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 15

System / cell line: chicken ✕ Assay: family ✕ Clear

Insights into vertebrate evolution from the chicken genome sequence.

PMID 15693954 · PMC551526 · Genome biology · 2005 · 8 claims · 6 setups

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Chicken has expanded gene families involved in egg production (e.g., avidin) and feather/scale/claw formation (avian-specific keratins) not present or lost in mammals

red chicken whole-genome comparative synteny
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 novel mutation in FRMD7 causing X-linked idiopathic congenital nystagmus in a large family.

PMID 18246032 · PMC2267738 · Molecular vision · 2008 · 8 claims · 6 setups

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A novel c.812G>T transversion in exon 9 of FRMD7, causing p.C271F, is the causative mutation for XLICN in this family

affected family blood frmd7 microsatellite direct denaturing
Mutations in TRPV4 cause Charcot-Marie-Tooth disease type 2C.

PMID 20037586 · PMC2812627 · Nature genetics · 2010 · 8 claims · 8 setups

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Heterozygous missense mutations in TRPV4 (c.805C>T/R269C and c.806G>A/R269H) cause CMT2C

cmt2c affected spinal drg genetic sanger quantitative
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
Pseudofam: the pseudogene families database.

PMID 18957444 · PMC2686518 · Nucleic acids research · 2009 · 8 claims · 7 setups

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Pseudofam is an online database of pseudogene families built by mapping pseudogenes to Pfam protein families, providing query tools, statistics, and sequence alignments

eukaryotic over pseudogenes pseudogene blast family sequence
Genes at human chromosome 5q31.1 regulate delayed-type hypersensitivity responses associated with Leishmania chagasi infection.

PMID 17713557 · PMC2435172 · Genes and immunity · 2007 · 7 claims · 8 setups

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SNPs in LECT2 and TGFBI show independent associations with the DTH+ phenotype, indicating two separate genes in this region control DTH+

blood family unrelated subjects snp family-based linkage
Comparative genomic analysis of prion genes.

PMID 17199895 · PMC1781936 · BMC genomics · 2007 · 8 claims · 8 setups

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SPRN and PRNP homologues are present in all vertebrates, whereas PRND is restricted to tetrapods and PRNT is restricted to primates

vertebrate multi-tissue aligned sprn comparative gene cdna
Genomic analysis of a heterogeneous Mendelian phenotype: multiple novel alleles for inherited hearing loss in the Palestinian population.

PMID 16460646 · PMC3525152 · Human genomics · 2006 · 8 claims · 8 setups

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GJB2 (connexin 26) mutations account for hearing loss in only 17 of 156 families (11%), a smaller fraction than reported in other populations.

palestinian genomic probands lymphoblasts targeted sanger pcr
Novel mutations in BBS5 highlight the importance of this gene in non-Caucasian Bardet-Biedl syndrome patients.

PMID 18203199 · PMC2578871 · American journal of medical genetics. Part A · 2008 · 6 claims · 8 setups

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Two novel homozygous missense mutations in BBS5 (p.Gly72Ser and p.Thr183Ala) were identified in non-Caucasian BBS patients (Somali and Sri Lankan)

genomic somali sri ethnically dhplc snp sanger
New mutations in the PKD1 gene in Czech population with autosomal dominant polycystic kidney disease.

PMID 19686598 · PMC2736583 · BMC medical genetics · 2009 · 8 claims · 7 setups

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DGGE screening of the non-duplicated PKD1 region detects likely pathogenic mutations in Czech ADPKD patients

genomic pcr polycystin-1 czech denaturing sanger family
Conservation and losses of non-coding RNAs in avian genomes.

PMID 25822729 · PMC4378963 · PloS one · 2015 · 8 claims · 6 setups

Has reproduction · 100

Homology-based covariance model (Rfam CM) annotation, combined with tRNAscan-SE and miRBase-derived models, identifies ncRNA loci across 48 avian genomes

avian bird chicken covariance trna microrna
How accurately is ncRNA aligned within whole-genome multiple alignments?

PMID 17963514 · PMC2206062 · BMC bioinformatics · 2007 · 7 claims · 4 setups

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MULTIZ does a fairly accurate job of aligning ncRNA regions across 17 vertebrate genomes, but better alignments exist in some regions.

genome vertebrate nonhuman genomic sequence whole-genome covariance
Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3'-end of genes.

PMID 18757892 · PMC2553571 · Nucleic acids research · 2008 · 8 claims · 6 setups

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3'-most (L type) poly(A) sites are more conserved than upstream F/M type sites, while intronic (C/H type) sites are the least conserved

consensus poly comparative transposable
BHD mutations, clinical and molecular genetic investigations of Birt-Hogg-Dubé syndrome: a new series of 50 families and a review of published reports.

PMID 18234728 · PMC2564862 · Journal of medical genetics · 2008 · 8 claims · 7 setups

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BHD germline mutation detection rate was 88% (51/58 families) using direct DNA sequencing

peripheral blood-derived folliculin chest direct subcloning sequence

Experiments

Insights into vertebrate evolution from the chicken genome sequence.

Genomic view of the evolution of the complement system.

A novel mutation in FRMD7 causing X-linked idiopathic congenital nystagmus in a large family.

Mutations in TRPV4 cause Charcot-Marie-Tooth disease type 2C.

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

Pseudofam: the pseudogene families database.

Genes at human chromosome 5q31.1 regulate delayed-type hypersensitivity responses associated with Leishmania chagasi infection.

Comparative genomic analysis of prion genes.

Genomic analysis of a heterogeneous Mendelian phenotype: multiple novel alleles for inherited hearing loss in the Palestinian population.

Novel mutations in BBS5 highlight the importance of this gene in non-Caucasian Bardet-Biedl syndrome patients.

New mutations in the PKD1 gene in Czech population with autosomal dominant polycystic kidney disease.

Conservation and losses of non-coding RNAs in avian genomes.

How accurately is ncRNA aligned within whole-genome multiple alignments?

Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3'-end of genes.

BHD mutations, clinical and molecular genetic investigations of Birt-Hogg-Dubé syndrome: a new series of 50 families and a review of published reports.