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 220

Assay: regulatory ✕ Clear

The cohesin complex: sequence homologies, interaction networks and shared motifs.

PMID 11276426 · PMC30708 · Genome biology · 2001 · 8 claims · 8 setups

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Mouse Mmip1 and Smc3 (SMCD) share 99% sequence identity and are products of the same gene

smc1 smc3 mmip1 smc psi-blast phylogenetic sequence
Genome informatics: taming the avalanche of genomic data.

PMID 15642109 · PMC549058 · Genome biology · 2005 · 8 claims · 7 setups

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Ultraconserved regions (>100 bp, 100% conserved among mammals) exist in the genome and their function remains unknown

genes arabidopsis genome vertebrate comparative conservation whole-genome
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
The MAPPER database: a multi-genome catalog of putative transcription factor binding sites.

PMID 15608292 · PMC540057 · Nucleic acids research · 2005 · 8 claims · 6 setups

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Built a library of 1134 HMM models (359 matrix-derived, 718 factor-derived, 57 JASPAR-derived), corresponding to 863 distinct TF names, from TRANSFAC and JASPAR binding site data

genome drosophila transfac b99 profile sequence case-study
Epigenetics and phenotypic variation in mammals.

PMID 16688527 · PMC3906716 · Mammalian genome : official journal of the International Mammalian Genome Society · 2006 · 8 claims · 8 setups

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Epigenetic modifications are mitotically heritable, but the fidelity of meiotic/transgenerational inheritance in mammals is poorly understood and evidence in mammals is scanty.

mammalian mhc chromosomes embryonic methylation high-throughput chip
MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data.

PMID 16381984 · PMC1347458 · Nucleic acids research · 2006 · 8 claims · 5 setups

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MPromDb is a novel database integrating experimentally supported gene promoters, TSS annotation, cis-regulatory elements, CpG islands, and ChIP-chip data with an integrated visualization interface.

chip-chip sequence genbank
F-SNP: computationally predicted functional SNPs for disease association studies.

PMID 17986460 · PMC2238878 · Nucleic acids research · 2008 · 6 claims · 8 setups

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F-SNP is a database integrating functional effect predictions for SNPs from 16 bioinformatics tools/databases across four categories: splicing, transcription, translation, and post-translation

genome protein-coding genomic genome-wide non-synonymous exonic nonsense
Population genomics of human gene expression.

PMID 17873874 · PMC2683249 · Nature genetics · 2007 · 8 claims · 8 setups

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Gene expression levels in lymphoblastoid cell lines are a heritable trait

ebv-transformed ceu lymphoblastoid unrelated genome-wide custom cis-eqtl
Inference of transcriptional regulation using gene expression data from the bovine and human genomes.

PMID 17683551 · PMC1978505 · BMC genomics · 2007 · 7 claims · 8 setups

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Using human reference promoter sequences is a useful approach for studying gene expression regulation in species with limited or non-existing genomic sequence, such as cattle.

muscle-specific bovine refseq cardiac novo est blastn
In silico whole-genome screening for cancer-related single-nucleotide polymorphisms located in human mRNA untranslated regions.

PMID 17201911 · PMC1774567 · BMC genomics · 2007 · 8 claims · 5 setups

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A computational EST-based pipeline can identify UTR-SNPs that are statistically over-represented in cancerous versus normal tissue libraries

est acute 100-nt whole-genome est-based pcr-based secondary
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
Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research.

PMID 18831773 · PMC3226104 · BMC genomics · 2008 · 8 claims · 8 setups

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Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare

mcf7 arabidopsis specified different chip-seq microarray array-based
Complete genome of Phenylobacterium zucineum--a novel facultative intracellular bacterium isolated from human erythroleukemia cell line K562.

PMID 18700039 · PMC2529317 · BMC genomics · 2008 · 8 claims · 6 setups

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Complete genome of P. zucineum HLK1T consists of a 3,996,255 bp circular chromosome and a 382,976 bp circular plasmid encoding 3,861 proteins, 42 tRNAs, and one 16S-23S-5S rRNA operon

phenylobacterium zucineum bacteria genome cog comparative
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

PMID 18515841 · PMC2447758 · Nucleic acids research · 2008 · 8 claims · 5 setups

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Babelomics is a web suite offering both conventional functional enrichment methods and more advanced gene set analysis (GSA) methods, a combination offered by only one other tool (FuncAssociate) among competitors.

user-supplied ranked gene fasta-formatted functional gene novo
Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes.

PMID 18187510 · PMC2275096 · Nucleic acids research · 2008 · 8 claims · 6 setups

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G-richness downstream of the TSS is strand-biased, concentrated on the nontemplate strand, with a peak at +200 to +300 bp

refseq chicken random genome-wide quadparser regulatory
Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns.

PMID 19906709 · PMC2811022 · Nucleic acids research · 2010 · 8 claims · 5 setups

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A genome-wide catalog of up to ~9000 overlapping antisense loci (23,782 non-redundant SAT pairs, clustered into 8894) was compiled and stored in the USAGP database

genome affymetrix antisense mirna computational microarray sage
Mutation analysis in primary immunodeficiency diseases: case studies.

PMID 19841577 · PMC2774237 · Current opinion in allergy and clinical immunology · 2009 · 8 claims · 8 setups

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Genomic DNA Sanger sequencing is the standard first-line approach for identifying PIDD-causing mutations but has limitations that can yield false-negative or false-positive results

mother parents ebv-transformed nemo genomic flow northern
Identification of a novel functional deletion variant in the 5'-UTR of the DJ-1 gene.

PMID 19825160 · PMC2767350 · BMC medical genetics · 2009 · 8 claims · 6 setups

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A novel 16 bp deletion variant (g.-6_+10del) was identified in the DJ-1 5'-UTR, spanning the transcription start site, 93 bp downstream of a known Sp1 site.

genomic hek293 m17 south sscp dual-luciferase pcr-rflp
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
Unveiling the NEFH+ malignant cell subtype: Insights from single-cell RNA sequencing in prostate cancer progression and tumor microenvironment interactions.

PMID 39759507 · PMC11695424 · Frontiers in immunology · 2024 · 8 claims · 8 setups

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A malignant cell subtype in PCa with high expression of NEFH was identified, located at the differentiation terminal, showing higher malignancy and association with advanced tumor lesions.

pca malignant tcga mda single-cell infercnv pseudotime

Experiments

The cohesin complex: sequence homologies, interaction networks and shared motifs.

Genome informatics: taming the avalanche of genomic data.

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

The MAPPER database: a multi-genome catalog of putative transcription factor binding sites.

Epigenetics and phenotypic variation in mammals.

MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data.

F-SNP: computationally predicted functional SNPs for disease association studies.

Population genomics of human gene expression.

Inference of transcriptional regulation using gene expression data from the bovine and human genomes.

In silico whole-genome screening for cancer-related single-nucleotide polymorphisms located in human mRNA untranslated regions.

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

Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research.

Complete genome of Phenylobacterium zucineum--a novel facultative intracellular bacterium isolated from human erythroleukemia cell line K562.

Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes.

Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns.

Mutation analysis in primary immunodeficiency diseases: case studies.

Identification of a novel functional deletion variant in the 5'-UTR of the DJ-1 gene.

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

Unveiling the NEFH+ malignant cell subtype: Insights from single-cell RNA sequencing in prostate cancer progression and tumor microenvironment interactions.