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: cdna ✕ Assay: splice ✕ Clear

Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles.

PMID 16195578 · PMC1240112 · Nucleic acids research · 2005 · 8 claims · 5 setups

Full-text index only

Alternative splices in 10,818 human-mouse gene pairs can be classified as conserved, novel, or diverged based on genomic and transcript-level cross-species comparison.

orthologous diverse tissues gene comparative est microarray
Genome-wide survey of allele-specific splicing in humans.

PMID 18518984 · PMC2427040 · BMC genomics · 2008 · 8 claims · 5 setups

Full-text index only

A genome-wide computational scan identified 30,977 SNPs located within predicted splicing regulatory sequences (donor sites, acceptor sites, branch points, and ESEs)

genome cdna hapmap computational est exon
Computational analysis of splicing errors and mutations in human transcripts.

PMID 18194514 · PMC2234086 · BMC genomics · 2008 · 8 claims · 4 setups

Full-text index only

Retained introns are significantly shorter than constitutively spliced introns

refseq genes intron exon computational splice prediction
Pairagon+N-SCAN_EST: a model-based gene annotation pipeline.

PMID 16925839 · PMC1810554 · Genome biology · 2006 · 7 claims · 5 setups

Full-text index only

Pairagon+N-SCAN_EST, using only native alignments, was as accurate as ENSEMBL and ExoGean in the EGASP mRNA/EST evidence assessment

encode genome cdna-to-genome novo comparative
Accurate splice site prediction using support vector machines.

PMID 18269701 · PMC2230508 · BMC bioinformatics · 2007 · 8 claims · 5 setups

Full-text index only

Weighted degree (WD) kernel SVMs outperform Markov Chains, GeneSplicer and SpliceMachine for genome-wide splice site recognition

nn269 dgsplicer caenorhabditis arabidopsis svm genome-wide
Alzheimer's disease biomarker discovery in symptomatic and asymptomatic patients: experimental approaches and future clinical applications.

PMID 19796674 · PMC2840994 · Experimental gerontology · 2010 · 8 claims · 4 setups

Full-text index only

cDNA microarray screening of 6794 genes identified 32 genes aberrantly expressed (>1.8-fold) in the superior temporal gyrus of moderate dementia cases versus cognitively normal controls

post-mortem cortico-hippocampal cdna western culture
Identification of herpesvirus transcripts from genomic regions around the replication origins.

PMID 37773348 · PMC10541914 · Scientific reports · 2023 · 8 claims · 8 setups

Has reproduction · 59

Herpesviruses display distinct patterns of transcriptional overlaps near or at the replication origins (Oris)

nine same vzv prv direct cage-seq qrt-pcr
Genome annotation of a 1.5 Mb region of human chromosome 6q23 encompassing a quantitative trait locus for fetal hemoglobin expression in adults.

PMID 15169551 · PMC441375 · BMC genomics · 2004 · 8 claims · 8 setups

Full-text index only

A very large, previously uncharacterized gene, AHI1, containing WD40 and SH3 domains was discovered in the candidate interval

cdna image hbs1l ahi1 rt-pcr est northern
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

Full-text index only

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
Modification of the Creator recombination system for proteomics applications--improved expression by addition of splice sites.

PMID 16519801 · PMC1421398 · BMC biotechnology · 2006 · 8 claims · 8 setups

Full-text index only

The Creator Splice system (5' intron splicing) significantly increases protein expression levels compared to the standard Creator system

hek293t mammalian coli vector immunoblot fluorescence bacterial
Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse.

PMID 18439302 · PMC2432081 · BMC genomics · 2008 · 8 claims · 7 setups

Full-text index only

Adjacent cassette exon pairs can be categorized by EST-derived correlation coefficient into three groups: mutually exclusive (ME, r<=-0.7), independent (IND, -0.2<=r<=0.2), and linked (LNK, r>=0.7)

human-mouse adjacent est genome splice
Alternative splicing of human peroxisome proliferator-activated receptor delta (PPAR delta): effects on translation efficiency and trans-activation ability.

PMID 17705821 · PMC2045109 · BMC molecular biology · 2007 · 8 claims · 8 setups

Full-text index only

Multiple alternatively spliced 5'-UTR isoforms of human PPARdelta mRNA differ in translation efficiency

placenta five lines huh7 5'-race rt-pcr real-time
Identification of a novel splice-site mutation in the Lebercilin (LCA5) gene causing Leber congenital amaurosis.

PMID 18334959 · PMC2268850 · Molecular vision · 2008 · 7 claims · 5 setups

Full-text index only

A homozygous c.955G>A mutation at the last base of exon 6 of LCA5 disrupts the normal splice donor site.

genomic lca5 lymphocyte affected snp sanger splice
Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts.

PMID 19835606 · PMC2784330 · Genome biology · 2009 · 7 claims · 2 setups

Full-text index only

Hybrid selection of cDNA dramatically increases the specificity of sequencing reads mapping to targeted cancer-related transcripts.

k-562 targeted sanger
Combined subtractive cDNA cloning and array CGH: an efficient approach for identification of overexpressed genes in DNA amplicons.

PMID 15018647 · PMC365025 · BMC genomics · 2004 · 8 claims · 8 setups

Full-text index only

Combined SSH subtractive cloning and array CGH is an efficient strategy to identify overexpressed genes located within DNA amplicons.

imr-32 subtracted mycn-amplified suppression differential array
ECgene: genome annotation for alternative splicing.

PMID 15608289 · PMC540072 · Nucleic acids research · 2005 · 8 claims · 5 setups

Full-text index only

ECgene combines genome-based EST clustering with a graph-theoretic transcript assembly procedure to predict gene models including alternative splicing events.

brca2 rgs17 organs cdna genomic genome transcript
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

Full-text index only

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

lncap lncap-derived r1881-treated massively blast blat
Genome Network and FANTOM3: assessing the complexity of the transcriptome.

PMID 16683037 · PMC1449904 · PLoS genetics · 2006 · 8 claims · 7 setups

Full-text index only

63% of the genome is transcribed from at least one strand, versus the earlier belief that only 2% is transcribed into protein-coding mRNA

fantom3 genome large-scale mammalian cage full-length genome
GENCODE: producing a reference annotation for ENCODE.

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

Full-text index only

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
Mutation analysis of SDHB and SDHC: novel germline mutations in sporadic head and neck paraganglioma and familial paraganglioma and/or pheochromocytoma.

PMID 16405730 · PMC1343542 · BMC medical genetics · 2006 · 8 claims · 4 setups

Full-text index only

Germline mutations of SDHB and SDHC play a minor role in sporadic head and neck paraganglioma

peripheral genomic ebv-transformed conformation pira-pcr rt-pcr

Experiments

Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles.

Genome-wide survey of allele-specific splicing in humans.

Computational analysis of splicing errors and mutations in human transcripts.

Pairagon+N-SCAN_EST: a model-based gene annotation pipeline.

Accurate splice site prediction using support vector machines.

Alzheimer's disease biomarker discovery in symptomatic and asymptomatic patients: experimental approaches and future clinical applications.

Identification of herpesvirus transcripts from genomic regions around the replication origins.

Genome annotation of a 1.5 Mb region of human chromosome 6q23 encompassing a quantitative trait locus for fetal hemoglobin expression in adults.

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

Modification of the Creator recombination system for proteomics applications--improved expression by addition of splice sites.

Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse.

Alternative splicing of human peroxisome proliferator-activated receptor delta (PPAR delta): effects on translation efficiency and trans-activation ability.

Identification of a novel splice-site mutation in the Lebercilin (LCA5) gene causing Leber congenital amaurosis.

Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts.

Combined subtractive cDNA cloning and array CGH: an efficient approach for identification of overexpressed genes in DNA amplicons.

ECgene: genome annotation for alternative splicing.

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

Genome Network and FANTOM3: assessing the complexity of the transcriptome.

GENCODE: producing a reference annotation for ENCODE.

Mutation analysis of SDHB and SDHC: novel germline mutations in sporadic head and neck paraganglioma and familial paraganglioma and/or pheochromocytoma.