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: orthologs ✕ Assay: ratio ✕ Clear

Evidence for positive selection in putative virulence factors within the Paracoccidioides brasiliensis species complex.

PMID 18820744 · PMC2553485 · PLoS neglected tropical diseases · 2008 · 8 claims · 8 setups

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Positive selection has played an important role in the molecular evolution of putative virulence factors of P. brasiliensis

brasiliensis gp43 ratio codon-based mutational
Natural selection of protein structural and functional properties: a single nucleotide polymorphism perspective.

PMID 18397526 · PMC2643940 · Genome biology · 2008 · 8 claims · 8 setups

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The SNP A/S ratio is a robust measure of selective constraint, correlating with interspecies Ka/Ks ratios and with protein sequence conservation.

sequence genes proteins sequences snp interspecies sequence
A map of human protein interactions derived from co-expression of human mRNAs and their orthologs.

PMID 18414481 · PMC2387231 · Molecular systems biology · 2008 · 8 claims · 6 setups

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Comparing human mRNA co-expression with co-expression of orthologous gene pairs in five other organisms identifies proteins that physically associate

genes hela proteins worm co-expression quantitative functional
Functional characterisation of the TSC1-TSC2 complex to assess multiple TSC2 variants identified in single families affected by tuberous sclerosis complex.

PMID 18302728 · PMC2291454 · BMC medical genetics · 2008 · 8 claims · 8 setups

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Functional assays of TSC1–TSC2 complex activity can distinguish pathogenic TSC2 mutations from rare polymorphisms when multiple variants segregate in one family

hek immunoprecipitated tsc2 peripheral coimmunoprecipitation rheb s6k-t389
A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation.

PMID 16423292 · PMC1382217 · BMC genomics · 2006 · 7 claims · 6 setups

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Expression context is largely conserved between orthologs across four eukaryote species.

elegans pairwise orthologs cerevisiae microarray ortholog functional
Human PAML browser: a database of positive selection on human genes using phylogenetic methods.

PMID 17962310 · PMC2238824 · Nucleic acids research · 2008 · 8 claims · 5 setups

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The Human PAML Browser is a web-accessible database of codeml-based positive selection test results for 13,721 human genes with orthologs in UCSC multispecies alignments.

same genes orangutan codeml gene sequence
Programmed genetic instability: a tumor-permissive mechanism for maintaining the evolvability of higher species through methylation-dependent mutation of DNA repair genes in the male germ line.

PMID 18535014 · PMC2464741 · Molecular biology and evolution · 2008 · 8 claims · 7 setups

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Repair genes are numerically less common than apoptosis genes in the genomes of multicellular organisms

yeast familial human-mouse comparative gene mutation
Organismal complexity, cell differentiation and gene expression: human over mouse.

PMID 17881362 · PMC2095826 · Nucleic acids research · 2007 · 8 claims · 7 setups

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Human shows a greater fraction of tissue-specific genes and a greater ratio of total expression of tissue-specific to housekeeping genes than mouse across 32 homologous tissues

human-mouse oligonucleotide exon comparative
Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G.

PMID 15269786 · PMC479043 · PLoS biology · 2004 · 7 claims · 6 setups

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APOBEC3G has been under strong, recurrent positive selection throughout primate evolution (~33 million years)

apobec3g pairwise human-chimpanzee apobec1 pcr phylogenetic sliding
Adaptive history of single copy genes highly expressed in the term human placenta.

PMID 18848617 · PMC2759754 · Genomics · 2009 · 8 claims · 6 setups

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222 single copy eutherian genes are highly expressed (>=3x median) in the term human placenta

term single same lists microarray comparative site
Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons.

PMID 19969543 · PMC2831330 · Nucleic acids research · 2010 · 8 claims · 8 setups

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38 candidate cis-regulatory coding exons (RCEs) with predicted target genes were identified genome-wide

hg18 zebrafish bystander human-mouse comparative synteny orthologous
The excess of 5' introns in eukaryotic genomes.

PMID 16314314 · PMC1292992 · Nucleic acids research · 2005 · 7 claims · 4 setups

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All 21 eukaryotic genomes studied show a statistically significant 5′-biased distribution of introns in protein-coding genes

eukaryotic same housekeeping comparative chi-square bidirectional
Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase.

PMID 17316440 · PMC1852407 · Genome biology · 2007 · 8 claims · 6 setups

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CDK consensus motifs are frequently clustered (closely spaced) in known CDK substrate proteins rather than uniformly distributed

cerevisiae cycle reanalysis statistical optimal
Presence of myocilin sequence variants in Japanese patients with open-angle glaucoma.

PMID 18334962 · PMC2268858 · Molecular vision · 2008 · 8 claims · 4 setups

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Two MYOC sequence variants were identified in Japanese POAG patients: a novel non-synonymous variant p.Gln297His and a previously reported variant p.Ala363Thr.

genomic myoc poag pcr amino clinical
Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness.

PMID 19895688 · PMC3091318 · Genome biology · 2009 · 8 claims · 6 setups

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MacroRNA and lincRNA exons are subject to the same relatively low degree of sequence constraint, contrary to prior reports that lincRNAs are far more conserved

macrorna sequence comparative mouse-human population
Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.

PMID 17982176 · PMC2238928 · Nucleic acids research · 2008 · 6 claims · 7 setups

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Evola combines genome synteny-based computational ortholog detection with manual curation of phylogenetic trees by experts to yield more reliable orthologs than automated pairwise methods

genome h-invdb gene sets genome transcript-to-genome coding
Identification and characterization of insect-specific proteins by genome data analysis.

PMID 17407609 · PMC1852559 · BMC genomics · 2007 · 8 claims · 7 setups

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Comparative genome analysis across five holometabolous insects and three non-insect eukaryotes (opisthokonts) identifies 154 insect-specific orthologous groups (refined to 51 proteins) and 466 eukaryote/opisthokont-core orthologous groups

drosophila insect-core locusta insect-specific comparative est functional
Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

PMID 19754956 · PMC2753554 · BMC genomics · 2009 · 8 claims · 8 setups

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1750 transcribed pseudogene annotations (TPAs) were identified in the human genome, ~11.5% of all human pseudogene annotations.

genome rhesus vega-annotated tpas transcript-to-genome same synteny
Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes.

PMID 16150157 · PMC1236922 · BMC genomics · 2005 · 8 claims · 5 setups

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HERV-W (envW) and HERV-FRD (envFRD) envelope genes, both specifically expressed in placenta, show strong sequence conservation with only two nonsynonymous SNPs identified across 91 individuals

genomic genotype 293t pcr-amplified pcr haplotype cell-cell

Experiments

Evidence for positive selection in putative virulence factors within the Paracoccidioides brasiliensis species complex.

Natural selection of protein structural and functional properties: a single nucleotide polymorphism perspective.

A map of human protein interactions derived from co-expression of human mRNAs and their orthologs.

Functional characterisation of the TSC1-TSC2 complex to assess multiple TSC2 variants identified in single families affected by tuberous sclerosis complex.

A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation.

Human PAML browser: a database of positive selection on human genes using phylogenetic methods.

Programmed genetic instability: a tumor-permissive mechanism for maintaining the evolvability of higher species through methylation-dependent mutation of DNA repair genes in the male germ line.

Organismal complexity, cell differentiation and gene expression: human over mouse.

Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G.

Adaptive history of single copy genes highly expressed in the term human placenta.

Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons.

The excess of 5' introns in eukaryotic genomes.

Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase.

Presence of myocilin sequence variants in Japanese patients with open-angle glaucoma.

Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness.

Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.

Identification and characterization of insect-specific proteins by genome data analysis.

Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes.