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 80

Assay: exon-intron ✕ Clear

A novel splice-site mutation of TULP1 underlies severe early-onset retinitis pigmentosa in a consanguineous Israeli Muslim Arab family.

PMID 18432314 · PMC2329669 · Molecular vision · 2008 · 6 claims · 5 setups

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A novel homozygous splice-site mutation, c.1495+2_1495+3insT, in the donor splice-site of TULP1 intron 14 underlies autosomal recessive early-onset RP in family TB13.

genomic tulp1 y79 haplotype direct mismatch-primer
A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence.

PMID 18344523 · PMC2377433 · Nucleic acids research · 2008 · 7 claims · 6 setups

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Spaln maps and aligns large cDNA sequence sets onto whole mammalian genomes using substantially less memory than comparable existing tools

unigene shuffled real genomes genome-wide alignment gene
Comparative genomic analysis and evolution of the T cell receptor loci in the opossum Monodelphis domestica.

PMID 18312668 · PMC2275272 · BMC genomics · 2008 · 8 claims · 5 setups

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The conventional TCR loci (TRA/D, TRB, TRG) in opossum are highly conserved in organization and complexity with those of eutherian mammals.

monodelphis 23-day-old trav trbv comparative rt-pcr phylogenetic
Mutation analysis of the AATF gene in breast cancer families.

PMID 20025740 · PMC2806411 · BMC cancer · 2009 · 6 claims · 6 setups

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No AATF sequence alteration identified was predicted to be pathogenic or showed significant association with breast cancer risk

genomic showing aatf case conformation direct pathogenicity
Searching for genes for cleft lip and/or palate based on breakpoint analysis of a balanced translocation t(9;17)(q32;q12).

PMID 19929093 · PMC2945731 · The Cleft palate-craniofacial journal : official publication of the American Cleft Palate-Craniofacial Association · 2009 · 8 claims · 4 setups

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The translocation breakpoints disrupt SLC31A1 (intron 1) on chromosome 9 and a predicted gene containing CCL2 (5'UTR/exons) on chromosome 17

family genomic case-control case fluorescence long-range mutation
A role of SCN9A in human epilepsies, as a cause of febrile seizures and as a potential modifier of Dravet syndrome.

PMID 19763161 · PMC2730533 · PLoS genetics · 2009 · 7 claims · 8 setups

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A heterozygous SCN9A missense mutation (p.N641Y) cosegregates with febrile seizures in the large K4425 family and is absent from ethnically matched population controls

family k4425 embryonic scn9a-n641y linkage copy deletion
Compound heterozygosity for a novel and a recurrent MFRP gene mutation in a family with the nanophthalmos-retinitis pigmentosa complex.

PMID 19753314 · PMC2742641 · Molecular vision · 2009 · 8 claims · 8 setups

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Compound heterozygosity for two distinct MFRP mutations (a novel nonsense mutation and a recurrent frameshift mutation) causes the nanophthalmos-retinitis pigmentosa-foveoschisis-optic disc drusen complex in this sibling pair

patients eyes genomic ophthalmological a-mode electroretinogram
Homozygous P86S mutation of the human glucagon receptor is associated with hyperglucagonemia, alpha cell hyperplasia, and islet cell tumor.

PMID 19657311 · PMC2767399 · Pancreas · 2009 · 8 claims · 6 setups

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A homozygous P86S mutation in GCGR is associated with hyperglucagonemia and α cell hyperplasia in the patient

patient's hek293 pancreatic sanger radioligand camp
Target SNP selection in complex disease association studies.

PMID 15248903 · PMC487897 · BMC bioinformatics · 2004 · 7 claims · 3 setups

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A computational pipeline can retrieve gene sequence, collect SNP variation data, and annotate SNPs falling in functional motifs (promoter, exon-intron structure, AU-rich elements, TF binding sites, splice sites) with expression in target tissue

genes pooled primer computational maldi-tof blast
FGF: a web tool for Fishing Gene Family in a whole genome database.

PMID 17584790 · PMC1933194 · Nucleic acids research · 2007 · 6 claims · 3 setups

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FGF efficiently searches and identifies gene families in whole-genome databases and outputs visual phylogenetic trees annotated with gene structure, chromosome position, duplication fate, and selective pressure (Ka/Ks)

genome rice gene large-scale
saseR: juggling offsets unlocks RNA-seq tools for fast and scalable differential usage, aberrant splicing and expression retrieval.

PMID 41709279 · PMC13019952 · Genome biology · 2026 · 8 claims · 5 setups

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Replacing the library-size offset with the log of the total gene count in NB-based bulk RNA-seq models (edgeR/DESeq2) lets the mean-model parameters be interpreted as transcript/exon usage, unlocking these tools for differential usage and aberrant splicing without DEXSeq-style subject-specific blocking covariates.

simulated bulk cohort aberrant differential exon
Genomic approaches to the genetics of alcoholism.

PMID 12875046 · PMC6683845 · Alcohol research & health : the journal of the National Institute on Alcohol Abuse and Alcoholism · 2002 · 8 claims · 4 setups

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Alcoholism is a complex disease that develops from a combination of numerous genetic and environmental factors, unlike single-gene disorders such as cystic fibrosis or Huntington's disease.

specified genomic gene genomic exon
Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella).

PMID 26248502 · PMC4528194 · Scientific reports · 2015 · 8 claims · 8 setups

Has reproduction · 70

AS events, including differentially-expressed-transcript-containing genes (DETs), are ubiquitous in head-kidney and spleen transcriptomes of C. idella

head-kidney idella assembled il-12p40α rna-seq rt-qpcr pcr
Systematic analysis of CNGCs in cotton and the positive role of GhCNGC32 and GhCNGC35 in salt tolerance.

PMID 35931984 · PMC9356423 · BMC genomics · 2022 · 8 claims · 8 setups

Has reproduction

114 CNGC genes were identified across the genomes of four cotton species (G. arboreum, G. raimondii, G. barbadense, G. hirsutum)

arboreum cotton hirsutum ghcngc genome-wide phylogenetic gene
The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.

PMID 38245722 · PMC10800049 · BMC genomics · 2024 · 8 claims · 8 setups

Has reproduction · 100

44 venom peptide genes were identified, distributed across four of the eleven chromosomes and organized in tandem repeat clusters.

tetramorium bicarinatum vpg venom whole-genome blast gene
Identification of the Wheat (Triticum aestivum) IQD Gene Family and an Expression Analysis of Candidate Genes Associated with Seed Dormancy and Germination.

PMID 35456910 · PMC9025732 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

Has reproduction · 78

73 IQD gene family members were identified in the wheat genome and classified into six phylogenetic groups

triticum taiqd wheat rice genome-wide phylogenetic gene
Identification of a novel spliced variant of the SYT gene expressed in normal tissues and in synovial sarcoma.

PMID 11308259 · PMC2363857 · British journal of cancer · 2001 · 8 claims · 8 setups

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Two forms of SYT mRNA, N-SYT and a novel form I-SYT, are co-expressed in normal human tissues and in synovial sarcomas

synovial ss-derived normal liver rt-pcr cloning densitometric
Molecular genetics and structural genomics of the human protein kinase C gene module.

PMID 11897026 · PMC88812 · Genome biology · 2002 · 8 claims · 4 setups

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The nine human PKC genes are dispersed throughout the genome, with five isotypes (α, β, δ, ζ, ι) previously incorrectly assigned to chromosomes in the literature.

metaphase genome pkc genomic fluorescence bioinformatic snp
Analyses of apoptotic regulators CASP9 and DFFA at 1P36.2, reveal rare allele variants in human neuroblastoma tumours.

PMID 11870543 · PMC2375272 · British journal of cancer · 2002 · 8 claims · 5 setups

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DFFA is localized within the 1p36.2-3 smallest region of overlap (SRO) of deletions defined in Scandinavian neuroblastoma tumours, distal to marker D1S244

scandinavian chromosome unfinished neuroblastoma pcr bac-library in-silico
Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.

PMID 12908878 · PMC194569 · BMC genomics · 2003 · 8 claims · 7 setups

Full-text index only

XRRA1 is a novel gene down-regulated ~2-fold in XR-resistant HCT116 Clone2_XRR relative to HCT116 Clone10, identified via cDNA microarray

hct116 macaque cos-7 genomic cdna est molecular

Experiments

A novel splice-site mutation of TULP1 underlies severe early-onset retinitis pigmentosa in a consanguineous Israeli Muslim Arab family.

A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence.

Comparative genomic analysis and evolution of the T cell receptor loci in the opossum Monodelphis domestica.

Mutation analysis of the AATF gene in breast cancer families.

Searching for genes for cleft lip and/or palate based on breakpoint analysis of a balanced translocation t(9;17)(q32;q12).

A role of SCN9A in human epilepsies, as a cause of febrile seizures and as a potential modifier of Dravet syndrome.

Compound heterozygosity for a novel and a recurrent MFRP gene mutation in a family with the nanophthalmos-retinitis pigmentosa complex.

Homozygous P86S mutation of the human glucagon receptor is associated with hyperglucagonemia, alpha cell hyperplasia, and islet cell tumor.

Target SNP selection in complex disease association studies.

FGF: a web tool for Fishing Gene Family in a whole genome database.

saseR: juggling offsets unlocks RNA-seq tools for fast and scalable differential usage, aberrant splicing and expression retrieval.

Genomic approaches to the genetics of alcoholism.

Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella).

Systematic analysis of CNGCs in cotton and the positive role of GhCNGC32 and GhCNGC35 in salt tolerance.

The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.

Identification of the Wheat (Triticum aestivum) IQD Gene Family and an Expression Analysis of Candidate Genes Associated with Seed Dormancy and Germination.

Identification of a novel spliced variant of the SYT gene expressed in normal tissues and in synovial sarcoma.

Molecular genetics and structural genomics of the human protein kinase C gene module.

Analyses of apoptotic regulators CASP9 and DFFA at 1P36.2, reveal rare allele variants in human neuroblastoma tumours.

Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.