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 36

System / cell line: independent ✕ Assay: profiling ✕ Clear

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
CCL8 as a promising prognostic factor in diffuse large B-cell lymphoma via M2 macrophage interactions: A bioinformatic analysis of the tumor microenvironment.

PMID 36072582 · PMC9441746 · Frontiers in immunology · 2022 · 7 claims · 4 setups

Has reproduction · 81

CCL8 is a promising independent prognostic factor in DLBCL associated with M2 macrophage interactions

dlbcl ffpe paraffin-embedded bulk quantitative immunofluorescent
Logical Analysis of Data (LAD) model for the early diagnosis of acute ischemic stroke.

PMID 18616825 · PMC2492849 · BMC medical informatics and decision making · 2008 · 7 claims · 5 setups

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An LAD classification model built from a support-set of 3 peptide peaks can distinguish stroke patients from controls with 75% accuracy on an independent validation set

plasma discretized seldi-tof serum logical
Novel MEK1 mutation identified by mutational analysis of epidermal growth factor receptor signaling pathway genes in lung adenocarcinoma.

PMID 18632602 · PMC2586155 · Cancer research · 2008 · 8 claims · 7 setups

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A novel somatic MEK1 K57N mutation was identified in 2 of 207 primary lung adenocarcinomas

nsclc 293t il-3-independent mutational site-directed cytokine-independence
Bayesian prediction of RNA translation from ribosome profiling.

PMID 28126919 · PMC5389577 · Nucleic acids research · 2017 · 8 claims · 4 setups

Has reproduction · 62

Rp-Bp is an unsupervised Bayesian approach that uses a two-component 'high-low-low' mixture model to predict translated ORFs from ribosome profiles

hek293 ribo-seq ribosome proteomics quantitative
Integrated genomics identifies five medulloblastoma subtypes with distinct genetic profiles, pathway signatures and clinicopathological features.

PMID 18769486 · PMC2518524 · PloS one · 2008 · 8 claims · 4 setups

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Unsupervised clustering of expression profiles from 62 medulloblastomas identifies 5 molecular subtypes (A–E)

relapsed medulloblastoma independent expression array targeted
Genomic transcriptional profiling identifies a candidate blood biomarker signature for the diagnosis of septicemic melioidosis.

PMID 19903332 · PMC3091321 · Genome biology · 2009 · 6 claims · 5 setups

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A candidate 37-transcript diagnostic signature distinguishes septicemic melioidosis from sepsis caused by other organisms with 100% accuracy in the training set and 78%/80% accuracy in two independent validation sets

blood whole-genome unsupervised class
CLEAN: CLustering Enrichment ANalysis.

PMID 19640299 · PMC2734555 · BMC bioinformatics · 2009 · 8 claims · 4 setups

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The gene-specific CLEAN score improves reproducibility of cluster analysis conclusions across independent datasets compared to the traditional cluster-wide score (cwCLEAN).

four breast combined hierarchical cluster csimm-based
Topologically inferring pathway activity toward precise cancer classification via integrating genomic and metabolomic data: prostate cancer as a case.

PMID 26286638 · PMC4541321 · Scientific reports · 2015 · 6 claims · 4 setups

Has reproduction · 76

DRW-GM integrates gene expression and metabolomic profiles via directed random walk on a global gene–metabolite pathway graph to weight genes by topological importance and infer reproducible pathway activities

prostate global gene metabolomic computational
Integrative analyses reveal signaling pathways underlying familial breast cancer susceptibility.

PMID 26969729 · PMC4812528 · Molecular systems biology · 2016 · 7 claims · 6 setups

Has reproduction · 67

Cell adhesion (cell-cell and cell-ECM) pathways are significantly and consistently dysregulated in women who develop familial breast cancer across multiple omic data types and tissues.

peripheral pbmcs normal snap-frozen gene exome western
Canine tumor cross-species genomics uncovers targets linked to osteosarcoma progression.

PMID 20028558 · PMC2803201 · BMC genomics · 2009 · 8 claims · 7 setups

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High expression of IL-8 and SLC1A3, identified via cross-species mining, is associated with poor outcome in an independent population of human osteosarcoma patients

canine osteosarcoma independent third oligonucleotide cross-species quantitative
Cross species genomic analysis identifies a mouse model as undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma.

PMID 19956606 · PMC2779485 · PloS one · 2009 · 8 claims · 7 setups

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A 100-gene signature from LSL-KrasG12D;Trp53Flox/Flox mouse sarcomas (vs normal muscle) is specifically and significantly enriched in human MFH but not other soft tissue sarcoma subtypes across three independent human datasets.

lsl-krasg12d soft combined mfh microarray gene oncogenic
Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling.

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

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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
ResnetAge: A Resnet-Based DNA Methylation Age Prediction Method.

PMID 38247911 · PMC10813502 · Bioengineering (Basel, Switzerland) · 2023 · 8 claims · 4 setups

Has reproduction · 75

ResnetAge, a ResNet-based neural network using 22,278 shared Illumina 27K/450K CpG sites, predicts DNA methylation age from beta values.

shared independent methylation resnet comparative
A Decentralized Kidney Transplant Biopsy Classifier for Transplant Rejection Developed Using Genes of the Banff-Human Organ Transplant Panel.

PMID 35619722 · PMC9128066 · Frontiers in immunology · 2022 · 6 claims · 6 setups

Has reproduction · 90

A random forest model trained solely on B-HOT panel genes (B-HOT Model) accurately classifies kidney transplant biopsies as NR, ABMR, or TCMR.

kidney gene combined microarray machine sequential
Application of functional genomics to primate endometrium: insights into biological processes.

PMID 17118168 · PMC1775064 · Reproductive biology and endocrinology : RB&E · 2006 · 8 claims · 7 setups

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Gene expression profiles differ distinctly across proliferative, early-, mid-, and late-secretory phases of the human menstrual cycle, reflecting sequential estradiol and progesterone action.

endometrial uterus whole-genome cdna oligonucleotide
Adipose proteome analysis: focus on mediators of insulin resistance.

PMID 19086862 · PMC2651673 · Expert review of proteomics · 2008 · 8 claims · 5 setups

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Ectopic lipid accumulation in liver and muscle, resulting from impaired adipose tissue lipid-storage capacity, is more directly associated with insulin resistance than adipose tissue mass itself.

3t3-l1 adipose visceral 35s-radiolabeling gel seldi-tof
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

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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
Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis.

PMID 20003344 · PMC2801700 · BMC genomics · 2009 · 7 claims · 8 setups

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Meta-analysis of 16 microarray datasets across human, mouse, rat and yeast identifies 164 genes (MDEGs) consistently differentially expressed in response to high fat diet or PPAR signaling perturbation.

liver saccharomyces mdeg independent microarray transcription chromosomal
Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: the Stockholm Atherosclerosis Gene Expression (STAGE) study.

PMID 19997623 · PMC2780352 · PLoS genetics · 2009 · 8 claims · 6 setups

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Functionally associated gene modules, not individual genes, underlie CAD development and can be identified via multi-organ expression clustering

liver atherosclerotic 128-gene independent two-way gene bioinformatic

Experiments

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

CCL8 as a promising prognostic factor in diffuse large B-cell lymphoma via M2 macrophage interactions: A bioinformatic analysis of the tumor microenvironment.

Logical Analysis of Data (LAD) model for the early diagnosis of acute ischemic stroke.

Novel MEK1 mutation identified by mutational analysis of epidermal growth factor receptor signaling pathway genes in lung adenocarcinoma.

Bayesian prediction of RNA translation from ribosome profiling.

Integrated genomics identifies five medulloblastoma subtypes with distinct genetic profiles, pathway signatures and clinicopathological features.

Genomic transcriptional profiling identifies a candidate blood biomarker signature for the diagnosis of septicemic melioidosis.

CLEAN: CLustering Enrichment ANalysis.

Topologically inferring pathway activity toward precise cancer classification via integrating genomic and metabolomic data: prostate cancer as a case.

Integrative analyses reveal signaling pathways underlying familial breast cancer susceptibility.

Canine tumor cross-species genomics uncovers targets linked to osteosarcoma progression.

Cross species genomic analysis identifies a mouse model as undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma.

Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling.

ResnetAge: A Resnet-Based DNA Methylation Age Prediction Method.

A Decentralized Kidney Transplant Biopsy Classifier for Transplant Rejection Developed Using Genes of the Banff-Human Organ Transplant Panel.

Application of functional genomics to primate endometrium: insights into biological processes.

Adipose proteome analysis: focus on mediators of insulin resistance.

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

Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis.

Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: the Stockholm Atherosclerosis Gene Expression (STAGE) study.