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 81

System / cell line: allele ✕ Assay: in-silico ✕ Clear

Replication of association between schizophrenia and ZNF804A in the Irish Case-Control Study of Schizophrenia sample.

PMID 19844207 · PMC2797562 · Molecular psychiatry · 2010 · 8 claims · 7 setups

Full-text index only

rs1344706 in ZNF804A is associated with schizophrenia in the Irish ICCSS sample, replicating the original Cardiff finding

irish iccss postmortem genomic snp haplotype logistic
Implication of BRCA2 -26G>A 5' untranslated region polymorphism in susceptibility to sporadic breast cancer and its modulation by p53 codon 72 Arg>Pro polymorphism.

PMID 17945002 · PMC2242669 · Breast cancer research : BCR · 2007 · 8 claims · 7 setups

Full-text index only

-26G>A polymorphism in the BRCA2 5' UTR is functional: the A allele drives roughly twice the reporter gene expression of the G allele in MCF-7 and HeLa cells

mcf-7 hela brca2 peripheral luciferase transcription genotyping
Genes implicated in multiple sclerosis pathogenesis from consilience of genotyping and expression profiles in relapse and remission.

PMID 18366677 · PMC2324081 · BMC medical genetics · 2008 · 8 claims · 7 setups

Full-text index only

Distinct sets of dysregulated genes are found in peripheral blood during the relapse phase versus the remission phase of RRMS

peripheral blood pooled trio gene quantitative promoter
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

Full-text index only

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
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

Full-text index only

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
Resequencing PNMT in European hypertensive and normotensive individuals: no common susceptibilily variants for hypertension and purifying selection on intron 1.

PMID 17645789 · PMC1947951 · BMC medical genetics · 2007 · 7 claims · 7 setups

Full-text index only

Resequencing of PNMT found no common susceptibility variants that distinguish hypertensive from normotensive individuals

genomic pnmt promoter pcr population haplotype
In silico whole-genome screening for cancer-related single-nucleotide polymorphisms located in human mRNA untranslated regions.

PMID 17201911 · PMC1774567 · BMC genomics · 2007 · 8 claims · 5 setups

Full-text index only

A computational EST-based pipeline can identify UTR-SNPs that are statistically over-represented in cancerous versus normal tissue libraries

est acute 100-nt whole-genome est-based pcr-based secondary
BCoR-L1 variation and breast cancer.

PMID 17697391 · PMC2206730 · Breast cancer research : BCR · 2007 · 8 claims · 7 setups

Full-text index only

BCoR-L1 expression does not play a large role in predisposition to familial breast cancer

genomic aberrant lymphoblastoid mouse-human dhplc sanger qrt-pcr
A novel polymorphism in the 1A promoter region of the vitamin D receptor is associated with altered susceptibilty and prognosis in malignant melanoma.

PMID 15238985 · PMC2364794 · British journal of cancer · 2004 · 7 claims · 6 setups

Full-text index only

A novel A-1012G (adenine-guanine) polymorphism exists in the VDR exon 1a promoter region, identified by SSCP screening and sequencing

blood variant patients same sscp sanger pcr-rflp
Variants in the estrogen receptor alpha gene and its mRNA contribute to risk for schizophrenia.

PMID 18424448 · PMC2465798 · Human molecular genetics · 2008 · 8 claims · 8 setups

Full-text index only

Genotype CC (rs2234693/PvuII) and C-allele-containing haplotypes in ESR1 intron 1 are more frequent in African American schizophrenics than controls

genomic postmortem nimhgi esr1 targeted case-control family-based
Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

PMID 18710585 · PMC2533671 · BMC microbiology · 2008 · 7 claims · 6 setups

Full-text index only

A four-SNP set (glnA36, glnA429, glcK180, adhP111) identified via the Not-N algorithm plus empirical testing divides GBS into 10 groups concordant with eBURST-defined population structure.

gbs clinical bioinformatic eburst kinetic
Genome-wide survey of allele-specific splicing in humans.

PMID 18518984 · PMC2427040 · BMC genomics · 2008 · 8 claims · 5 setups

Full-text index only

A genome-wide computational scan identified 30,977 SNPs located within predicted splicing regulatory sequences (donor sites, acceptor sites, branch points, and ESEs)

genome cdna hapmap computational est exon
Protective effect of paraoxonase 1 gene variant Gln192Arg in age-related macular degeneration.

PMID 20042177 · PMC3026437 · American journal of ophthalmology · 2010 · 6 claims · 4 setups

Full-text index only

The Gln192Arg PON1 polymorphism is associated with decreased susceptibility to AMD, particularly wet AMD, indicating a protective effect

genomic pcr-amplified case-control pon1 single-strand direct genetic
Identification of functional SNPs in the 5-prime flanking sequences of human genes.

PMID 15717931 · PMC550646 · BMC genomics · 2005 · 6 claims · 5 setups

Full-text index only

7 of 10 candidate SNPs tested by EMSA showed reproducible allele-specific differences in TF-DNA complex binding/stability

flanking synthetic genomic cloned comparative electrophoretic rflp
Sequence variation and linkage disequilibrium in the GABA transporter-1 gene (SLC6A1) in five populations: implications for pharmacogenetic research.

PMID 17941974 · PMC2175509 · BMC genetics · 2007 · 8 claims · 7 setups

Full-text index only

SLC6A1 shows low levels of LD and an absence of major LD blocks across all five populations studied

african-american thai same study sanger snp genotyping
Molecular and clinical genetics of mitochondrial diseases due to POLG mutations.

PMID 18546365 · PMC2891192 · Human mutation · 2008 · 8 claims · 4 setups

Full-text index only

POLG mutations cause at least 6 major heterogeneous phenotypes of neurodegenerative mitochondrial disease (MCHS, Alpers syndrome, ANS, MEMSA, arPEO, adPEO)

blood parental model sanger parental microsatellite
Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.

PMID 25122667 · PMC4232532 · G3 (Bethesda, Md.) · 2014 · 8 claims · 8 setups

Has reproduction · 50

330,995 SNPs were identified in transcribed regions between B. rapa genotypes R500 and IMB211, at an average frequency of one SNP per 200 bases.

brassica r500 rapa genomic bulk reference-based snp
Identification of the imprinted KLF14 transcription factor undergoing human-specific accelerated evolution.

PMID 17480121 · PMC1865561 · PLoS genetics · 2007 · 7 claims · 8 setups

Full-text index only

KLF14 is a novel imprinted gene showing monoallelic maternal expression in embryonic and extra-embryonic tissues of both human and mouse

embryonic fetal monochromosomal fibroblasts allele-specific rt-pcr chromatin
Quality control method for RNA-seq using single nucleotide polymorphism allele frequency.

PMID 25243705 · PMC4231238 · Genes to cells : devoted to molecular & cellular mechanisms · 2014 · 8 claims · 8 setups

Has reproduction · 50

SNP allele frequency distributions from RNA-seq reads can detect contaminating cells whose genomic background differs from the target cells; the mode of the distribution reflects the cellular composition while its variance reflects PCR bias.

mathematical escs pure stap simulation rna-seq contamination
Common variants of the beta and gamma subunits of the epithelial sodium channel and their relation to plasma renin and aldosterone levels in essential hypertension.

PMID 15661075 · PMC547905 · BMC medical genetics · 2005 · 8 claims · 7 setups

Full-text index only

Heterozygous carriage of common βENaC/γENaC variants (G589S, i12-17CT, V546I) is significantly more prevalent in essential hypertension patients (9.2%) than in normotensive males (2.9%) or blood donors (3.0%)

hypertensive lymphocytes βenac xenopus targeted pcr-rflp plasma

Experiments

Replication of association between schizophrenia and ZNF804A in the Irish Case-Control Study of Schizophrenia sample.

Implication of BRCA2 -26G>A 5' untranslated region polymorphism in susceptibility to sporadic breast cancer and its modulation by p53 codon 72 Arg>Pro polymorphism.

Genes implicated in multiple sclerosis pathogenesis from consilience of genotyping and expression profiles in relapse and remission.

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

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

Resequencing PNMT in European hypertensive and normotensive individuals: no common susceptibilily variants for hypertension and purifying selection on intron 1.

In silico whole-genome screening for cancer-related single-nucleotide polymorphisms located in human mRNA untranslated regions.

BCoR-L1 variation and breast cancer.

A novel polymorphism in the 1A promoter region of the vitamin D receptor is associated with altered susceptibilty and prognosis in malignant melanoma.

Variants in the estrogen receptor alpha gene and its mRNA contribute to risk for schizophrenia.

Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

Genome-wide survey of allele-specific splicing in humans.

Protective effect of paraoxonase 1 gene variant Gln192Arg in age-related macular degeneration.

Identification of functional SNPs in the 5-prime flanking sequences of human genes.

Sequence variation and linkage disequilibrium in the GABA transporter-1 gene (SLC6A1) in five populations: implications for pharmacogenetic research.

Molecular and clinical genetics of mitochondrial diseases due to POLG mutations.

Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.

Identification of the imprinted KLF14 transcription factor undergoing human-specific accelerated evolution.

Quality control method for RNA-seq using single nucleotide polymorphism allele frequency.

Common variants of the beta and gamma subunits of the epithelial sodium channel and their relation to plasma renin and aldosterone levels in essential hypertension.