2024
Detecting Boolean Asymmetric Relationships with a Loop Counting Technique and its Implications for Analyzing Heterogeneity within Gene Expression Datasets
Zhou H, Lin W, Labra S, Lipton S, Elman J, Schork N, Rangan A. Detecting Boolean Asymmetric Relationships with a Loop Counting Technique and its Implications for Analyzing Heterogeneity within Gene Expression Datasets. IEEE/ACM Transactions On Computational Biology And Bioinformatics 2024, PP: 1-12. PMID: 39471117, DOI: 10.1109/tcbb.2024.3487434.Peer-Reviewed Original ResearchSubsets of genesGene-gene relationshipsGene expression dataGene-gene interactionsGene expression datasetsRNA-sequencing data setsDetected biclustersExpression datasetsGene pathwaysSubsets of cellsGenesRegulatory effectsBiclusteringCorrelated expressionAsymmetric interactionsSymmetric interactionsInteractionExpressionCells
2000
How Are Neuronal Genes Expressed in Neurons? Regulation of NMDA Receptor Subunit Type 1 Gene as a Model
Okamoto S, Sherman K, Lipton S. How Are Neuronal Genes Expressed in Neurons? Regulation of NMDA Receptor Subunit Type 1 Gene as a Model. 2000, 355-360. DOI: 10.1007/978-4-431-66973-9_47.Peer-Reviewed Original ResearchType 1 geneRegulation of expressionGene regulationNeuronal genesEssential subunitDifferentiation proceedsTranscriptional levelFunctional NMDA receptorsNeuronal differentiationGenesVariety of moleculesNR1 geneNeuronal functionRegulationCentral nervous systemNR1ExpressionSynaptic responsesNMDA receptorsNeuronal activityNervous systemSubunitsNeuronsDifferentiationBest model
1999
Absence of binding activity of neuron-restrictive silencer factor is necessary, but not sufficient for transcription of NMDA receptor subunit type 1 in neuronal cells
Okamoto S, Sherman K, Lipton S. Absence of binding activity of neuron-restrictive silencer factor is necessary, but not sufficient for transcription of NMDA receptor subunit type 1 in neuronal cells. Brain Research 1999, 74: 44-54. PMID: 10640675, DOI: 10.1016/s0169-328x(99)00250-8.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceCell DifferentiationDown-RegulationGene Expression RegulationHeLa CellsHumansLuciferasesMutationNeuronsPromoter Regions, GeneticProtein BindingReceptors, N-Methyl-D-AspartateRecombinant Fusion ProteinsRepressor ProteinsResponse ElementsRNA, MessengerSequence Homology, Nucleic AcidTranscription FactorsTranscription, GeneticTumor Cells, CulturedConceptsNRSF/RESTNeuron-restrictive silencer factorPromoter activityNR1 geneSilencer factorCell linesNRSE/RE1Set of genesNeuronal cellsType I geneNonneuronal cell linesREST proteinNeuronal cell lineI geneP19 cellsConsensus sequenceNeuronal differentiationGenesHeLa cellsTranscriptionNonneuronal cellsIndependent mannerNeuronal specificityMRNA levelsExpression
1993
hMEF2C gene encodes skeletal muscle- and brain-specific transcription factors.
McDermott J, Cardoso M, Yu Y, Andres V, Leifer D, Krainc D, Lipton S, Nadal-Ginard B. hMEF2C gene encodes skeletal muscle- and brain-specific transcription factors. Molecular And Cellular Biology 1993, 13: 2564-2577. PMID: 8455629, PMCID: PMC359588, DOI: 10.1128/mcb.13.4.2564.Peer-Reviewed Original ResearchMeSH KeywordsAlternative SplicingAmino Acid SequenceAnimalsBase SequenceBrainCells, CulturedCloning, MolecularConsensus SequenceDNA-Binding ProteinsGene ExpressionGenesHumansImmunologic TechniquesIn Vitro TechniquesMEF2 Transcription FactorsMiceMolecular Sequence DataMusclesMyogenic Regulatory FactorsNeuronsOligodeoxyribonucleotidesPolymerase Chain ReactionRNA, MessengerSequence AlignmentTissue DistributionTranscription FactorsTranscription, GeneticConceptsSkeletal muscleSubset of neuronsCortical neuronsBrain-specific transcription factorTranscription factorsMRNA levelsPotential targetTrans-activating activityMuscleMEF2 transcription factorsNeuronsBrainBrain transcriptsMEF2 factorsMuscle-specific enhancerExpressionMyogenic differentiationTissue-specific isoformsUbiquitous expressionFactorsTissue-specific patternsGenesNeurogenesishMEF2C Gene Encodes Skeletal Muscle- and Brain-Specific Transcription Factors
McDermott J, Cardoso M, Yu Y, Andres V, Leifer D, Krainc D, Lipton S, Nadal-Ginard B. hMEF2C Gene Encodes Skeletal Muscle- and Brain-Specific Transcription Factors. Molecular And Cellular Biology 1993, 13: 2564-2577. DOI: 10.1128/mcb.13.4.2564-2577.1993.Peer-Reviewed Original ResearchSkeletal muscleSubset of neuronsCortical neuronsBrain-specific transcription factorTranscription factorsMRNA levelsPotential targetTrans-activating activityMuscleMEF2 transcription factorsNeuronsBrainBrain transcriptsMEF2 factorsMuscle-specific enhancerExpressionMyogenic differentiationTissue-specific isoformsUbiquitous expressionFactorsTissue-specific patternsGenesNeurogenesishMEF2C Gene Encodes Skeletal Muscle- and Brain-Specific Transcription Factors
McDermott J, Cardoso M, Yu Y, Andres V, Leifer D, Krainc D, Lipton S, Nadal-Ginard B. hMEF2C Gene Encodes Skeletal Muscle- and Brain-Specific Transcription Factors. Molecular And Cellular Biology 1993, 13: 2564-2577. DOI: 10.1128/mcb.13.4.2564-2577.1993.Peer-Reviewed Original ResearchMyocyte enhancer-binding factor 2Transcription factorsCharacterization of cDNA clonesBind nuclear proteinsTissue-specific patternsTissue-specific isoformsTrans-activation activityBrain-specific transcription factorMode of regulationMEF2 transcription factorsMuscle-specific enhancerCDNA clonesAlternative exonsNuclear proteinsDNA bindingPosttranscriptional processesFunctional characterizationBrain transcriptsGenesSkeletal muscle-TranscriptionMyogenic differentiationCortical neuronsPotential targetMRNA levels