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 62

System / cell line: orthologs ✕ Assay: sequence ✕ Clear

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
The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species.

PMID 20003425 · PMC2808326 · BMC genomics · 2009 · 7 claims · 4 setups

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3,801 bovine genes have no orthologs in human, mouse and dog, and 1,010 human genes have no orthologs in cow despite having orthologs in mouse and dog

bovine cow coding blast-based ensembl gene
Evolution of insect proteomes: insights into synapse organization and synaptic vesicle life cycle.

PMID 18257909 · PMC2374702 · Genome biology · 2008 · 8 claims · 3 setups

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Compiled a list of 120 core presynaptic gene prototypes (PS120) and catalogued their conservation across insect proteomes.

insect vamp2 ps120 comparative sequence protein-protein
Structural organization and interactions of transmembrane domains in tetraspanin proteins.

PMID 15985154 · PMC1190194 · BMC structural biology · 2005 · 8 claims · 5 setups

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TM1, TM2 and TM3 of human tetraspanins display a distinct heptad repeat motif (abcdefg)n, while TM4 lacks this motif.

tetraspanin cd9 gfp single-cysteine sequence cross-species fluorescence
GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.

PMID 17178752 · PMC1781107 · Nucleic acids research · 2007 · 8 claims · 5 setups

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GenomeTrafac is a web-accessible database enabling genome-wide detection of conserved cis-element clusters in human-mouse gene orthologs, covering both conventional and microRNA genes

human-mouse genome blastz-aligned itgb1bp2 comparative transcription sequence
Comparative analysis of cancer genes in the human and chimpanzee genomes.

PMID 16438707 · PMC1382208 · BMC genomics · 2006 · 7 claims · 6 setups

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All 333 examined human cancer genes have intact, highly conserved orthologs in the chimpanzee genome (99.38% protein identity).

chimpanzee non-human cancer comparative pcr targeted
Divergence of exonic splicing elements after gene duplication and the impact on gene structures.

PMID 19883501 · PMC3091315 · Genome biology · 2009 · 8 claims · 7 setups

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ESEs and ESSs diverge especially fast shortly after gene duplication, correlating with time since duplication (Ks)

paralogous human-mouse duplicated comparative ortholog binomial
A novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31.

PMID 11305939 · PMC31480 · Genome biology · 2001 · 8 claims · 8 setups

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SLC4A9 is a novel human NBC-like gene on chromosome 5q31 encoding a 990-amino-acid, 12-transmembrane-domain protein with high similarity to other sodium bicarbonate cotransporters

bac kidney genomic marathon genomic cdna pcr
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
Correlation of microsynteny conservation and disease gene distribution in mammalian genomes.

PMID 19909546 · PMC2779822 · BMC genomics · 2009 · 7 claims · 8 setups

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Density of mouse orthologs of human disease genes correlates with regions of conserved microsynteny in the mouse genome

genes autosomes dog genome comparative blat sliding-window
Recent segmental and gene duplications in the mouse genome.

PMID 12914656 · PMC193640 · Genome biology · 2003 · 8 claims · 8 setups

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33.6 Mb (1.2%) of the February 2003 mouse genome assembly (2,695 Mb) is involved in recent segmental duplications

genome gene ensembl-annotated chromosome pairwise gene blat
Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics.

PMID 15790398 · PMC1082905 · BMC genomics · 2005 · 8 claims · 6 setups

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Twenty-three chemokine genes and 14 chemokine receptor genes were identified in the chicken genome, including 12 new chemokines and 7 new receptors beyond prior reports.

chicken comparative amino phylogenetic
Genomic view of the evolution of the complement system.

PMID 16896831 · PMC2480602 · Immunogenetics · 2006 · 8 claims · 6 setups

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Bony fish and higher vertebrates share practically the same set of complement genes, indicating most complement gene duplications occurred by the teleost/mammalian divergence (~500 MYA)

chicken complement sponge shark comparative phylogenetic reverse
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
Evolutionary history of the UCP gene family: gene duplication and selection.

PMID 18980678 · PMC2584656 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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The UCP gene family arose through two ancestral gene duplications early in vertebrate evolution, producing the UCP1, UCP2 and UCP3 lineages.

vertebrate ucp human-mouse ucp1 sequence phylogenetic gene
Comparative genomics of the neglected human malaria parasite Plasmodium vivax.

PMID 18843361 · PMC2651158 · Nature · 2008 · 8 claims · 8 setups

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P. vivax resembles other sequenced malaria parasites (P. falciparum, P. knowlesi, P. yoelii) in gene content and metabolic potential

vivax genome comparative microsatellite
Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina.

PMID 14519200 · PMC328454 · Genome biology · 2003 · 8 claims · 5 setups

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Annotation of 8,633 high-quality non-mitochondrial/non-ribosomal ESTs shows 57% represent known genes and 43% are unknown or novel, with M15E having the highest proportion of novel ESTs

embryonic high-quality unique m15e est sequence 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
Computing Ka and Ks with a consideration of unequal transitional substitutions.

PMID 16740169 · PMC1552089 · BMC evolutionary biology · 2006 · 7 claims · 7 setups

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MYN, a modified version of the Yang-Nielsen (YN) algorithm based on the Tamura-Nei Model, allows unequal transitional substitution rates between purines (κR) and pyrimidines (κY) plus codon frequency bias

simulated pairs human-mouse human-dog computer comparative
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

Experiments

Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species.

Evolution of insect proteomes: insights into synapse organization and synaptic vesicle life cycle.

Structural organization and interactions of transmembrane domains in tetraspanin proteins.

GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.

Comparative analysis of cancer genes in the human and chimpanzee genomes.

Divergence of exonic splicing elements after gene duplication and the impact on gene structures.

A novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31.

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

Correlation of microsynteny conservation and disease gene distribution in mammalian genomes.

Recent segmental and gene duplications in the mouse genome.

Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics.

Genomic view of the evolution of the complement system.

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

Evolutionary history of the UCP gene family: gene duplication and selection.

Comparative genomics of the neglected human malaria parasite Plasmodium vivax.

Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina.

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

Computing Ka and Ks with a consideration of unequal transitional substitutions.

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.