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 268

System / cell line: liver ✕ Clear

Functional module detection through integration of single-cell RNA sequencing data with protein-protein interaction networks.

PMID 33138772 · PMC7607865 · BMC genomics · 2020 · 8 claims · 6 setups

Has reproduction · 83

scPPIN integrates scRNA-seq-derived p-values with PPINs to detect maximum-weight connected subgraphs (active/functional modules) via an exact Steiner-tree approach

liver hepatocyte detected adipose single-cell differential protein-protein
Detection of Virus-Related Sequences Associated With Potential Etiologies of Hepatitis in Liver Tissue Samples From Rats, Mice, Shrews, and Bats.

PMID 34177835 · PMC8221242 · Frontiers in microbiology · 2021 · 8 claims · 6 setups

Has reproduction · 79

Viral metagenomics of liver tissue from rats, mice, shrews, and bats revealed a diverse set of sequences related to herpesviruses, orthomyxoviruses, anelloviruses, hepeviruses, hepadnaviruses, flaviviruses, parvoviruses, and picornaviruses

pooled individual liver serum viral pcr strand-specific
Systematic Analysis of Long Non-Coding RNA Genes in Nonalcoholic Fatty Liver Disease.

PMID 35893239 · PMC9332188 · Non-coding RNA · 2022 · 6 claims · 5 setups

Has reproduction · 85

Many lncRNAs, like protein-coding genes, are differentially expressed in NAFLD patients compared to healthy normal-weight and obese individuals.

liver huh-7 bulk sirna lipid
The seeker R package: simplified fetching and processing of transcriptome data.

PMID 36389425 · PMC9648347 · PeerJ · 2022 · 8 claims · 4 setups

Has reproduction · 84

seeker is an R package that wraps existing tools to fetch and process RNA-seq and microarray data, providing a standard interface, simple parallelization, and detailed logging

liver microarray rna-seq
An atlas of the human liver diurnal transcriptome and its perturbation by hepatitis C virus infection.

PMID 39209804 · PMC11362569 · Nature communications · 2024 · 7 claims · 7 setups

Has reproduction · 50

Human hepatocytes engrafted in liver chimeric mice display a large rhythmic transcriptome of ~1700 protein-coding orthologous genes, including transcription factors, chromatin modifiers, and metabolic enzymes.

liver hcv-infected serum bulk chip-seq serum
A missense mutation (Q279R) in the fumarylacetoacetate hydrolase gene, responsible for hereditary tyrosinemia, acts as a splicing mutation.

PMID 11476670 · PMC35353 · BMC genetics · 2001 · 8 claims · 7 setups

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The Q279R missense mutation acts as a splicing mutation in vivo, causing skipping of exon 9 (alone or with exon 8) rather than simply altering the encoded amino acid.

microdissected resected non-tumor liver pcr-rflp immunohistochemistry western
Large-scale discovery and validation of functional elements in the human genome.

PMID 15774039 · PMC1088940 · Genome biology · 2005 · 8 claims · 8 setups

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Genome-wide tiling microarray hybridization reveals large, diverse sets of transcripts, many of which lack existing gene annotations

liver genome yeast lines tiling computational dnase
Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

PMID 15757516 · PMC555945 · BMC genomics · 2005 · 8 claims · 8 setups

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Mouse has a transcribed, 7-exon L-threonine aldolase (GLY1) gene on chromosome 11 encoding a 400-residue protein homologous to bacterial threonine aldolase

liver genomic tissues embryos rt-pcr genomic secondary
Adaptively inferring human transcriptional subnetworks.

PMID 16760900 · PMC1681499 · Molecular systems biology · 2006 · 8 claims · 7 setups

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A multivariate linear spline (MARS-based) model correlating PWM binding scores with log expression ratios can identify active cis-motif combinations in mammalian promoters without requiring gene clustering.

liver proximal hela predicted microarray computational novo
Application of functional genomics to the chimeric mouse model of HCV infection: optimization of microarray protocols and genomics analysis.

PMID 16725047 · PMC1482685 · Virology journal · 2006 · 6 claims · 4 setups

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Mouse liver mRNA cross-hybridizes to corresponding human gene probes on the Agilent Human 22K oligonucleotide microarray

liver genomic hcv-infected agilent two-color semi-quantitative real-time
Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human.

PMID 17288572 · PMC1796608 · BMC evolutionary biology · 2007 · 8 claims · 6 setups

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Widespread transcription occurs across the human genome outside known gene annotations, and the bulk of TARs represent genuine transcripts rather than experimental artifacts

liver chimpanzee h-invitational tar genome blastn secondary
Genome-scale validation of deep-sequencing libraries.

PMID 19002256 · PMC2577887 · PloS one · 2008 · 6 claims · 4 setups

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Mab-seq allows a small aliquot of a ChIP-seq sequencing library to be labeled and hybridized to commercial microarrays for quality control before deep sequencing, without compromising the library for subsequent sequencing.

liver chip-chip chip-seq
Proteomics of the lysosome.

PMID 18977398 · PMC2684028 · Biochimica et biophysica acta · 2009 · 8 claims · 8 setups

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The mammalian lysosome has been shown to contain ~60 soluble luminal proteins and ~25 transmembrane proteins

liver placenta brain conditioned lc-ms n-terminal man6-p
Single nucleotide polymorphism discovery and functional assessment of variation in the UDP-glucuronosyltransferase 2B7 gene.

PMID 18622261 · PMC2680356 · Pharmacogenetics and genomics · 2008 · 7 claims · 7 setups

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UGT2B7 haplotype 4 is associated with increased enzyme activity (M3G and M6G formation)

liver caucasian ugt2b7 gene snp enzymatic
DiRE: identifying distant regulatory elements of co-expressed genes.

PMID 18487623 · PMC2447744 · Nucleic acids research · 2008 · 8 claims · 4 setups

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DiRE predicts distant regulatory elements by combining gene co-expression data, comparative genomics and TFBS profiles to determine TFBS-association signatures

liver myod transgenic microarray tfbs enhancer
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
Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing.

PMID 19822575 · PMC2794179 · Nucleic acids research · 2009 · 8 claims · 6 setups

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ChIP-seq identified 3064 GABP peaks, 7266 FOXA2 peaks and 18783 HNF4a peaks in HepG2 cells

hepg2 liver chip-seq quantitative co-immunoprecipitation
A protein-based set of reference markers for liver tissues and hepatocellular carcinoma.

PMID 19725976 · PMC2742551 · BMC cancer · 2009 · 7 claims · 5 setups

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Three protein spots (beta-actin, HSP60, PDI) show low expression variability across tumourous, non-tumourous cirrhotic, and normal liver tissues by 2-DE (ANOVA p>0.99 ranking)

liver 2-de western immunohistochemistry
MIMIC: a flexible pipeline to register and summarize IMC-MSI experiments.

PMID 41917425 · PMC13201759 · Communications biology · 2026 · 7 claims · 6 setups

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MIMIC is a reproducible, semi-automated workflow that co-registers and jointly analyzes MALDI-MSI and IMC data using a chain of before/after microscopy images.

liver regions artificial maldi-msi imaging multi-step
Alternative polyadenylation mediated the downregulation of lysophosphatidylglycerol acyltransferase 1 in metabolic dysfunction-associated steatotic liver disease.

PMID 41507908 · PMC12879358 · Lipids in health and disease · 2026 · 8 claims · 8 setups

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Early hepatocyte-specific APA remodeling, characterized by 3' UTR lengthening of metabolism-related genes (especially LPGAT1), occurs in MASLD and is established before fibrosis progression

liver hepg2 293t serum bulk single-cell oil

Experiments

Functional module detection through integration of single-cell RNA sequencing data with protein-protein interaction networks.

Detection of Virus-Related Sequences Associated With Potential Etiologies of Hepatitis in Liver Tissue Samples From Rats, Mice, Shrews, and Bats.

Systematic Analysis of Long Non-Coding RNA Genes in Nonalcoholic Fatty Liver Disease.

The seeker R package: simplified fetching and processing of transcriptome data.

An atlas of the human liver diurnal transcriptome and its perturbation by hepatitis C virus infection.

A missense mutation (Q279R) in the fumarylacetoacetate hydrolase gene, responsible for hereditary tyrosinemia, acts as a splicing mutation.

Large-scale discovery and validation of functional elements in the human genome.

Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

Adaptively inferring human transcriptional subnetworks.

Application of functional genomics to the chimeric mouse model of HCV infection: optimization of microarray protocols and genomics analysis.

Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human.

Genome-scale validation of deep-sequencing libraries.

Proteomics of the lysosome.

Single nucleotide polymorphism discovery and functional assessment of variation in the UDP-glucuronosyltransferase 2B7 gene.

DiRE: identifying distant regulatory elements of co-expressed genes.

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.

Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing.

A protein-based set of reference markers for liver tissues and hepatocellular carcinoma.

MIMIC: a flexible pipeline to register and summarize IMC-MSI experiments.

Alternative polyadenylation mediated the downregulation of lysophosphatidylglycerol acyltransferase 1 in metabolic dysfunction-associated steatotic liver disease.