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 21

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

The UCSC Proteome Browser.

PMID 15608236 · PMC540054 · Nucleic acids research · 2005 · 8 claims · 5 setups

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The UCSC Proteome Browser is tightly integrated with the UCSC Genome Browser, giving users simultaneous access to genome and proteome data.

swiss-prot sequence domain isoelectric
Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex.

PMID 18515835 · PMC2475620 · Nucleic acids research · 2008 · 8 claims · 6 setups

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Yeast Med2, Med3/Pgd1 and Med5/Nut1 (Tail module) are homologs of human Med29, Med27 and Med24, respectively

eukaryotic med genuine psi-blast mafft pssm-based
Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms.

PMID 15629046 · PMC5172449 · Genomics, proteomics & bioinformatics · 2004 · 8 claims · 7 setups

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Sequence-based molecular phylogenies widely support a sister relationship between animals and fungi, grouped as the Opisthokonta

nine animals completed fungal combined sequence biochemical
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
Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.

PMID 16351747 · PMC1866387 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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Systematic in silico search identified 5 novel human kinase genes (on chromosomes 1, 11, 13, 15, 16) and 1 pseudogene (chromosome X) absent from KinBase

genome genomic kinase psi-blast comparative genscan
Evolutionary genomics reveals lineage-specific gene loss and rapid evolution of a sperm-specific ion channel complex: CatSpers and CatSperbeta.

PMID 18974790 · PMC2572835 · PloS one · 2008 · 8 claims · 6 setups

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The CatSper channel complex (four CatSpers plus CatSperβ) originated as early as primitive metazoans such as the Cnidarian Nematostella vectensis

metazoan catsper pore chicken tblastn maximum sequence
Molecular evolution of Cide family proteins: novel domain formation in early vertebrates and the subsequent divergence.

PMID 18500987 · PMC2426694 · BMC evolutionary biology · 2008 · 8 claims · 5 setups

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Sequences homologous to the CIDE-N domain/NCD show a wide phylogenetic distribution, from hydra and sea anemone to mammals, while true Cide proteins are restricted to vertebrates.

organisms cide cideb hmmer tblastn sequence
Comparison of complete nuclear receptor sets from the human, Caenorhabditis elegans and Drosophila genomes.

PMID 11532213 · PMC55326 · Genome biology · 2001 · 7 claims · 5 setups

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The human genome contains fewer than 50 functional nuclear receptors, far fewer than C. elegans and about twice as many as Drosophila

genome elegans genomic panel tblastn hmmer pcr
The repertoire of G protein-coupled receptors in the sea squirt Ciona intestinalis.

PMID 18452600 · PMC2396169 · BMC evolutionary biology · 2008 · 8 claims · 5 setups

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169 gene products in the Ciona genome were identified as putative GPCRs

ciona sequence molecular est
Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses.

PMID 16805923 · PMC1779541 · Genome biology · 2006 · 8 claims · 6 setups

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The chimpanzee genome contains at least 42 separate families of endogenous retroviruses, 9 newly identified

chimpanzee domains genomic hg16 genome-wide sequence ltr-ltr
Assessing the gene space in draft genomes.

PMID 19042974 · PMC2615622 · Nucleic acids research · 2009 · 6 claims · 7 setups

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The proportion of mapped CEGs in a draft genome assembly is a useful metric for describing gene space completeness, complementing N50 and x-fold coverage.

caenorhabditis toxoplasma homo briggsae cegma blast tblastn
The UCSC genome browser database: update 2007.

PMID 17142222 · PMC1669757 · Nucleic acids research · 2007 · 8 claims · 8 setups

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The UCSC Genome Browser Database provides sequence and annotation data for 13 vertebrate and 19 invertebrate species as of September 2006.

hg17 genome lines xenopus comparative snp linkage
Protein coding potential of retroviruses and other transposable elements in vertebrate genomes.

PMID 15716312 · PMC549403 · Nucleic acids research · 2005 · 8 claims · 5 setups

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About 1000 genes across four vertebrate gene sets analyzed contain at least one RETRA marker protein domain

predicted non-masked genome interpro hmm tblastn inter-species
Dyneins across eukaryotes: a comparative genomic analysis.

PMID 17897317 · PMC2239267 · Traffic (Copenhagen, Denmark) · 2007 · 8 claims · 6 setups

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Phylogenetic inference identified nine DHC families (two cytoplasmic, seven axonemal) and six IC families (one cytoplasmic)

predicted dhc non-redundant arabidopsis hmm-based bayesian tblastn
auts2 Features and Expression Are Highly Conserved during Evolution Despite Different Evolutionary Fates Following Whole Genome Duplication.

PMID 36078102 · PMC9454499 · Cells · 2022 · 8 claims · 7 setups

Has reproduction · 50

auts2a and auts2b originate from the teleost-specific whole genome duplication (TGD)

fish genomic auts2 tissues comparative tblastn phylogenetic
The UCSC Genome Browser Database: 2008 update.

PMID 18086701 · PMC2238835 · Nucleic acids research · 2008 · 8 claims · 8 setups

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The UCSC Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes.

zebrafish yale vertebrate non-human sage expression snp
Multiple distinct sets of stereotyped antigen receptors indicate a role for antigen in promoting chronic lymphocytic leukemia.

PMID 15314077 · PMC2211936 · The Journal of experimental medicine · 2004 · 7 claims · 5 setups

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Five distinct sets of B-CLL patients express strikingly similar (stereotyped) BCRs sharing common H and L chain V region gene segments and similar CDR3 length, composition, and junctional residues.

b-cll sequence cd5+ igv blast phylogenetic
What makes species unique? The contribution of proteins with obscure features.

PMID 16859532 · PMC1779552 · Genome biology · 2006 · 7 claims · 8 setups

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POFs constitute 18-38% (average 26%) of a typical eukaryotic proteome

eukaryotic animal cerevisiae homo hmmpfam blast tblastn
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
Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider.

PMID 36203191 · PMC9535882 · BMC biology · 2022 · 8 claims · 8 setups

Has reproduction · 65

Comparative RNA-seq of cells isolated from central, intermediate, and peripheral regions of stage-3 embryos identifies genes with locally restricted expression genome-wide

tepidariorum drosophila rna-seq whole-mount parental

Experiments

The UCSC Proteome Browser.

Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex.

Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms.

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

Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.

Evolutionary genomics reveals lineage-specific gene loss and rapid evolution of a sperm-specific ion channel complex: CatSpers and CatSperbeta.

Molecular evolution of Cide family proteins: novel domain formation in early vertebrates and the subsequent divergence.

Comparison of complete nuclear receptor sets from the human, Caenorhabditis elegans and Drosophila genomes.

The repertoire of G protein-coupled receptors in the sea squirt Ciona intestinalis.

Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses.

Assessing the gene space in draft genomes.

The UCSC genome browser database: update 2007.

Protein coding potential of retroviruses and other transposable elements in vertebrate genomes.

Dyneins across eukaryotes: a comparative genomic analysis.

auts2 Features and Expression Are Highly Conserved during Evolution Despite Different Evolutionary Fates Following Whole Genome Duplication.

The UCSC Genome Browser Database: 2008 update.

Multiple distinct sets of stereotyped antigen receptors indicate a role for antigen in promoting chronic lymphocytic leukemia.

What makes species unique? The contribution of proteins with obscure features.

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

Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider.