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 293

System / cell line: domain ✕ Clear

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
A screen for proteins that interact with PAX6: C-terminal mutations disrupt interaction with HOMER3, DNCL1 and TRIM11.

PMID 16098226 · PMC1208879 · BMC genetics · 2005 · 8 claims · 7 setups

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PAX6 interacts with three novel proteins: HOMER3, DNCL1 and TRIM11

pax6 brain yeast sequence yeast semi-quantitative
Benchmarking ortholog identification methods using functional genomics data.

PMID 16613613 · PMC1557999 · Genome biology · 2006 · 8 claims · 7 setups

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InParanoid is the best overall ortholog identification method for identifying functionally equivalent proteins when sensitivity and selectivity are combined into an overall score.

known human-mouse expression interpro co-expression
Early onset familial Alzheimer Disease with spastic paraparesis, dysarthria, and seizures and N135S mutation in PSEN1.

PMID 18580586 · PMC2750842 · Alzheimer disease and associated disorders · 2008 · 8 claims · 8 setups

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The PSEN1 N135S mutation causes EOFAD with an atypical phenotype including spastic dysarthria, limb spasticity, and seizures in addition to typical cognitive deficits

archival medulla cortex hippocampus immunohistochemistry thioflavin-s pcr
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
MEROPS: the peptidase database.

PMID 19892822 · PMC2808883 · Nucleic acids research · 2010 · 8 claims · 5 setups

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MEROPS is a manually curated hierarchical classification of peptidases and protein inhibitors organized into protein species, families, and clans based on sequence and structural homology.

archaean holotype c-x-c proteins comparative domain substrate
In Silico screening for functional candidates amongst hypothetical proteins.

PMID 19754976 · PMC2758874 · BMC bioinformatics · 2009 · 7 claims · 6 setups

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An in silico selection strategy combining subcellular targeting-signal prediction with protein domain identification can enrich for true functional proteins among hypothetical proteins

hypothetical targetp-selected mitochondria-predicted subcellular domain database
Advances in the study of SR protein family.

PMID 15626328 · PMC5172405 · Genomics, proteomics & bioinformatics · 2003 · 8 claims · 8 setups

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SR proteins promote assembly of the early splicesome via protein-protein interactions in their RS-domain that recruit components of the splicing machinery.

nuclear bovine drosophila caenorhabditis selex rna-binding splicing
Enthoprotin: a novel clathrin-associated protein identified through subcellular proteomics.

PMID 12213833 · PMC2173151 · The Journal of cell biology · 2002 · 8 claims · 8 setups

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Subcellular proteomics of purified CCVs identifies enthoprotin (encoded by KIAA0171), a novel ENTH domain-containing protein not previously detected at the protein level.

brain cos-7 hek-293 clathrin subcellular western ccv
Molecular phylogeny of the kelch-repeat superfamily reveals an expansion of BTB/kelch proteins in animals.

PMID 13678422 · PMC222960 · BMC bioinformatics · 2003 · 8 claims · 8 setups

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The human genome encodes at least 71 kelch-repeat proteins

genome yeast kelch-repeat full-length blast blastp cross-referencing
CpG island methylation status and mutation analysis of the RB1 gene essential promoter region and protein-binding pocket domain in nervous system tumours.

PMID 12556968 · PMC2376780 · British journal of cancer · 2003 · 8 claims · 4 setups

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RB1 CpG island hypermethylation is a common epigenetic event associated with development of malignant nervous system tumours

nervous bisulphite-modified same pcr-sscp methylation-specific bisulphite
Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level.

PMID 17090320 · PMC1654190 · BMC evolutionary biology · 2006 · 8 claims · 5 setups

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HHpred (HMM-HMM comparison) detects remote homologs in the human proteome with higher sensitivity than hmmpfam (HMMER), giving 10% more functional domain coverage and 20% higher residue coverage against Pfam-A families.

proteome homo domains hmm-hmm hmm subtractive
Analysis of protein sequence and interaction data for candidate disease gene prediction.

PMID 17020920 · PMC1636487 · Nucleic acids research · 2006 · 8 claims · 7 setups

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Combining CPS and CMP using known disease genes as input achieves sensitivity 0.52 and specificity 0.97, reducing candidate lists 13-fold

ophid biocarta kegg pfam-annotated common benchmarking multiple-interval
Mutations in PIK3CA are infrequent in neuroblastoma.

PMID 16822308 · PMC1533846 · BMC cancer · 2006 · 8 claims · 6 setups

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PIK3CA activating mutations are infrequent in human neuroblastoma (2.9%, 2/69 tumors)

neuroblastoma neuroblastoma-derived patients th-mycn targeted sanger rt-pcr
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
The 10 sea urchin receptor for egg jelly proteins (SpREJ) are members of the polycystic kidney disease-1 (PKD1) family.

PMID 17629917 · PMC1934368 · BMC genomics · 2007 · 8 claims · 5 setups

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Sea urchins possess 10 SpREJ (PKD1 family) genes, compared to five in humans, all defined by possession of a ~600 residue REJ domain

strongylocentrotus sprej purpuratus full-length cdna secondary real-time
Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.

PMID 19756158 · PMC2742196 · PLoS computational biology · 2009 · 8 claims · 4 setups

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MIP active learning is a novel active learning method that preferentially seeks informative Positive (functionally active) examples rather than only maximizing classifier accuracy.

engineered p53 computational yeast-based regional homology
The genome of the simian and human malaria parasite Plasmodium knowlesi.

PMID 18843368 · PMC2656934 · Nature · 2008 · 8 claims · 7 setups

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The P. knowlesi (H strain) nuclear genome was sequenced and assembled: 23.5 Mb across 14 chromosomes with 5,188 predicted protein-encoding genes.

knowlesi predicted type whole-genome comparative pfam
Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties.

PMID 18673550 · PMC2533329 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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The human TRIM family is split into two groups (group 1 and group 2) that differ in domain structure, genomic organization, and evolutionary properties.

redundant mammalian genomic vertebrates blast pattern-hit tblastn
Evaluation of the genetic polymorphism of Plasmodium falciparum P126 protein (SERA or SERP) and its influence on naturally acquired specific antibody responses in malaria-infected individuals living in the Brazilian Amazon.

PMID 18667071 · PMC2515332 · Malaria journal · 2008 · 8 claims · 4 setups

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Only two OR fragment types were identified in P. falciparum isolates from the Brazilian Amazon: OR-I (175 bp) and OR-II (199 bp)

falciparum pcr-amplified p126 sera nested agarose sequencing

Experiments

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

A screen for proteins that interact with PAX6: C-terminal mutations disrupt interaction with HOMER3, DNCL1 and TRIM11.

Benchmarking ortholog identification methods using functional genomics data.

Early onset familial Alzheimer Disease with spastic paraparesis, dysarthria, and seizures and N135S mutation in PSEN1.

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

MEROPS: the peptidase database.

In Silico screening for functional candidates amongst hypothetical proteins.

Advances in the study of SR protein family.

Enthoprotin: a novel clathrin-associated protein identified through subcellular proteomics.

Molecular phylogeny of the kelch-repeat superfamily reveals an expansion of BTB/kelch proteins in animals.

CpG island methylation status and mutation analysis of the RB1 gene essential promoter region and protein-binding pocket domain in nervous system tumours.

Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level.

Analysis of protein sequence and interaction data for candidate disease gene prediction.

Mutations in PIK3CA are infrequent in neuroblastoma.

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

The 10 sea urchin receptor for egg jelly proteins (SpREJ) are members of the polycystic kidney disease-1 (PKD1) family.

Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.

The genome of the simian and human malaria parasite Plasmodium knowlesi.

Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties.

Evaluation of the genetic polymorphism of Plasmodium falciparum P126 protein (SERA or SERP) and its influence on naturally acquired specific antibody responses in malaria-infected individuals living in the Brazilian Amazon.