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 23

System / cell line: alternative ✕ Assay: cdna ✕ Clear

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

Full-text index only

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
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
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
Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals.

PMID 15860772 · PMC1087780 · Nucleic acids research · 2005 · 8 claims · 8 setups

Full-text index only

Constructed a large-scale dataset of 6876 human alternative protein isoforms from 2624 genes by combining H-Invitational full-length cDNA data and SwissProt VARSPLIC entries

full-length alternative refseq genome pairwise mitochondrial signal
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
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
Visualizing the genome: techniques for presenting human genome data and annotations.

PMID 12149135 · PMC119855 · BMC bioinformatics · 2002 · 8 claims · 4 setups

Full-text index only

Web-based client-server genome browsers (e.g., LocusLink evidence viewer, UCSC genome browser) are limited by lack of true interactivity, requiring server round-trips for navigation

flj22324 snurf arg1 plat cdna-to-genomic multi-track frame-of-translation
Forseti: a mechanistic and predictive model of the splicing status of scRNA-seq reads.

PMID 38940130 · PMC11256924 · Bioinformatics (Oxford, England) · 2024 · 7 claims · 5 setups

Has reproduction · 87

Forseti is the first probabilistic model for resolving the splicing status of exonic scRNA-seq reads by scoring putative fragments linking read alignments to proximate priming sites

training simulated held-out paired-end cubic mlp
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
Characterization of the human DYRK1A promoter and its regulation by the transcription factor E2F1.

PMID 18366763 · PMC2292204 · BMC molecular biology · 2008 · 8 claims · 8 setups

Full-text index only

Transcription start sites of human DYRK1A are distributed over an 800 bp region within an unmethylated CpG island

pc3 saos2 resting phoenix 5'-race-pcr rt-pcr chip-seq
DBTSS provides a tissue specific dynamic view of Transcription Start Sites.

PMID 19910371 · PMC2808897 · Nucleic acids research · 2010 · 8 claims · 8 setups

Full-text index only

DBTSS update adds ~330 million new TSS Seq tags from 31 different human/mouse cell types or culture conditions.

normal dld1 beas2b ramos tss comparative
ECgene: an alternative splicing database update.

PMID 17132829 · PMC1716719 · Nucleic acids research · 2007 · 8 claims · 5 setups

Full-text index only

ECgene provides functional annotation (domain, GO, expression pattern) for alternatively spliced genes

nine genome sage cdna genome-based chi-squared sage
Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella).

PMID 26248502 · PMC4528194 · Scientific reports · 2015 · 8 claims · 8 setups

Has reproduction · 70

AS events, including differentially-expressed-transcript-containing genes (DETs), are ubiquitous in head-kidney and spleen transcriptomes of C. idella

head-kidney idella assembled il-12p40α rna-seq rt-qpcr pcr
Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome.

PMID 32536962 · PMC7291481 · Plant methods · 2020 · 8 claims · 8 setups

Has reproduction · 57

ONT Pc produces higher raw data quality (higher alignment rate, lower error rate) than ONT Dc, while PacBio generates the longest reads

arabidopsis pacbio randomly illumina pacbio nanopore
SMRT and Illumina RNA sequencing reveal novel insights into the heat stress response and crosstalk with leaf senescence in tall fescue.

PMID 32746857 · PMC7397585 · BMC plant biology · 2020 · 7 claims · 5 setups

Has reproduction · 30

Short-term heat stress strongly and specifically activates Hsps, Hsfs, FKBPs, calcium signaling, glutathione S-transferase, photosynthesis, and phytohormone signaling genes.

tall tobacco illumina smrt electrolyte
Defective splicing, disease and therapy: searching for master checkpoints in exon definition.

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

Full-text index only

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
The VIZIER project: preparedness against pathogenic RNA viruses.

PMID 18083241 · PMC7114271 · Antiviral research · 2008 · 8 claims · 6 setups

Full-text index only

Almost all newly emerging human pathogenic viruses are RNA viruses, largely because their error-prone RNA-dependent RNA polymerases and zoonotic reservoirs allow rapid adaptation to new hosts.

viruses virus coli soluble large-scale bioinformatic recombinant
In silico comparative genomic analysis of GABAA receptor transcriptional regulation.

PMID 17603907 · PMC1934366 · BMC genomics · 2007 · 8 claims · 8 setups

Full-text index only

Previously unreported putative promoters were identified for the β2, γ1, γ3, ε, θ and π GABA A receptor subunit genes

subunit mammalian α1-β2-γ2-α6 cross-species promoter transcription
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

Full-text index only

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
Genomic analysis of the chromosome 15q11-q13 Prader-Willi syndrome region and characterization of transcripts for GOLGA8E and WHCD1L1 from the proximal breakpoint region.

PMID 18226259 · PMC2268926 · BMC genomics · 2008 · 8 claims · 7 setups

Full-text index only

GOLGA8E and WHDC1L1 are characterized for the first time as protein-coding transcripts from the PWS proximal breakpoint region.

genomic chromosome lymphoblasts multi-tissue bioinformatic fish rt-pcr

Experiments

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

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

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

Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals.

ECgene: genome annotation for alternative splicing.

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

Visualizing the genome: techniques for presenting human genome data and annotations.

Forseti: a mechanistic and predictive model of the splicing status of scRNA-seq reads.

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

Characterization of the human DYRK1A promoter and its regulation by the transcription factor E2F1.

DBTSS provides a tissue specific dynamic view of Transcription Start Sites.

ECgene: an alternative splicing database update.

Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella).

Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome.

SMRT and Illumina RNA sequencing reveal novel insights into the heat stress response and crosstalk with leaf senescence in tall fescue.

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

The VIZIER project: preparedness against pathogenic RNA viruses.

In silico comparative genomic analysis of GABAA receptor transcriptional regulation.

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.

Genomic analysis of the chromosome 15q11-q13 Prader-Willi syndrome region and characterization of transcripts for GOLGA8E and WHCD1L1 from the proximal breakpoint region.