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 15

System / cell line: genome-wide ✕ Assay: splicing ✕ Clear

The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species.

PMID 17108355 · PMC1669709 · Nucleic acids research · 2007 · 8 claims · 4 setups

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ASAP II expands human alternative splicing data ~3-fold over the previous ASAP database, to ~89,078 distinct alternative splicing relationships in 11,717 genes

genome animal aligned est genome-wide comparative est
Extending Asia Pacific bioinformatics into new realms in the "-omics" era.

PMID 19958472 · PMC2788361 · BMC genomics · 2009 · 8 claims · 6 setups

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88 full paper submissions were peer-reviewed for InCoB2009, with 49 shortlisted for oral presentation and 34 accepted into this BMC Genomics supplement, reflecting an overall acceptance rate of 50% across venues.

nhe1 cancer mammalian bovine computational microarray quantile
Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches.

PMID 19773805 · PMC2958924 · Nature reviews. Molecular cell biology · 2009 · 8 claims · 6 setups

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Alternative splicing occurs in the expression of nearly 95% of human multi-exon genes

gria2 drosophila nova1 cd45 splicing sirna hits-clip
Splicing bioinformatics to biology.

PMID 16732900 · PMC1779529 · Genome biology · 2006 · 8 claims · 8 setups

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Mutually exclusive selection of Dscam exon 6 variants is governed by base pairing between a conserved intronic docking site and selector sequences adjacent to each alternative exon.

dscam alternative heterologous expressing comparative dicodon reporter
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
Twin peaks: the draft human genome sequence.

PMID 11276423 · PMC138909 · Genome biology · 2001 · 8 claims · 8 setups

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The predicted number of human genes (~26,000-40,000) is far lower than the widely assumed ~100,000, though downstream RNA/protein complexity can still generate substantial biological complexity.

genome genomic genes yeast whole-genome bac computational
In vitro and in silico analysis reveals an efficient algorithm to predict the splicing consequences of mutations at the 5' splice sites.

PMID 17726045 · PMC2094079 · Nucleic acids research · 2007 · 8 claims · 6 setups

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Two exonic mutations, PINK1 E417G and PARK7 E64D, disrupt binding to U1 snRNA and cause skipping of the mutation-harboring exon

hek293 genome lymphocytes minigene artificial genome-wide
Spontaneous symmetry breaking in genome evolution.

PMID 18367477 · PMC2377439 · Nucleic acids research · 2008 · 6 claims · 3 setups

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Exon size distributions in sequenced genomes follow a lognormal pattern typical of a random Kolmogoroff fractioning process

animal homo model genome-wide alternatively computational
Phenotypic variation meets systems biology.

PMID 19664197 · PMC2745761 · Genome biology · 2009 · 8 claims · 8 setups

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Cellular differentiation states are constrained by complex networks with substantial positive and negative regulation, challenging the concept of single 'master regulators'

thp-1 arabidopsis unspecified mammalian deepcage protein-protein sequencing
X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis.

PMID 17932061 · PMC2238884 · Nucleic acids research · 2008 · 7 claims · 4 setups

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X:Map is a genome annotation database that maps every Affymetrix exon array probeset to Ensembl genome features (genes, ESTs, GenScan predictions) and supports both high-throughput and gene-centric analysis.

ensembl breast mcf7 25-mer probe-to-transcript microarray
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
HITS-CLIP yields genome-wide insights into brain alternative RNA processing.

PMID 18978773 · PMC2597294 · Nature · 2008 · 8 claims · 8 setups

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HITS-CLIP, combining CLIP with high-throughput sequencing, provides a genome-wide, unbiased method to map protein-RNA interactions in vivo.

neocortex brain 293t hits-clip traditional exon
Cohesin regulates alternative splicing.

PMID 36857449 · PMC9977177 · Science advances · 2023 · 7 claims · 8 setups

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Cohesin regulates alternative splicing independently of its effects on transcription.

hct116rmac hct116 recombinant hek293 bulk rt-pcr proximity
Identification of common genetic variation that modulates alternative splicing.

PMID 17571926 · PMC1904363 · PLoS genetics · 2007 · 7 claims · 8 setups

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Common SNPs located close to intron-exon boundaries are associated with and causally modulate alternative splicing patterns in human genes

ceph lcls skipped additional rt-pcr snp resequencing
Mutation screen and association studies in the diacylglycerol O-acyltransferase homolog 2 gene (DGAT2), a positional candidate gene for early onset obesity on chromosome 11q13.

PMID 17477860 · PMC1871603 · BMC genetics · 2007 · 7 claims · 5 setups

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DGAT2 is a plausible positional and functional candidate gene for obesity due to its localization at chr.11q13 (a linkage region) and its key role in triglyceride synthesis

extremely families genome sanger case-control family-based

Experiments

The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species.

Extending Asia Pacific bioinformatics into new realms in the "-omics" era.

Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches.

Splicing bioinformatics to biology.

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

Twin peaks: the draft human genome sequence.

In vitro and in silico analysis reveals an efficient algorithm to predict the splicing consequences of mutations at the 5' splice sites.

Spontaneous symmetry breaking in genome evolution.

Phenotypic variation meets systems biology.

X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis.

Population genomics of human gene expression.

HITS-CLIP yields genome-wide insights into brain alternative RNA processing.

Cohesin regulates alternative splicing.

Identification of common genetic variation that modulates alternative splicing.

Mutation screen and association studies in the diacylglycerol O-acyltransferase homolog 2 gene (DGAT2), a positional candidate gene for early onset obesity on chromosome 11q13.