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 265

System / cell line: enriched ✕ Clear

CompMoby: comparative MobyDick for detection of cis-regulatory motifs.

PMID 18950538 · PMC2605473 · BMC bioinformatics · 2008 · 7 claims · 4 setups

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CompMoby identifies cis-regulatory binding sites at both transcriptional and post-transcriptional levels in metazoans without prior knowledge of the trans-acting factor

embryonic hela novo genome-wide
Decision tree-driven tandem mass spectrometry for shotgun proteomics.

PMID 18931669 · PMC2597439 · Nature methods · 2008 · 8 claims · 5 setups

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A decision tree (DT) algorithm that selects CAD or ETD per precursor based on z and m/z yields more peptide identifications than either CAD or ETD alone

saccharomyces proteome embryonic nlc-ms phosphoproteomics sequential
Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases.

PMID 18842138 · PMC2760875 · Genome biology · 2008 · 8 claims · 6 setups

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AD-related genes (APOE, A2M, PON2, MAP4) and CVD-associated genes (COMT, CBS, WNK1) congregate in a single co-expression module, linking AD and CVD at the transcriptional level

entorhinal subjects expression differentially microarray significance principal
Integrative analysis of RUNX1 downstream pathways and target genes.

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

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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
Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation.

PMID 18653530 · PMC2528163 · Nucleic acids research · 2008 · 8 claims · 7 setups

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A new computational pipeline identifies trans-SAs using ESTs (not just mRNAs) across 10 animal species, improving coverage over prior methods

est unannotated trans-sa tus computational coding hybridization
Dissecting microregulation of a master regulatory network.

PMID 18294391 · PMC2289817 · BMC genomics · 2008 · 8 claims · 6 setups

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143 human miRNAs (termed p53-miRs) each contain at least one putative p53 binding site within 10 kb flanking sequence and are predicted to target at least one known gene

genome mirnas mirna-target predicted p53 mirna cross-referencing
Commonality of functional annotation: a method for prioritization of candidate genes from genome-wide linkage studies.

PMID 18263617 · PMC2275105 · Nucleic acids research · 2008 · 8 claims · 7 setups

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Genes correlated with a common complex trait are more likely to share GO functional annotations than genes not correlated with that trait

genes candidate simulated alzheimer's genome-wide term null-hypothesis
Proteomic analysis of human aqueous humor using multidimensional protein identification technology.

PMID 20019884 · PMC2793904 · Molecular vision · 2009 · 8 claims · 4 setups

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Albumin/IgG depletion combined with MudPIT (2D-LC-MS/MS) enables high-confidence, extensive characterization of the human AH proteome

pooled albumin-bound analysis mudpit immunoaffinity bca
SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells.

PMID 20008100 · PMC2836562 · Nucleic acids research · 2010 · 8 claims · 6 setups

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SeqBuster is a versatile web-based and stand-alone bioinformatic toolkit for processing and analyzing large-scale small RNA deep sequencing datasets.

embryonic hesc small sequence adapter
Gene- and evidence-based candidate gene selection for schizophrenia and gene feature analysis.

PMID 19944577 · PMC2826526 · Artificial intelligence in medicine · 2010 · 8 claims · 5 setups

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The SCOR method outperforms the CCOR method for prioritizing schizophrenia candidate genes

schizophrenia genes ranked gene-based gene expression
MALDI profiling of human lung cancer subtypes.

PMID 19890392 · PMC2767501 · PloS one · 2009 · 8 claims · 8 setups

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PIMAC/MALDI-TOF peptide profiles combined with classification models can distinguish normal lung from tumor and differentiate NSCLC histological subtypes

lung tryptic peak ffpe maldi-tof parallel stepwise
A key role for mitochondria in endothelial signaling by plasma cysteine/cystine redox potential.

PMID 19879942 · PMC3057402 · Free radical biology & medicine · 2010 · 8 claims · 8 setups

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Mitochondria are a major source of ROS in the endothelial signaling response to a more oxidized extracellular EhCySS

maec monocyte dcf mitosox
Liquid chromatography-tandem and MALDI imaging mass spectrometry analyses of RCL2/CS100-fixed, paraffin-embedded tissues: proteomics evaluation of an alternate fixative for biomarker discovery.

PMID 19856998 · PMC2924679 · Journal of proteome research · 2009 · 7 claims · 4 setups

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RCL2/CS100-fixed tissues yield peptide and protein identifications by nanoRPLC-MS/MS comparable to matched fresh-frozen tissues, with proteome coverage not obviously compromised by fixation.

colonic rcl2 colon nanorplc-ms extraction laser
Enrichment of sequencing targets from the human genome by solution hybridization.

PMID 19835619 · PMC2784331 · Genome biology · 2009 · 8 claims · 5 setups

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Solution hybridization with 120-mer capture probes efficiently enriches targeted genomic sequences for next-generation sequencing

genome genomic same technical capture solution-hybridization sequence
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
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

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

dermal same fibroblasts analysis microarray quantitative rt-pcr
Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases.

PMID 19763266 · PMC2740864 · PloS one · 2009 · 8 claims · 8 setups

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Androgen treatment alters the whole-cell proteome of LNCaP prostate cancer cells

lncap androgen prostate itraq mudpit immunoblot
Identification of Key Genes in Atherosclerosis by Combined DNA Methylation and miRNA Expression Analyses.

PMID 35949126 · PMC9682560 · Anatolian journal of cardiology · 2022 · 7 claims · 7 setups

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10 key genes (TCF7L2, CACNA1C, NRP1, GABBR2, FANCC, DCK, CCDC88C, TCF12, ABLIM1, PBX1) are regulated by both aberrant DNA methylation and miRNA activity in atherosclerosis

aorta cardiovascular peripheral blood methylation mirna expression
Cancer-wide in silico analyses using differentially expressed genes demonstrate the functions and clinical relevance of JAG, DLL, and NOTCH.

PMID 39074091 · PMC11285958 · PloS one · 2024 · 7 claims · 8 setups

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JAG, DLL, and NOTCH family gene/protein expression varies diversely across 15 cancer types relative to normal tissue, sometimes discordant between mRNA and protein levels.

tumor degs cancer jag bulk proteomics gene
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

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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

Experiments

CompMoby: comparative MobyDick for detection of cis-regulatory motifs.

Decision tree-driven tandem mass spectrometry for shotgun proteomics.

Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases.

Integrative analysis of RUNX1 downstream pathways and target genes.

Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation.

Dissecting microregulation of a master regulatory network.

Commonality of functional annotation: a method for prioritization of candidate genes from genome-wide linkage studies.

Proteomic analysis of human aqueous humor using multidimensional protein identification technology.

SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells.

Gene- and evidence-based candidate gene selection for schizophrenia and gene feature analysis.

MALDI profiling of human lung cancer subtypes.

A key role for mitochondria in endothelial signaling by plasma cysteine/cystine redox potential.

Liquid chromatography-tandem and MALDI imaging mass spectrometry analyses of RCL2/CS100-fixed, paraffin-embedded tissues: proteomics evaluation of an alternate fixative for biomarker discovery.

Enrichment of sequencing targets from the human genome by solution hybridization.

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

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

Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases.

Identification of Key Genes in Atherosclerosis by Combined DNA Methylation and miRNA Expression Analyses.

Cancer-wide in silico analyses using differentially expressed genes demonstrate the functions and clinical relevance of JAG, DLL, and NOTCH.

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