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 16

System / cell line: transcripts ✕ Assay: genbank ✕ Clear

Human SNPs resulting in premature stop codons and protein truncation.

PMID 16595072 · PMC3500177 · Human genomics · 2006 · 8 claims · 6 setups

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Genome-wide screening of dbSNP identified 28 validated X-SNPs from 28 genes with known minor allele frequencies.

genome transcripts validated x-snp-encoded database blast exon-intron
ChimerDB 2.0--a knowledgebase for fusion genes updated.

PMID 19906715 · PMC2808913 · Nucleic acids research · 2010 · 8 claims · 4 setups

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ChimerDB 2.0 is an updated knowledgebase integrating fusion transcripts from GenBank transcriptome analysis with Sanger CGP, OMIM, PubMed, and Mitelman's database data.

genbank sra pubmed transcript-to-genome ngs literature
ChimerDB--a knowledgebase for fusion sequences.

PMID 16381848 · PMC1347382 · Nucleic acids research · 2006 · 8 claims · 6 setups

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ChimerDB integrates bioinformatics analysis of mRNA/EST sequences, manually collected literature data, and OMIM translocation data into a single fusion sequence knowledgebase

genome candidate pubmed omim blat splice-site ecgene
Non-EST based prediction of exon skipping and intron retention events using Pfam information.

PMID 16204458 · PMC1243800 · Nucleic acids research · 2005 · 7 claims · 5 setups

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A novel ab initio method predicts exon skipping and intron retention events using only Pfam domain annotation, via a Viterbi-like dynamic programming algorithm applied to the Pfam alignment.

refseq dbest genome pfam initio est comparative
ARED 3.0: the large and diverse AU-rich transcriptome.

PMID 16381826 · PMC1347415 · Nucleic acids research · 2006 · 7 claims · 6 setups

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ARED 3.0 computationally mapped more than 4000 ARE-mRNAs to the human genome, representing 5-8% of human genes.

records est est-derived combined computational est sequence
Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription.

PMID 17386095 · PMC1868932 · Genome biology · 2007 · 8 claims · 4 setups

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More than 55,000 totally intronic noncoding (TIN) RNAs are transcribed from the introns of 74% of unique RefSeq genes.

dbest liver cultures refseq est oligoarray polymerase
AceView: a comprehensive cDNA-supported gene and transcripts annotation.

PMID 16925834 · PMC1810549 · Genome biology · 2006 · 8 claims · 4 setups

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At the mRNA level, AceView transcripts are the closest match to Gencode transcripts among all evaluated methods, including alternative splice variants

genome encode caenorhabditis comparative n-to-n cds
Identification of transcription start sites and preferential expression of select CB2 transcripts in mouse and human B lymphocytes.

PMID 19757078 · PMC2843092 · Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology · 2009 · 7 claims · 8 setups

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Human B cells express one CB2 transcript while mouse B cells express three CB2 transcripts

splenocytes pbmc-derived splenic genbank race pcr quantitative
Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes.

PMID 17447839 · PMC1853124 · PLoS computational biology · 2007 · 8 claims · 8 setups

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A new algorithm using spliced ESTs (cross-validated against Known Genes and GenBank mRNA) comprehensively maps bidirectional promoters in the human genome

genome transcripts tissues proteins comparative taf250 cpg
Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.

PMID 18564434 · PMC2453528 · BMC genomics · 2008 · 8 claims · 6 setups

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Jmjd6 has been misleadingly annotated as a transmembrane receptor for engulfment of apoptotic cells; recent evidence contradicts this transmembrane receptor function

species genomic jmjd6 jmjc reciprocal comparative est
Prediction-based approaches to characterize bidirectional promoters in the mammalian genome.

PMID 18366609 · PMC2386062 · BMC genomics · 2008 · 8 claims · 7 setups

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The mapping algorithm identified 5,647 candidate bidirectional promoter regions in the mouse genome, similar in number to those previously found in human.

genome seven genes computational cage comparative
A third approach to gene prediction suggests thousands of additional human transcribed regions.

PMID 16543943 · PMC1391917 · PLoS computational biology · 2006 · 8 claims · 7 setups

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A third basic concept for gene prediction exists, based on detecting strand-specific 'transcription footprints' (mutational and selectional biases) rather than gene structure or sequence similarity.

genome 4.4-mb known nucleotide repeat polyadenylation
Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.

PMID 17010196 · PMC1592491 · BMC genomics · 2006 · 8 claims · 7 setups

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High-throughput 454 sequencing-by-synthesis of LNCaP cDNA can profile transcript abundance across the transcriptome

lncap lncap-derived r1881-treated massively blast blat
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
SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis.

PMID 17338820 · PMC1839109 · BMC bioinformatics · 2007 · 6 claims · 4 setups

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EVDB is a comprehensive, non-redundant relational database of known human splice variants built from NCBI Entrez Gene and Evidence Viewer data

genome affymetrix probe database microarray interactive
Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses.

PMID 24236165 · PMC3827447 · PloS one · 2013 · 8 claims · 8 setups

Has reproduction · 82

An ordinal-level phylogeny of Diplopoda reconstructed from 221 nuclear protein-coding loci (61,641 aligned amino acid columns) differs from existing classifications in fundamental ways.

exemplar paired-end cleaned assembled transcriptome read novo

Experiments

Human SNPs resulting in premature stop codons and protein truncation.

ChimerDB 2.0--a knowledgebase for fusion genes updated.

ChimerDB--a knowledgebase for fusion sequences.

Non-EST based prediction of exon skipping and intron retention events using Pfam information.

ARED 3.0: the large and diverse AU-rich transcriptome.

Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription.

AceView: a comprehensive cDNA-supported gene and transcripts annotation.

Identification of transcription start sites and preferential expression of select CB2 transcripts in mouse and human B lymphocytes.

Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes.

Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.

Prediction-based approaches to characterize bidirectional promoters in the mammalian genome.

A third approach to gene prediction suggests thousands of additional human transcribed regions.

Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.

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

SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis.

Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses.