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 26

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

Identification of HNPCC by molecular analysis of colorectal and endometrial tumors.

PMID 15528786 · PMC3839268 · Disease markers · 2004 · 8 claims · 5 setups

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The Bethesda criteria, with a few modifications, are appropriate to identify families eligible for MMR mutation genetic testing

colorectal endometrial microsatellite immunohistochemistry germline
Comprehensive analysis of peroxisome proliferator-activated receptors to predict the drug resistance, immune microenvironment, and prognosis in stomach adenocarcinomas.

PMID 38529307 · PMC10962337 · PeerJ · 2024 · 8 claims · 8 setups

Has reproduction · 58

PPARA, PPARD and PPARG are more abnormally expressed in STAD samples and cell lines compared to most of 32 cancer types in TCGA

cancer tcga-stad stomach ges1 rna-seq pearson gsva
Association between telomere length and V(H) gene mutation status in chronic lymphocytic leukaemia: clinical and biological implications.

PMID 12592375 · PMC2377180 · British journal of cancer · 2003 · 7 claims · 5 setups

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Unmutated VH gene CLL cases have significantly shorter telomeres than mutated VH gene CLL cases

cll subset pcr southern real-time
Does tumorigenesis select for or against mutations of the DNA repair-associated genes BRCA2 and MRE11?: considerations from somatic mutations in microsatellite unstable (MSI) gastrointestinal cancers.

PMID 16417627 · PMC1382246 · BMC genetics · 2006 · 8 claims · 7 setups

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Heterozygous truncating BRCA2 mutations occur in 47% (7/15) of gastrointestinal MSI cancer cell lines/xenografts, a higher rate than previously reported

gastrointestinal ls174t pl3 msi gene rt-pcr rad51
An integrated genomic analysis of human glioblastoma multiforme.

PMID 18772396 · PMC2820389 · Science (New York, N.Y.) · 2008 · 8 claims · 7 setups

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IDH1 is recurrently mutated at its active site (R132) in 12% of GBM patients, a previously unrecognized alteration in GBM.

gbm additional missense exome targeted snp
With the finished human genome in hand, what next?

PMID 12844356 · PMC193627 · Genome biology · 2003 · 8 claims · 8 setups

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Gene Ontology (GO) provides a syntax/query framework for functional classification of genes, expanding beyond E. coli origins into anatomy, pathology, and phenotype data.

domestic saccharomyces systemic schistosoma comparative functional genetic
Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals.

PMID 15882449 · PMC1134656 · BMC genomics · 2005 · 8 claims · 4 setups

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A predictive computational screen covering ~40% of annotated protein-coding genes identified 21 co-expressed gene clusters with statistically supported sharing of cis-regulatory motifs.

upstream co-expression pre-b microarray-based motif gene
Somatic mutations in mitochondria: the chicken or the egg?

PMID 16207343 · PMC1257449 · Arthritis research & therapy · 2005 · 6 claims · 6 setups

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Patients with RA have a higher incidence of somatic mtDNA mutations (in MT-ND1 transcripts) in synoviocytes and synovial tissue compared with OA patients

mutated synovial sequencing mhc expression
Description of a PCR-based technique for DNA splicing and mutagenesis by producing 5' overhangs with run through stop DNA synthesis utilizing Ara-C.

PMID 16137330 · PMC1208860 · BMC biotechnology · 2005 · 7 claims · 7 setups

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Two adjacent Ara-C molecules incorporated into a PCR primer produce mild template-dependent polymerization termination, generating 5' overhangs usable for cohesive-end ligation.

plasmid pcr gel-isolated ligated pcr gel ligation
Expression of RAB4B, a protein governing endocytic recycling, is co-regulated with MHC class II genes.

PMID 17175541 · PMC1802633 · Nucleic acids research · 2007 · 7 claims · 7 setups

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A typical MHC-II-like S-Y module is present upstream of the RAB4B transcription start site, identified by genome-wide profile scanning

genomic raji monocyte-derived rj2.2.5 computational chip-on-chip chromatin
Eight previously unidentified mutations found in the OA1 ocular albinism gene.

PMID 16646960 · PMC1468396 · BMC medical genetics · 2006 · 7 claims · 5 setups

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Sequencing of the nine OA1 exons in 72 individuals identified ten different mutations across seven unrelated families and three sporadic cases.

genomic oa1 direct long-range splice-site
Patterns of somatic mutation in human cancer genomes.

PMID 17344846 · PMC2712719 · Nature · 2007 · 8 claims · 5 setups

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Systematic resequencing of a large gene family (protein kinases) across diverse cancers reveals a larger repertoire of cancer genes than previously anticipated

cancers additional computational combined targeted follow-up statistical
Comprehensive genomic characterization defines human glioblastoma genes and core pathways.

PMID 18772890 · PMC2671642 · Nature · 2008 · 8 claims · 5 setups

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NF1 is a genuine human glioblastoma suppressor gene, inactivated by mutation, deletion, or expression loss in at least 23% of GBM samples

glioblastoma gbm matched sequenced copy gene methylation
Design and analysis issues in genome-wide somatic mutation studies of cancer.

PMID 18692126 · PMC2820387 · Genomics · 2009 · 6 claims · 4 setups

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Two-stage (discovery + validation) sequencing designs efficiently allocate resources and can produce highly informative candidate driver gene lists even with relatively small sample sizes.

hypothetical panel colorectal germline simulation targeted genome-wide
Mechanisms of relapse in acute leukaemia: involvement of p53 mutated subclones in disease progression in acute lymphoblastic leukaemia.

PMID 10098750 · PMC2362216 · British journal of cancer · 1999 · 6 claims · 4 setups

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p53 mutations are detected at relapse far more frequently in ALL (28.6%) than in AML (7.3%)

bone presentation b-cells direct allele-specific igh
Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.

PMID 19756158 · PMC2742196 · PLoS computational biology · 2009 · 8 claims · 4 setups

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MIP active learning is a novel active learning method that preferentially seeks informative Positive (functionally active) examples rather than only maximizing classifier accuracy.

engineered p53 computational yeast-based regional homology
Genome wide identification of recessive cancer genes by combinatorial mutation analysis.

PMID 18846217 · PMC2557123 · PloS one · 2008 · 7 claims · 4 setups

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A combinatorial mutation analysis identified 154 candidate recessive cancer genes (pRecessiveCancer<1.5x10-7, FDR=0.39)

refseq tp53 tumor 154-gene est paired array
Preponderance of the oncogenic V599E and V599K mutations in B-raf kinase domain is enhanced in melanoma cutaneous/subcutaneous metastases.

PMID 15935100 · PMC1164406 · BMC cancer · 2005 · 8 claims · 4 setups

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B-raf exon 15 somatic mutations occur in 24/60 (40%) of cutaneous/subcutaneous melanoma metastases, similar to the frequency in primary melanomas

paraffin-embedded cloned same predicted pcr cloning blastx
A high throughput method for genome-wide analysis of retroviral integration.

PMID 17028098 · PMC1636494 · Nucleic acids research · 2006 · 8 claims · 8 setups

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VITA uses MmeI to cleave DNA at a fixed distance from its recognition site, generating 21-22 bp genomic tags that serve as signatures of lentiviral integration sites.

hela ht3 genome chromosomes isf vita sanger
Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

PMID 17576681 · PMC1934990 · Nucleic acids research · 2007 · 8 claims · 4 setups

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Cryptic 5'ss are best predicted by computational algorithms that accommodate nucleotide dependencies (e.g., Markov model, maximum entropy, maximum dependence decomposition) rather than by weight-matrix models

disease mammalian compiled literature minigene computational

Experiments

Identification of HNPCC by molecular analysis of colorectal and endometrial tumors.

Comprehensive analysis of peroxisome proliferator-activated receptors to predict the drug resistance, immune microenvironment, and prognosis in stomach adenocarcinomas.

Association between telomere length and V(H) gene mutation status in chronic lymphocytic leukaemia: clinical and biological implications.

Does tumorigenesis select for or against mutations of the DNA repair-associated genes BRCA2 and MRE11?: considerations from somatic mutations in microsatellite unstable (MSI) gastrointestinal cancers.

An integrated genomic analysis of human glioblastoma multiforme.

With the finished human genome in hand, what next?

Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals.

Somatic mutations in mitochondria: the chicken or the egg?

Description of a PCR-based technique for DNA splicing and mutagenesis by producing 5' overhangs with run through stop DNA synthesis utilizing Ara-C.

Expression of RAB4B, a protein governing endocytic recycling, is co-regulated with MHC class II genes.

Eight previously unidentified mutations found in the OA1 ocular albinism gene.

Patterns of somatic mutation in human cancer genomes.

Comprehensive genomic characterization defines human glioblastoma genes and core pathways.

Design and analysis issues in genome-wide somatic mutation studies of cancer.

Mechanisms of relapse in acute leukaemia: involvement of p53 mutated subclones in disease progression in acute lymphoblastic leukaemia.

Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.

Genome wide identification of recessive cancer genes by combinatorial mutation analysis.

Preponderance of the oncogenic V599E and V599K mutations in B-raf kinase domain is enhanced in melanoma cutaneous/subcutaneous metastases.

A high throughput method for genome-wide analysis of retroviral integration.

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.