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 687

System / cell line: predicted ✕ Clear

GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.

PMID 17178752 · PMC1781107 · Nucleic acids research · 2007 · 8 claims · 5 setups

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GenomeTrafac is a web-accessible database enabling genome-wide detection of conserved cis-element clusters in human-mouse gene orthologs, covering both conventional and microRNA genes

human-mouse genome blastz-aligned itgb1bp2 comparative transcription sequence
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
Expression of full-length p53 and its isoform Deltap53 in breast carcinomas in relation to mutation status and clinical parameters.

PMID 17054774 · PMC1636663 · Molecular cancer · 2006 · 7 claims · 7 setups

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The alternative splice isoform Δp53 mRNA is co-expressed with full-length p53 mRNA in breast tumors and cell lines

breast universal p53 subset qrt-pcr bioinformatic structure
Rubinstein-Taybi Syndrome: spectrum of CREBBP mutations in Italian patients.

PMID 17052327 · PMC1626071 · BMC medical genetics · 2006 · 8 claims · 8 setups

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RSTS is caused by chromosomal microdeletions and point mutations in one copy of CREBBP (16p13.3), consistent with haploinsufficiency of this dosage-sensitive gene

peripheral patient-parent genomic crebbp karyotyping bac microsatellite
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
Evaluation of models to predict BRCA germline mutations.

PMID 17016486 · PMC2360540 · British journal of cancer · 2006 · 7 claims · 7 setups

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Four commonly used BRCA risk prediction models (BRCAPRO, Manchester, Penn, Myriad-Frank) have only modest ability to rule in or rule out BRCA1/2 germline mutation carrier status at a 10% probability threshold.

proband pedigrees randomly brca1 brcapro manchester
Novel STAT1 alleles in otherwise healthy patients with mycobacterial disease.

PMID 16934001 · PMC1550284 · PLoS genetics · 2006 · 7 claims · 6 setups

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The E320Q, Q463H, and L706S STAT1 alleles are intrinsically deleterious for both IFNG/GAF-mediated and IFNA/ISGF3-mediated immunity when tested in STAT1-deficient transfected cells

ebv-transformed sv40-transformed nuclear stat1-deficient cdna western immunofluorescence
GENCODE: producing a reference annotation for ENCODE.

PMID 16925838 · PMC1810553 · Genome biology · 2006 · 8 claims · 8 setups

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GENCODE annotation combines initial manual annotation by HAVANA, experimental validation, and refinement based on results to identify protein-coding genes in ENCODE regions

tissues encode rt-pcr comparative automated
Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.

PMID 16914452 · PMC1557807 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Analysis of 56,419 full-length cDNAs identified 6877 alternative splicing genes encoding 18,297 alternative splicing variants made of 37,670 exons.

full-length deduced alternative panel cdna-to-genome manual motif
ATM variants and cancer risk in breast cancer patients from Southern Finland.

PMID 16914028 · PMC1592307 · BMC cancer · 2006 · 8 claims · 6 setups

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Neither 5557G>A nor ivs38-8T>C, nor any haplotype containing them, was significantly associated with breast cancer risk in any patient group

familial brca1 same genotype genotyping denaturing direct
V-MitoSNP: visualization of human mitochondrial SNPs.

PMID 16907992 · PMC1564046 · BMC bioinformatics · 2006 · 6 claims · 4 setups

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V-MitoSNP integrates RFLP genotyping information with mitochondria-related cancer/disease data in a user-friendly, interactive, color-coded visual web interface

blood blood-derived mtdna standard agarose rflp
Genomic view of the evolution of the complement system.

PMID 16896831 · PMC2480602 · Immunogenetics · 2006 · 8 claims · 6 setups

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Bony fish and higher vertebrates share practically the same set of complement genes, indicating most complement gene duplications occurred by the teleost/mammalian divergence (~500 MYA)

chicken complement sponge shark comparative phylogenetic reverse
What makes species unique? The contribution of proteins with obscure features.

PMID 16859532 · PMC1779552 · Genome biology · 2006 · 7 claims · 8 setups

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POFs constitute 18-38% (average 26%) of a typical eukaryotic proteome

eukaryotic animal cerevisiae homo hmmpfam blast tblastn
GeneAlign: a coding exon prediction tool based on phylogenetical comparisons.

PMID 16845010 · PMC1538901 · Nucleic acids research · 2006 · 8 claims · 5 setups

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GeneAlign predicts coding exons by using signal detection (GeneSplicer/WMM) combined with CORAL, a heuristic linear-time alignment tool, to align candidate signal-flanked regions against annotated exons of a homologous organism's genes

homologous human-mouse same gene comparative parameter micro-exon
MACSIMS: multiple alignment of complete sequences information management system.

PMID 16792820 · PMC1539025 · BMC bioinformatics · 2006 · 8 claims · 5 setups

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MACSIMS is a multiple alignment-based information management system combining knowledge-based database mining with ab initio sequence predictions

balibase-derived sequences same query automatic database initio
Genetic diversity among five T4-like bacteriophages.

PMID 16716236 · PMC1524935 · Virology journal · 2006 · 8 claims · 8 setups

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A core set of 82 conserved genes (T4-like genes) is present in all five genomes analyzed, clustered in large collinear blocks.

bacteriophages five conserved aeh1 genome orf trna
Nucleotide sequence analyses of the MRP1 gene in four populations suggest negative selection on its coding region.

PMID 16684361 · PMC1488846 · BMC genomics · 2006 · 8 claims · 5 setups

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The coding region of MRP1 shows evidence of negative selection or recent population expansion based on nucleotide diversity statistics

healthy mrp1 population novo population functional
Eight previously unidentified mutations found in the OA1 ocular albinism gene.

PMID 16646960 · PMC1468396 · BMC medical genetics · 2006 · 7 claims · 5 setups

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Sequencing of the nine OA1 exons in 72 individuals identified ten different mutations across seven unrelated families and three sporadic cases.

genomic oa1 direct long-range splice-site
Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging.

PMID 16646632 · PMC1450327 · PLoS biology · 2006 · 8 claims · 5 setups

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The C-terminal domain of the gE ectodomain (CgE) is the minimal Fc-binding domain of gE-gI

recombinant selenomethionine-substituted ge-gi models surface x-ray computational
Fabry disease: identification of 50 novel alpha-galactosidase A mutations causing the classic phenotype and three-dimensional structural analysis of 29 missense mutations.

PMID 16595074 · PMC3500179 · Human genomics · 2006 · 8 claims · 7 setups

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50 novel α-Gal A mutations were identified in 49 of 66 unrelated families with classic Fabry disease.

genomic α-gal cos-7 transcripts pcr southern microsatellite

Experiments

GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.

The evolution and genomic landscape of CGB1 and CGB2 genes.

Expression of full-length p53 and its isoform Deltap53 in breast carcinomas in relation to mutation status and clinical parameters.

Rubinstein-Taybi Syndrome: spectrum of CREBBP mutations in Italian patients.

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

Evaluation of models to predict BRCA germline mutations.

Novel STAT1 alleles in otherwise healthy patients with mycobacterial disease.

GENCODE: producing a reference annotation for ENCODE.

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.

ATM variants and cancer risk in breast cancer patients from Southern Finland.

V-MitoSNP: visualization of human mitochondrial SNPs.

Genomic view of the evolution of the complement system.

What makes species unique? The contribution of proteins with obscure features.

GeneAlign: a coding exon prediction tool based on phylogenetical comparisons.

MACSIMS: multiple alignment of complete sequences information management system.

Genetic diversity among five T4-like bacteriophages.

Nucleotide sequence analyses of the MRP1 gene in four populations suggest negative selection on its coding region.

Eight previously unidentified mutations found in the OA1 ocular albinism gene.

Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging.

Fabry disease: identification of 50 novel alpha-galactosidase A mutations causing the classic phenotype and three-dimensional structural analysis of 29 missense mutations.