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 19

System / cell line: network ✕ Assay: domain ✕ Clear

Evolutionary cores of domain co-occurrence networks.

PMID 15788102 · PMC1079808 · BMC evolutionary biology · 2005 · 8 claims · 4 setups

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The innermost (globally central) cores of protein domain co-occurrence networks gradually grow in size with increasing evolutionary/developmental complexity of the organism.

cerevisiae domain weighted comparative
Discovering cancer genes by integrating network and functional properties.

PMID 19765316 · PMC2758898 · BMC medical genomics · 2009 · 8 claims · 6 setups

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Cancer genes have distinct PPI network topology (higher connectivity, higher clustering coefficient, shorter path length to known cancer genes) compared to non-cancer genes

genes gene colon ppi pfam term
Sequence similarity network reveals common ancestry of multidomain proteins.

PMID 18475320 · PMC2377100 · PLoS computational biology · 2008 · 8 claims · 6 setups

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Traditional homology definitions do not capture multidomain evolution; the authors extend the definition to include domain insertion via a common ancestral locus model.

curated complete well-studied sequence alignment domain
The dystrobrevin-binding protein 1 gene: features and networks.

PMID 18663367 · PMC2859304 · Molecular psychiatry · 2009 · 8 claims · 6 setups

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DTNBP1 gene structure, protein-coding sequence, and dysbindin domain are conserved across 13 vertebrate species, while noncoding sequence is diverse.

vertebrate dtnbp1 comparative cross-species molecular
SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny.

PMID 19036790 · PMC2686452 · Nucleic acids research · 2009 · 7 claims · 6 setups

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SUPERFAMILY provides structural, functional and evolutionary annotation for proteins from all completely sequenced genomes using SCOP-based hidden Markov models

user-submitted query genomes proteins domain profile-profile comparative
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
NetworKIN: a resource for exploring cellular phosphorylation networks.

PMID 17981841 · PMC2238868 · Nucleic acids research · 2008 · 8 claims · 4 setups

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NetworKIN integrates consensus substrate motifs with probabilistic network context modelling to predict cellular kinase-substrate relations.

phosphoproteome kinome interactome 53bp1 consensus blastp probabilistic
The cohesin complex: sequence homologies, interaction networks and shared motifs.

PMID 11276426 · PMC30708 · Genome biology · 2001 · 8 claims · 8 setups

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Mouse Mmip1 and Smc3 (SMCD) share 99% sequence identity and are products of the same gene

smc1 smc3 mmip1 smc psi-blast phylogenetic sequence
InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale.

PMID 17868464 · PMC2375030 · Genome biology · 2007 · 8 claims · 8 setups

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InSite predicts protein-pair-specific binding motifs ('Motif M on protein A binds to protein B') by integrating heterogeneous PPI and motif-motif interaction evidence within a Bayesian network trained by EM

saccharomyces homo bank computational yeast tandem
The integrated world of functional genomics.

PMID 12537543 · PMC151279 · Genome biology · 2003 · 8 claims · 8 setups

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Integrating chromatin immunoprecipitation (promoter-binding) data with expression data reveals the yeast cell-cycle transcriptional regulatory network, including network motifs such as autoregulation, multi-component loops, and feedforward loops.

cerevisiae sequenced elegans drosophila chromatin integration comparative
'Genome design' model and multicellular complexity: golden middle.

PMID 17062620 · PMC1635334 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Intermediately expressed human genes are the longest genes genome-wide, in both coding and intronic sequence, longer than housekeeping or tissue-specific genes.

normal genes proteins encoded oligonucleotide gene functional
Bayesian prediction of microbial oxygen requirement.

PMID 26913185 · PMC4743139 · F1000Research · 2013 · 7 claims · 8 setups

Has reproduction · 76

A naive Bayesian classifier based on presence/absence of class-associated Pfam-A domains can distinguish three oxygen requirement classes (aerobe, anaerobe, facultative anaerobe) from genome sequence, unlike prior studies that only made pairwise distinctions.

bacterial selected predicted pfam-a genome gene domain
Interactome networks: the state of the science.

PMID 16515723 · PMC1431712 · Genome biology · 2006 · 8 claims · 8 setups

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Spastin interacts with CHMP1B, an ESCRT-III-associated protein, supporting a role for spastin in intracellular membrane trafficking relevant to hereditary spastic paraplegia

genes tnfα orf proteins yeast tandem interference
Phosphoproteomics: unraveling the signaling web.

PMID 18922462 · PMC2754874 · Molecular cell · 2008 · 8 claims · 8 setups

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Integrating discovery-based MS phosphoproteomics with targeted protein microarray technologies yields a more complete picture of signaling networks and improves clinical translation of findings.

ddr atr-deficient hela mammary phosphospecific phospho-motif scx
Prioritization of candidate cancer genes--an aid to oncogenomic studies.

PMID 18710882 · PMC2566894 · Nucleic acids research · 2008 · 8 claims · 8 setups

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Computational classifiers using combinations of protein conservation, gene structure, protein domains, protein interactions, and regulatory data can distinguish known cancer genes (CD/CR) from unlabelled human genes

genes cancer interpro interactome averaged cross-validation domain
Protein co-evolution, co-adaptation and interactions.

PMID 18818697 · PMC2556093 · The EMBO journal · 2008 · 8 claims · 6 setups

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The mirrortree method predicts protein-protein interactions by detecting pairs of protein families with similar phylogenetic trees (quantified as Pearson correlation of sequence similarity matrices).

nuoe intra-protein coli interacting phylogenetic correlated domain-restricted
Filtering high-throughput protein-protein interaction data using a combination of genomic features.

PMID 15833142 · PMC1127019 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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A combination of three genomic features (interacting Pfam domains, GO annotations, sequence homology) using naive Bayesian networks predicts true protein-protein interactions with high sensitivity and good specificity.

saccharomyces bank caenorhabditis homo yeast mass naive
NovelFam3000--uncharacterized human protein domains conserved across model organisms.

PMID 16533400 · PMC1440326 · BMC genomics · 2006 · 8 claims · 7 setups

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NovelFam3000 is an online data centre unifying bioinformatics resource links, news, comments, and user-submitted experimental data (including a Gene Characterization Index) for ~3000 uncharacterized Pfam-B/DUF domain families conserved across worm, fly, and human

lines mammalian hek drosophila rt-pcr immunofluorescence counterstaining
Sequence variation of PfEMP1-DBLalpha in association with rosette formation in Plasmodium falciparum isolates causing severe and uncomplicated malaria.

PMID 19650937 · PMC3224928 · Malaria journal · 2009 · 8 claims · 5 setups

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Sequence group 1 (mainly from uncomplicated malaria) is significantly different in distribution from sequence group 3 (mainly from severe malaria)

falciparum falciparum-infected pcr-amplified non-identical static rosette rt-pcr

Experiments

Evolutionary cores of domain co-occurrence networks.

Discovering cancer genes by integrating network and functional properties.

Sequence similarity network reveals common ancestry of multidomain proteins.

The dystrobrevin-binding protein 1 gene: features and networks.

SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny.

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

NetworKIN: a resource for exploring cellular phosphorylation networks.

The cohesin complex: sequence homologies, interaction networks and shared motifs.

InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale.

The integrated world of functional genomics.

'Genome design' model and multicellular complexity: golden middle.

Bayesian prediction of microbial oxygen requirement.

Interactome networks: the state of the science.

Phosphoproteomics: unraveling the signaling web.

Prioritization of candidate cancer genes--an aid to oncogenomic studies.

Protein co-evolution, co-adaptation and interactions.

Filtering high-throughput protein-protein interaction data using a combination of genomic features.

NovelFam3000--uncharacterized human protein domains conserved across model organisms.

Sequence variation of PfEMP1-DBLalpha in association with rosette formation in Plasmodium falciparum isolates causing severe and uncomplicated malaria.