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 20

System / cell line: corresponding ✕ Assay: comparison ✕ Clear

Codon usage comparison of novel genes in clinical isolates of Haemophilus influenzae.

PMID 15983137 · PMC1160521 · Nucleic acids research · 2005 · 8 claims · 4 setups

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A codon usage similarity statistic (ε, based on squared/absolute differences of codon frequencies with an optimized amino acid usage factor) was developed to compare ORFs against a set of 80 reference genomes.

influenzae novel reference codon phylogenetic comparative
Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

PMID 16536879 · PMC1479377 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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ENACE, a cross-species EST-to-genome comparison algorithm, can identify novel cassette-on exons and retained introns for EST-scanty species and distinguish conserved vs lineage-specific exons

presumably orthologous enace genes cross-species rt-pcr-sequencing nonsynonymous-to-synonymous
APC promoter methylation and protein expression in hepatocellular carcinoma.

PMID 17973119 · PMC2757596 · Journal of cancer research and clinical oncology · 2008 · 6 claims · 7 setups

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APC promoter methylation is significantly higher in HCC compared to non-cancerous liver tissue

hcc liver cholangiocellular benign methylight truncation western
DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues.

PMID 38600112 · PMC11006913 · Nature communications · 2024 · 8 claims · 5 setups

Has reproduction · 93

Many of the 92 assayed HD missense variants alter DNA binding affinity and/or specificity compared to their corresponding reference alleles

homeodomain hoxd13 cerevisiae amino universal chip-seq electrophoretic
Heterotachy in mammalian promoter evolution.

PMID 16683025 · PMC1449885 · PLoS genetics · 2006 · 8 claims · 5 setups

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The rate of promoter evolution relative to control sequences is not consistent between or within mammalian lineages over time (heterotachy)

promoter ancient chimpanzee comparative ancient micro-indel
Somatic mutations in RET exons 12 and 15 in sporadic medullary thyroid carcinomas: different spectrum of mutations in sporadic type from hereditary type.

PMID 10622534 · PMC5926019 · Japanese journal of cancer research : Gann · 1999 · 8 claims · 3 setups

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Novel somatic point mutations and an in-frame deletion were identified in RET exons 12 and 15 in sporadic MTC

formalin-fixed corresponding sporadic pcr clinical
Identification and analysis of co-occurrence networks with NetCutter.

PMID 18781200 · PMC2526157 · PloS one · 2008 · 8 claims · 4 setups

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Random sampling from a complete permutation set of the bipartite graph permits co-occurrence analysis with optimal stringency, and the edge-swapping (ES) model closely approximates this and is the preferred null-model among six tested.

publime bipartite randomized co-occurrence null-model signal-to-noise
Mutation and deletion analysis of GFR alpha-1, encoding the co-receptor for the GDNF/RET complex, in human brain tumours.

PMID 10408842 · PMC2362327 · British journal of cancer · 1999 · 8 claims · 3 setups

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No mutations were found in the coding region of GDNF in any of the 36 brain tumours analysed

sporadic tumour tumour-derived pcr loss semi-quantitative
Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

PMID 17452356 · PMC1904267 · Nucleic acids research · 2007 · 8 claims · 7 setups

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PASE (Prediction of Alternative Signaling Exons) is a computational algorithm combining Markov splice-site models, a Bayesian classifier, species conservation, and Scansite motif scoring to identify novel alternative cassette exons involved in cell signaling.

elegans pooled pcr known semi-nested cloning initio
High fidelity of whole-genome amplified DNA on high-density single nucleotide polymorphism arrays.

PMID 18786630 · PMC2659594 · Genomics · 2008 · 8 claims · 7 setups

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WGA product performs well on the Affymetrix 250K SNP array compared to genomic DNA, especially with the BRLMM calling algorithm.

genomic whole-genome same call snp technical genotype
Screening for microsatellite instability identifies frequent 3'-untranslated region mutation of the RB1-inducible coiled-coil 1 gene in colon tumors.

PMID 19888451 · PMC2766054 · PloS one · 2009 · 7 claims · 4 setups

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Somatic mutation frequency (%MSI) of 3'UTR microsatellites in MSI-H colorectal tumors correlates significantly with microsatellite length (r=0.86, p=7.2×10−13), following an exponential growth model.

msi-h computational rb1cc1 normal pcr nonlinear real-time
Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.

PMID 24715956 · PMC3962008 · F1000Research · 2013 · 8 claims · 6 setups

Has reproduction · 67

Cyrface is a Cytoscape app/Java library providing a general interface from Cytoscape (Java) to any R function or package.

cytoscape generated prior-knowledge iris software datarail logic
Mutations in the C-terminus of the X protein of hepatitis B virus regulate Wnt-5a expression in hepatoma Huh7 cells: cDNA microarray and proteomic analyses.

PMID 18477650 · PMC2443277 · Carcinogenesis · 2008 · 8 claims · 7 setups

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HBx C-terminal deletion mutants (HBx3'-30 and HBx3'-40) produce differentially expressed gene and protein profiles in transfected Huh7 HCC cells, mostly involving transcriptional regulation, oncogenes/tumor suppressors, cell junctions, signal transduction, metabolism and immune response

huh7 frozen hcc genomic cdna two-dimensional western
Evaluating native-like structures of RNA-protein complexes through the deep learning method.

PMID 36828844 · PMC9958188 · Nature communications · 2023 · 8 claims · 7 setups

Has reproduction · 67

DRPScore identifies native-like RNA-protein structures with higher success rates than ITScore-PR, DARS-RNP, and 3dRPC across bound and unbound testing sets.

bound-bound unbound-bound unbound-unbound bacillus structure interface secondary
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
Establishment and characterisation of six human biliary tract cancer cell lines.

PMID 12107841 · PMC2376107 · British journal of cancer · 2002 · 8 claims · 8 setups

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Six new human biliary tract cancer cell lines (SNU-245, SNU-308, SNU-478, SNU-869, SNU-1079, SNU-1196) were established and characterised from Korean patients

biliary snu lines microdissected culture fingerprinting pcr-sscp
Quasimonomorphic mononucleotide repeats for high-level microsatellite instability analysis.

PMID 15528790 · PMC3888729 · Disease markers · 2004 · 8 claims · 8 setups

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Mononucleotide repeats are more sensitive, specific, and easier to use than dinucleotide repeats for detecting MSI-H tumors

msi-h colon hmsh6-mutated tumors pentaplex pcr dinucleotide
A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

PMID 19923232 · PMC2817484 · Nucleic acids research · 2010 · 8 claims · 7 setups

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A Perl-based pipeline that BLASTs/BLATs Illumina probe sequences against genomes and transcript databases (RefSeq, UCSC Known Genes, UniGene/GenBank, Ensembl) can classify probes by quality grade (Perfect/Good/Bad/No match) and is applicable across 8 BeadArray platforms and other array types

maqc hepatocytes japanese illeum microarray dasl sequence
High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling.

PMID 16893952 · PMC1540726 · Nucleic acids research · 2006 · 7 claims · 6 setups

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Ecotilling can be adapted to accurately discover and genotype human SNPs, with error rates low relative to resequencing

genomic ecotilling non-synonymous ecotilling sanger universal-primer
Microsatellite instability analysis in hereditary non-polyposis colon cancer using the Bethesda consensus panel of microsatellite markers in the absence of proband normal tissue.

PMID 16426447 · PMC1373649 · BMC medical genetics · 2006 · 7 claims · 4 setups

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MSI status can be determined in the absence of proband non-tumor tissue by comparing tumor alleles to alleles carried by the proband's progenitors

proband's peripheral hmsh2 microsatellite direct targeted

Experiments

Codon usage comparison of novel genes in clinical isolates of Haemophilus influenzae.

Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

APC promoter methylation and protein expression in hepatocellular carcinoma.

DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues.

Heterotachy in mammalian promoter evolution.

Somatic mutations in RET exons 12 and 15 in sporadic medullary thyroid carcinomas: different spectrum of mutations in sporadic type from hereditary type.

Identification and analysis of co-occurrence networks with NetCutter.

Mutation and deletion analysis of GFR alpha-1, encoding the co-receptor for the GDNF/RET complex, in human brain tumours.

Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

High fidelity of whole-genome amplified DNA on high-density single nucleotide polymorphism arrays.

Screening for microsatellite instability identifies frequent 3'-untranslated region mutation of the RB1-inducible coiled-coil 1 gene in colon tumors.

Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.

Mutations in the C-terminus of the X protein of hepatitis B virus regulate Wnt-5a expression in hepatoma Huh7 cells: cDNA microarray and proteomic analyses.

Evaluating native-like structures of RNA-protein complexes through the deep learning method.

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

Establishment and characterisation of six human biliary tract cancer cell lines.

Quasimonomorphic mononucleotide repeats for high-level microsatellite instability analysis.

A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling.

Microsatellite instability analysis in hereditary non-polyposis colon cancer using the Bethesda consensus panel of microsatellite markers in the absence of proband normal tissue.