 · PMC2397510 · Genome biology · 2008 · 7 claims · 6 setups

Full-text index only

A novel methodology (dynamic path analysis combined with additive hazard survival regression) can detect and quantify indirect effects of gene expression on survival mediated through transcription factor target genes.

dutch uppsala dlbcl gene gene literature permutation
Proteomics as a method for early detection of cancer: a review of proteomics, exhaled breath condensate, and lung cancer screening.

PMID 18095050 · PMC2150625 · Journal of general internal medicine · 2008 · 8 claims · 7 setups

Full-text index only

Protein expression is closely aligned with cellular activity, unlike genomic changes which may have no functional significance

serum resected plasma lower microarray two-dimensional proteomic
Integrated Analysis of Multiple Microarrays Based on Raw Data Identified Novel Gene Signatures in Recurrent Implantation Failure.

PMID 35197930 · PMC8859149 · Frontiers in endocrinology · 2022 · 6 claims · 7 setups

Has reproduction · 85

Robust Rank Aggregation (RRA) can integrate DEG lists from multiple independent RIF microarray datasets to identify robust DEGs.

endometrium integrated robust ppi microarray robust gene
Developing a novel immune infiltration-associated mitophagy prediction model for amyotrophic lateral sclerosis using bioinformatics strategies.

PMID 38601155 · PMC11005030 · Frontiers in immunology · 2024 · 7 claims · 6 setups

Has reproduction · 71

An 18-gene mitophagy-related prognostic signature was identified by machine learning and used to build a prognostic risk score model for ALS.

peripheral als lumbar bulk cibersort gsea
Reduced expression of Axin correlates with tumour progression of oesophageal squamous cell carcinoma.

PMID 12771989 · PMC2377153 · British journal of cancer · 2003 · 7 claims · 6 setups

Full-text index only

Reduced Axin expression is correlated with tumour progression of oesophageal SCC

surgical oesophageal excised clinical immunohistochemistry western northern
Expression of full-length p53 and its isoform Deltap53 in breast carcinomas in relation to mutation status and clinical parameters.

PMID 17054774 · PMC1636663 · Molecular cancer · 2006 · 7 claims · 7 setups

Full-text index only

The alternative splice isoform Δp53 mRNA is co-expressed with full-length p53 mRNA in breast tumors and cell lines

breast universal p53 subset qrt-pcr bioinformatic structure
Is a genetic defect in Fkbp6 a common cause of azoospermia in humans?

PMID 16983454 · PMC6275806 · Cellular & molecular biology letters · 2006 · 7 claims · 7 setups

Full-text index only

Human FKBP6 expression is restricted to the testis among 15 adult tissues examined

genomic bilateral testicular rt-pcr mutation testicular
The proteogenomic path towards biomarker discovery.

PMID 18764911 · PMC2574627 · Pediatric transplantation · 2008 · 8 claims · 8 setups

Full-text index only

Serum creatinine is a widely used but non-ideal biomarker for renal transplant monitoring because it lacks specificity and sensitivity for graft injury

renal urine breast chronic microarray immunoassay gel
Peripheral blood B lymphocytes derived from patients with idiopathic pulmonary arterial hypertension express a different RNA pattern compared with healthy controls: a cross sectional study.

PMID 18269757 · PMC2262076 · Respiratory research · 2008 · 7 claims · 4 setups

Full-text index only

IPAH patients' peripheral blood B-lymphocytes express a distinct RNA profile compared with healthy controls

peripheral pbmc oligonucleotide flow density
Reduced transcription of TCOF1 in adult cells of Treacher Collins syndrome patients.

PMID 20003452 · PMC2801500 · BMC medical genetics · 2009 · 8 claims · 5 setups

Full-text index only

TCOF1 transcript levels are significantly reduced (~18%) in leucocytes of TCS patients compared to controls

leucocytes mesenchymal leucocyte real-time direct flow
Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling.

PMID 19901961 · PMC2820592 · Oncogene · 2010 · 8 claims · 6 setups

Full-text index only

Unsupervised gene expression clustering identifies 3 reproducible molecular subtypes of LMS (Group I/muscle-enriched, Group II, Group III)

lms independent soft gene array immunohistochemistry
Fibroblasts from patients with Diamond-Blackfan anaemia show abnormal expression of genes involved in protein synthesis, amino acid metabolism and cancer.

PMID 19765279 · PMC2760583 · BMC genomics · 2009 · 8 claims · 5 setups

Full-text index only

Global microarray profiling reveals 421 genes differentially expressed in DBA patient fibroblasts compared to healthy controls

dermal same fibroblasts analysis microarray quantitative rt-pcr

Experiments

Critical care: applying genomics to inflammation outcomes.

Integrative analysis of RUNX1 downstream pathways and target genes.

Systems biology approaches for the study of multiple sclerosis.

Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.

Distinct lncRNA transcriptional fingerprints characterize progressive stages of multiple myeloma.

Application of proteomics in the study of tumor metastasis.

Integrated weighted gene co-expression network analysis with an application to chronic fatigue syndrome.

Comparison of prognostic gene expression signatures for breast cancer.

Indirect genomic effects on survival from gene expression data.

Proteomics as a method for early detection of cancer: a review of proteomics, exhaled breath condensate, and lung cancer screening.

Integrated Analysis of Multiple Microarrays Based on Raw Data Identified Novel Gene Signatures in Recurrent Implantation Failure.

Developing a novel immune infiltration-associated mitophagy prediction model for amyotrophic lateral sclerosis using bioinformatics strategies.

Reduced expression of Axin correlates with tumour progression of oesophageal squamous cell carcinoma.

Expression of full-length p53 and its isoform Deltap53 in breast carcinomas in relation to mutation status and clinical parameters.

Is a genetic defect in Fkbp6 a common cause of azoospermia in humans?

The proteogenomic path towards biomarker discovery.

Peripheral blood B lymphocytes derived from patients with idiopathic pulmonary arterial hypertension express a different RNA pattern compared with healthy controls: a cross sectional study.

Reduced transcription of TCOF1 in adult cells of Treacher Collins syndrome patients.

Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling.

Fibroblasts from patients with Diamond-Blackfan anaemia show abnormal expression of genes involved in protein synthesis, amino acid metabolism and cancer.