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 41

System / cell line: upstream ✕ Assay: genomic ✕ Clear

Extreme conservation of noncoding DNA near HoxD complex of vertebrates.

PMID 15462684 · PMC524357 · BMC genomics · 2004 · 7 claims · 7 setups

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Three blocks of extremely conserved non-coding DNA (CR1, CR2, CR3) exist within 7 kb upstream of the HoxD complex, 3' of Evx-2, conserved from fish to human.

hoxd genomic pcr pcr-amplified comparative pcr southern
Ab initio identification of putative human transcription factor binding sites by comparative genomics.

PMID 15865625 · PMC1097714 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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An integrated algorithm combining human-mouse genomic comparison, motif overrepresentation, and coregulation filters (GO annotation and microarray coexpression) can identify candidate transcription factor binding sites genome-wide

human-mouse conserved gene consensus comparative statistical gene
Human CCS gene: genomic organization and exclusion as a candidate for amyotrophic lateral sclerosis (ALS).

PMID 11991808 · PMC107843 · BMC genetics · 2002 · 6 claims · 5 setups

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The genomic organization of human CCS was characterized, with the 823 bp coding region organized into 8 exons spanning 12798 bp of genomic DNA.

bac heart ccs genomic genomic rt-pcr transcription
The evolution and genomic landscape of CGB1 and CGB2 genes.

PMID 17055150 · PMC2599907 · Molecular and cellular endocrinology · 2007 · 8 claims · 5 setups

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CGB1 and CGB2 arose via insertion of a DNA fragment (736/724 bp) replacing part of the ancestral hCGβ promoter and 5'-UTR, creating a novel exon 1 and causing a frameshift that produces a completely different 132-aa protein unrelated to hCGβ

genomic great cgb1 chimpanzee pcr population hka
N-acetyltransferase 8, a positional candidate for blood pressure and renal regulation: resequencing, association and in silico study.

PMID 18402670 · PMC2330028 · BMC medical genetics · 2008 · 7 claims · 6 setups

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NAT8 is a novel positional candidate gene for blood pressure and renal function based on its chromosomal location within a BP linkage region and its expression in embryonic/adult kidney and liver

random reference healthy long-term resequencing quantitative sequence
Expression of RAB4B, a protein governing endocytic recycling, is co-regulated with MHC class II genes.

PMID 17175541 · PMC1802633 · Nucleic acids research · 2007 · 7 claims · 7 setups

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A typical MHC-II-like S-Y module is present upstream of the RAB4B transcription start site, identified by genome-wide profile scanning

genomic raji monocyte-derived rj2.2.5 computational chip-on-chip chromatin
Does distance matter? Variations in alternative 3' splicing regulation.

PMID 17704130 · PMC2018619 · Nucleic acids research · 2007 · 8 claims · 7 setups

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Alternative 3' splice sites can be distinguished from constitutive splice sites by a combination of sequence/conservation properties that vary depending on the distance between the splice sites.

intronic human-mouse same comparative polypyrimidine branch
Resequencing PNMT in European hypertensive and normotensive individuals: no common susceptibilily variants for hypertension and purifying selection on intron 1.

PMID 17645789 · PMC1947951 · BMC medical genetics · 2007 · 7 claims · 7 setups

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Resequencing of PNMT found no common susceptibility variants that distinguish hypertensive from normotensive individuals

genomic pnmt promoter pcr population haplotype
Highly individual methylation patterns of alternative glucocorticoid receptor promoters suggest individualized epigenetic regulatory mechanisms.

PMID 19004867 · PMC2602793 · Nucleic acids research · 2008 · 7 claims · 4 setups

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Methylation patterns of the five GR promoters activated in PBMCs are highly variable between individuals.

chromosome genomic pbmc multi-species phylogenetic bisulphite
VISTA Enhancer Browser--a database of tissue-specific human enhancers.

PMID 17130149 · PMC1716724 · Nucleic acids research · 2007 · 8 claims · 2 setups

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Comparative genome analysis can identify candidate human enhancer elements whose tissue-specific in vivo activity can then be experimentally validated in transgenic mice.

genomic genome transgenic comparative
Sequence changes in predicted promoter elements of STK11/LKB1 are unlikely to contribute to Peutz-Jeghers syndrome.

PMID 15774015 · PMC1084245 · BMC genomics · 2005 · 6 claims · 4 setups

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Integrated phylogenetic foot printing and transcription factor binding site (TFBS) prediction identified a consensus putative STK11/LKB1 promoter region between nucleotides -1090 and -1472

genomic phylogenetic direct high
Polymorphisms in the glucocerebrosidase gene and pseudogene urge caution in clinical analysis of Gaucher disease allele c.1448T>C (L444P).

PMID 16887033 · PMC1559599 · BMC medical genetics · 2006 · 6 claims · 5 setups

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A multiplexed suspension bead array (Luminex) assay was developed to genotype 8 Ashkenazi-prevalent disease alleles including GBA c.1448T>C

genomic de-identified multiplex sanger clinical
Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes.

PMID 18086709 · PMC2241899 · Nucleic acids research · 2008 · 8 claims · 5 setups

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Preferred nucleotide sequences around the initiation codon are diverse among eukaryote species, but differences roughly reflect evolutionary relationships between species

eukaryote genes hexanucleotide saccharomyces comparative cluster hexanucleotide
Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes.

PMID 17428321 · PMC1853088 · BMC genomics · 2007 · 8 claims · 7 setups

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Cis-regulatory elements responsible for liver-specific HL expression are conserved among mammalian HL genes

5'-flanking upstream transiently genomic comparative tfbs promoter-reporter
Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

PMID 17020603 · PMC1609119 · BMC genomics · 2006 · 8 claims · 8 setups

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A single PEDF gene is present in all examined vertebrate species but is absent from invertebrates (D. melanogaster, C. elegans, C. intestinalis)

vertebrate cdna pedf complete genomic rt-pcr phylogenetic
Defective splicing, disease and therapy: searching for master checkpoints in exon definition.

PMID 16855287 · PMC1524908 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Splicing-affecting genomic variations can account for up to 50% of mutations leading to gene dysfunction in some genes

random trans-acting tpo fibronectin minigene selex cdna
Five novel mutations of the FRMD7 gene in Chinese families with X-linked infantile nystagmus.

PMID 18431453 · PMC2324116 · Molecular vision · 2008 · 7 claims · 5 setups

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Five novel FRMD7 mutations were identified in five of seven Chinese families with X-linked infantile nystagmus.

genomic affected patients linkage direct snp
Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis.

PMID 18307801 · PMC2268679 · BMC genomics · 2008 · 8 claims · 8 setups

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eBLAT detects up to 75% more conserved bases than original BLAT alignments, with the largest gains between evolutionarily distant orthologs

drosophila caenorhabditis xenopus five pairwise evoprint comparison
CDKN2A and CDK4 mutation analysis in Italian melanoma-prone families: functional characterization of a novel CDKN2A germ line mutation.

PMID 11556834 · PMC2375081 · British journal of cancer · 2001 · 7 claims · 6 setups

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Germ line CDKN2A mutations were found in 5 of 15 (33.3%) Italian melanoma-prone families, including one novel mutation (P48T) and three known pathogenic mutations (R24P, G101W, N71S)

genomic radiolabelled tig-er u2os sscp protein-protein retroviral
ABO exon and intron analysis in individuals with the AweakB phenotype reveals a novel O1v-A2 hybrid allele that causes four missense mutations in the A transferase.

PMID 14617382 · PMC305365 · BMC genetics · 2003 · 8 claims · 7 setups

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A novel O1v-A2 hybrid allele, containing four missense mutations, causes the A weak B phenotype in five individuals of African descent

genomic red computational abo sequencing blood

Experiments

Extreme conservation of noncoding DNA near HoxD complex of vertebrates.

Ab initio identification of putative human transcription factor binding sites by comparative genomics.

Human CCS gene: genomic organization and exclusion as a candidate for amyotrophic lateral sclerosis (ALS).

The evolution and genomic landscape of CGB1 and CGB2 genes.

N-acetyltransferase 8, a positional candidate for blood pressure and renal regulation: resequencing, association and in silico study.

Expression of RAB4B, a protein governing endocytic recycling, is co-regulated with MHC class II genes.

Does distance matter? Variations in alternative 3' splicing regulation.

Resequencing PNMT in European hypertensive and normotensive individuals: no common susceptibilily variants for hypertension and purifying selection on intron 1.

Highly individual methylation patterns of alternative glucocorticoid receptor promoters suggest individualized epigenetic regulatory mechanisms.

VISTA Enhancer Browser--a database of tissue-specific human enhancers.

Sequence changes in predicted promoter elements of STK11/LKB1 are unlikely to contribute to Peutz-Jeghers syndrome.

Polymorphisms in the glucocerebrosidase gene and pseudogene urge caution in clinical analysis of Gaucher disease allele c.1448T>C (L444P).

Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes.

Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes.

Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

Defective splicing, disease and therapy: searching for master checkpoints in exon definition.

Five novel mutations of the FRMD7 gene in Chinese families with X-linked infantile nystagmus.

Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis.

CDKN2A and CDK4 mutation analysis in Italian melanoma-prone families: functional characterization of a novel CDKN2A germ line mutation.

ABO exon and intron analysis in individuals with the AweakB phenotype reveals a novel O1v-A2 hybrid allele that causes four missense mutations in the A transferase.