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 27

System / cell line: parental ✕ Assay: gene ✕ Clear

Systematic identification of pseudogenes through whole genome expression evidence profiling.

PMID 16945953 · PMC1636364 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Developed a novel bioinformatics method that identifies pseudogenes by profiling whole-genome transcript and protein expression evidence

genome ensembl vega celera spliced protein-to-genome pseudogene
Allelic imbalance in gene expression as a guide to cis-acting regulatory single nucleotide polymorphisms in cancer cells.

PMID 17267408 · PMC1865061 · Nucleic acids research · 2007 · 6 claims · 6 setups

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Measuring allelic imbalance (AI) of two SNP alleles within the same sample is an effective approach for identifying cis-acting rSNPs, since each allele serves as an internal control for the other.

tumor promoter hela cdna bead tag-microarray
Expression analysis of secreted and cell surface genes of five transformed human cell lines and derivative xenograft tumors.

PMID 15836779 · PMC1112590 · BMC genomics · 2005 · 8 claims · 3 setups

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A custom 60-mer oligonucleotide microarray covering 3531 secreted and cell surface genes was designed to profile 5 transformed human cell lines and their derivative xenograft tumors.

carcinoma derivative xenograft custom quantitative
Application of proteomics in the study of tumor metastasis.

PMID 15862116 · PMC5172469 · Genomics, proteomics & bioinformatics · 2004 · 8 claims · 8 setups

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Cell function is directly regulated through proteins, not genes or mRNA, so metastasis-related gene findings need protein-level validation via proteomics.

young metastatic hepatocellular lines microarray 2de cdna
Population genomics of human gene expression.

PMID 17873874 · PMC2683249 · Nature genetics · 2007 · 8 claims · 8 setups

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Gene expression levels in lymphoblastoid cell lines are a heritable trait

ebv-transformed ceu lymphoblastoid unrelated genome-wide custom cis-eqtl
Use of functional genomics to understand influenza-host interactions.

PMID 17765704 · PMC7112328 · Advances in virus research · 2007 · 8 claims · 8 setups

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Functional genomics/microarray analysis provides a global view of host response to influenza infection that reveals virus-host interaction mechanisms not accessible by conventional techniques

hela a549 lung texas cdna microarray infection
Ancient variation of the AvrPm17 gene in powdery mildew limits the effectiveness of the introgressed rye Pm17 resistance gene in wheat.

PMID 35857869 · PMC9335242 · Proceedings of the National Academy of Sciences of the United States of America · 2022 · 6 claims · 8 setups

Has reproduction · 80

AvrPm17 is encoded by a paralogous, tandemly duplicated effector gene pair located in a pericentromeric, mildew sublineage-specific effector cluster (family E003) showing signs of recurring gene conversion.

b.g parental nicotiana benthamiana qtl comparative rna-sequencing
Genotype differences in cognitive functioning in Noonan syndrome.

PMID 19077116 · PMC2760992 · Genes, brain, and behavior · 2009 · 8 claims · 6 setups

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Genotype differences account for some of the variation in cognitive ability in Noonan syndrome

individuals participants parents standardized genetic pure-tone
Genetic variation of St. Louis encephalitis virus.

PMID 18632961 · PMC2696384 · The Journal of general virology · 2008 · 8 claims · 4 setups

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Phylogenetic analysis of 106 SLEV E gene sequences confirms seven major lineages (I-VII) and refines them into 13 clades (IA, IB, IIA, IIB, IIC, IID, IIG, III, IV, VA, VB, VI, VII)

slev rt-pcr phylogenetic recombination
A novel role for mitochondria in regulating epigenetic modification in the nucleus.

PMID 18458531 · PMC2639623 · Cancer biology & therapy · 2008 · 8 claims · 6 setups

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Mitochondria regulate epigenetic (DNA methylation) modification in the nucleus

mcf12a mda-mb-435 143b restriction western bisulfite
Transcriptomic and functional analyses of the piRNA pathway in the Chagas disease vector Rhodnius prolixus.

PMID 30303955 · PMC6179187 · PLoS neglected tropical diseases · 2018 · 7 claims · 6 setups

Has reproduction · 94

Rhodnius prolixus genome harbors four putative piwi orthologs (three piwi genes plus one ago3 ortholog), and core piRNA pathway components are expressed during previtellogenic oogenesis

rhodnius piwi paired-end parental rt-pcr
Chromosomal phenotypes and submicroscopic abnormalities.

PMID 15601540 · PMC3525070 · Human genomics · 2004 · 8 claims · 8 setups

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Microdeletion syndromes are flanked by region-specific low-copy repeats (LCRs), and non-allelic homologous recombination (NAHR) between these LCRs, via interchromosomal or intrachromosomal mechanisms, causes the deletions.

patients parents vegf164 zebrafish breakpoint parental inversion
CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas.

PMID 18577749 · PMC2483574 · Journal of the National Cancer Institute · 2008 · 7 claims · 8 setups

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CHD5 promoter is highly methylated in neuroblastoma cell lines with 1p deletion and absent CHD5 expression (NLF, IMR5)

neuroblastoma nlf athymic methylation-specific quantitative soft
A novel HRAS substitution (c.266C>G; p.S89C) resulting in decreased downstream signaling suggests a new dimension of RAS pathway dysregulation in human development.

PMID 22821884 · PMC4166655 · American journal of medical genetics. Part A · 2012 · 8 claims · 6 setups

Has reproduction · 88

A novel heterozygous HRAS c.266C>G (p.S89C) germline mutation was identified in two siblings with severe fetal hydrops/pleural effusion (Patient 1) and polyhydramnios/Dandy-Walker malformation (Patient 2).

cos-7 parental hras genomic ras immunoblotting egf
6th annual meeting of the Complex Trait Consortium.

PMID 17906895 · PMC2042027 · Mammalian genome : official journal of the International Mammalian Genome Society · 2007 · 8 claims · 7 setups

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The NIEHS Perlegen/resequencing project has generated over 8.5 million SNPs from 15 inbred mouse strains but shows a high false-negative discovery rate, with an estimated 45 million SNPs actually present.

inbred recombinant yeast gallstone genome affymetrix microarray
Understanding sex differences in environmental health: a thought leaders' roundtable.

PMID 15064168 · PMC1241928 · Environmental health perspectives · 2004 · 8 claims · 8 setups

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Dioxin and corticosteroids both cause thymic atrophy but via distinct mechanisms; dioxin's atrophy kinetics resemble those induced by estrogen despite acting through a different receptor.

laboratory mice nzb c57bl thymus radiation autoimmune
Association of autism with polymorphisms in the paired-like homeodomain transcription factor 1 (PITX1) on chromosome 5q31: a candidate gene analysis.

PMID 18053270 · PMC2222245 · BMC medical genetics · 2007 · 8 claims · 6 setups

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PITX1 polymorphisms and haplotypes are significantly associated with autism

agre pitx1 parental family-based extended haplotype
Addressing the obesity epidemic: a genomics perspective.

PMID 17362622 · PMC1893129 · Preventing chronic disease · 2007 · 8 claims · 8 setups

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Obesity is a multifactorial disorder reflecting complex interactions of genes, environment, and lifestyle

identical fraternal children younger twin family longitudinal
Prenatal molecular diagnosis of beta-thalassemia: report on the first two cases in Romania.

PMID 20108460 · PMC5654072 · Journal of medicine and life · 2008 · 7 claims · 5 setups

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Combined DGGE, ARMS-PCR and PCR-RFLP molecular testing accurately detects β-thalassemia mutations in fetal DNA obtained by amniocentesis or CVS

fetal β-globin parental str denaturing amplification
Critical Role for the Human Cytomegalovirus Major Immediate Early Proteins in Recruitment of RNA Polymerase II and H3K27Ac To an Enhancer-Like Element in OriLyt.

PMID 36645269 · PMC9927211 · Microbiology spectrum · 2023 · 8 claims · 8 setups

Has reproduction · 93

An enhancer-like element in OriLyt (RNA4.9 promoter) is extraordinarily enriched in H3K27Ac compared to other viral loci.

hff mrc5 chip-qpcr rt-qpcr chipseq

Experiments

Systematic identification of pseudogenes through whole genome expression evidence profiling.

Allelic imbalance in gene expression as a guide to cis-acting regulatory single nucleotide polymorphisms in cancer cells.

Expression analysis of secreted and cell surface genes of five transformed human cell lines and derivative xenograft tumors.

Application of proteomics in the study of tumor metastasis.

Population genomics of human gene expression.

Use of functional genomics to understand influenza-host interactions.

Ancient variation of the AvrPm17 gene in powdery mildew limits the effectiveness of the introgressed rye Pm17 resistance gene in wheat.

Genotype differences in cognitive functioning in Noonan syndrome.

Genetic variation of St. Louis encephalitis virus.

A novel role for mitochondria in regulating epigenetic modification in the nucleus.

Transcriptomic and functional analyses of the piRNA pathway in the Chagas disease vector Rhodnius prolixus.

Chromosomal phenotypes and submicroscopic abnormalities.

CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas.

A novel HRAS substitution (c.266C>G; p.S89C) resulting in decreased downstream signaling suggests a new dimension of RAS pathway dysregulation in human development.

6th annual meeting of the Complex Trait Consortium.

Understanding sex differences in environmental health: a thought leaders' roundtable.

Association of autism with polymorphisms in the paired-like homeodomain transcription factor 1 (PITX1) on chromosome 5q31: a candidate gene analysis.

Addressing the obesity epidemic: a genomics perspective.

Prenatal molecular diagnosis of beta-thalassemia: report on the first two cases in Romania.

Critical Role for the Human Cytomegalovirus Major Immediate Early Proteins in Recruitment of RNA Polymerase II and H3K27Ac To an Enhancer-Like Element in OriLyt.