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 13

System / cell line: presence ✕ Assay: transmembrane ✕ 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

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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
Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space.

PMID 16481312 · PMC1373602 · Nucleic acids research · 2006 · 8 claims · 7 setups

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The number of protein families continues to expand steadily as more genomes are sequenced, showing no sign of saturation.

non-identical gene3d cath whole-gene domain transmembrane
MPLW515L is a novel somatic activating mutation in myelofibrosis with myeloid metaplasia.

PMID 16834459 · PMC1502153 · PLoS medicine · 2006 · 8 claims · 8 setups

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A somatic activating mutation in MPL (W515L, transmembrane domain) is present in 9% (4/45) of JAK2V617F-negative myelofibrosis (MF) patients

granulocyte hapmap 32d balb sequencing genotyping proliferation
A comprehensive proteomics and genomics analysis reveals novel transmembrane proteins in human platelets and mouse megakaryocytes including G6b-B, a novel immunoreceptor tyrosine-based inhibitory motif protein.

PMID 17186946 · PMC1860054 · Molecular & cellular proteomics : MCP · 2007 · 8 claims · 8 setups

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Three complementary membrane-enrichment proteomic methods (lectin affinity, biotin/NeutrAvidin affinity, free flow electrophoresis) combined with LC-MS/MS identify 136 transmembrane proteins in human platelets, including many novel ones.

washed platelets tryptic hek293t lc-ms free longsage
Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms?

PMID 15287975 · PMC507878 · Genome biology · 2004 · 8 claims · 6 setups

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3,848 Arabidopsis proteins were identified as likely plant-specific based on phylogenetic profiling and EST confirmation in multiple plant species

arabidopsis phylogenetic tblastn subcellular
Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms.

PMID 16569258 · PMC1557760 · Genome biology · 2006 · 8 claims · 7 setups

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An exon-gene-union (EGU) algorithm followed by an open-reading-frame-selection algorithm can synthesize ab initio (GENSCAN, GeneMark, SNAP) and comparative (Ensembl/Genewise) predictions into a single, more complete CDS set

anopheles gambiae reanocds05 initio full-length rt-pcr
LOCATE: a mammalian protein subcellular localization database.

PMID 17986452 · PMC2238969 · Nucleic acids research · 2008 · 8 claims · 6 setups

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LOCATE is a curated, web-accessible database housing membrane organization and subcellular localization data for mouse and human proteins.

hela proteome indirect automated computational
Genotypic analysis of two hypervariable human cytomegalovirus genes.

PMID 18649324 · PMC2658010 · Journal of medical virology · 2008 · 8 claims · 8 setups

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UL146 sequences from 184 samples fall into the same 14 genotypes (G1-G14) previously defined, with no new genotypes found.

hcmv clinical pcr ul146 pcr nested molecular
Coiled-coil protein composition of 22 proteomes--differences and common themes in subcellular infrastructure and traffic control.

PMID 16288662 · PMC1322226 · BMC evolutionary biology · 2005 · 7 claims · 5 setups

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Proteins with extended coiled-coil domains (>250 amino acids) are largely absent from bacterial genomes but present in archaea and eukaryotes.

proteomes predicted long prokaryotic coiled-coil all-against-all sequence
Comparative genomics search for losses of long-established genes on the human lineage.

PMID 18085818 · PMC2134963 · PLoS computational biology · 2007 · 8 claims · 6 setups

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A novel comparative genomics method (TransMap-based syntenic mapping of gene structures between human, mouse, and dog) can detect losses of well-established single-copy genes without relying on sequence homology to a parental gene, distinguishing them from typical duplication- or retrotransposition-derived pseudogenes.

dog genome chimp gorilla comparative overlap visual
Identification and characterisation of the angiotensin converting enzyme-3 (ACE3) gene: a novel mammalian homologue of ACE.

PMID 17597519 · PMC1925091 · BMC genomics · 2007 · 7 claims · 7 setups

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A novel single-domain ACE-like gene, ACE3, exists in mouse, rat, cow, dog and human genomes, located on the same chromosome downstream of ACE.

dog predicted ace3 panel blast sequence homology
Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs.

PMID 18838389 · PMC2582632 · Nucleic acids research · 2008 · 7 claims · 8 setups

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Although 86% of individual human exons are conserved in the mouse genome, only a small fraction (431/20392, ~2%) of human AS variants are perfectly conserved AS variants in mice.

genome full-length ~3x10^7 isoform whole-genome full-length polysome
Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.

PMID 19906316 · PMC2784480 · BMC genomics · 2009 · 8 claims · 7 setups

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Intronic single-block ESTs with poly(A/T) tails reveal previously unidentified novel transcript variants missed by existing databases.

genome poly est cdna est blast cdna

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.

Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space.

MPLW515L is a novel somatic activating mutation in myelofibrosis with myeloid metaplasia.

A comprehensive proteomics and genomics analysis reveals novel transmembrane proteins in human platelets and mouse megakaryocytes including G6b-B, a novel immunoreceptor tyrosine-based inhibitory motif protein.

Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms?

Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms.

LOCATE: a mammalian protein subcellular localization database.

Genotypic analysis of two hypervariable human cytomegalovirus genes.

Coiled-coil protein composition of 22 proteomes--differences and common themes in subcellular infrastructure and traffic control.

Comparative genomics search for losses of long-established genes on the human lineage.

Identification and characterisation of the angiotensin converting enzyme-3 (ACE3) gene: a novel mammalian homologue of ACE.

Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs.

Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.