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1. Full Text Comparing allele specific expression and local expression quantitative trait loci and the influence of gene expression on complex trait variation in cattle
by Khansefid, Majid and Pryce, Jennie E and Bolormaa, Sunduimijid and Chen, Yizhou and Millen, Catriona A and Chamberlain, Amanda J and Vander Jagt, Christy J and Goddard, Michael E
BMC genomics, ISSN 1471-2164, 11/2018, Volume 19, Issue 1, pp. 793 - 793
RNA-sequencing | Allele specific expression | ASE analysis | Genome-wide association study | eQTL mapping | Genetic variation of complex traits | Genetics & Heredity | Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Science & Technology | Gene Expression | Genome-Wide Association Study | Reproducibility of Results | Quantitative Trait, Heritable | Chromosome Mapping | Multifactorial Inheritance | Genetic Variation | Animals | Sequence Analysis, RNA | Cattle | Alleles | Polymorphism, Single Nucleotide | Quantitative Trait Loci | Quantitative trait loci | Genetic aspects | Research | Gene expression | Genes | Genomics | Genomes | Single-nucleotide polymorphism | Tissues | Ribonucleic acid--RNA | Loci | Gene sequencing | Genetic variance | Mutation | Feeds | Gene mapping | Variation | Bioinformatics | Chromosomes | Polymorphism | Index Medicus
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2. Full Text AlleleSeq: analysis of allele‐specific expression and binding in a network framework
by Rozowsky, Joel and Abyzov, Alexej and Wang, Jing and Alves, Pedro and Raha, Debasish and Harmanci, Arif and Leng, Jing and Bjornson, Robert and Kong, Yong and Kitabayashi, Naoki and Bhardwaj, Nitin and Rubin, Mark and Snyder, Michael and Gerstein, Mark
Molecular systems biology, ISSN 1744-4292, 2011, Volume 7, Issue 1, pp. 522 - n/a
allele‐specific | networks | RNA‐Seq | ChIP‐Seq | ChIP-Seq | RNA-Seq | allele-specific | Life Sciences & Biomedicine | Biochemistry & Molecular Biology | Science & Technology | Cell Line | Chromosomes, Human, X - genetics | Oligonucleotide Array Sequence Analysis | Humans | Molecular Sequence Annotation | Gene Expression Regulation | Databases, Genetic | Chromosome Mapping | Transcription Factors - genetics | DNA-Binding Proteins - genetics | Gene Regulatory Networks | Chromosomes, Human, Y - genetics | DNA-Binding Proteins - metabolism | Transcription Factors - metabolism | Sequence Analysis, RNA | Alleles | Polymorphism, Single Nucleotide | Genome, Human | Binding | Construction | Transcription factors | Deactivation | Nucleotide sequence | Pipelines | X chromosomes | Data processing | Genomes | Single-nucleotide polymorphism | Ribonucleic acid--RNA | Inactivation | Gene expression | X-chromosome inactivation | Annotations | Computation | Correlation analysis | Data sets | Computer applications | Gene mapping | Index Medicus
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3. Full Text Genome-wide allele-specific expression analysis using Massively Parallel Signature Sequencing (MPSS™) Reveals cis- and trans-effects on gene expression in maize hybrid meristem tissue
by Guo, Mei and Yang, Sean and Rupe, Mary and Hu, Bin and Bickel, David R and Arthur, Lane and Smith, Oscar
Plant molecular biology, ISSN 0167-4412, 3/2008, Volume 66, Issue 5, pp. 551 - 563
Life Sciences | Plant Pathology | Biochemistry, general | MPSS | Cis - and trans -regulation | Plant Sciences | Allele-specific expression | Heterosis | Zea mays L | Cis- and trans-regulation | Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Science & Technology | Zea mays - genetics | Genome, Plant - genetics | Meristem - genetics | Plants, Genetically Modified | RNA, Messenger - genetics | Alleles | Gene Expression Regulation, Plant - genetics | Gene Expression Profiling | Software | Zea mays - growth & development | Genetic research | Corn | Gene expression | Multiprocessing | Analysis | Hybridization | Transgenic plants | Genomics | Index Medicus
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4. Full Text Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression
by Ghavi-Helm, Yad and Jankowski, Aleksander and Meiers, Sascha and Viales, Rebecca R and Korbel, Jan O and Furlong, Eileen E. M
Nature genetics, ISSN 1061-4036, 08/2019, Volume 51, Issue 8, pp. 1272 - 1282
Life Sciences & Biomedicine | Genetics & Heredity | Science & Technology | Promoter Regions, Genetic | Animals | Enhancer Elements, Genetic | Chromosomes, Insect - genetics | Gene Rearrangement | Gene Expression Regulation | Female | Male | Chromosome Mapping | Genome, Insect | Chromatin - genetics | Drosophila melanogaster - genetics | Chromatin | Usage | Analysis | Drosophila | Physiological aspects | Influence | Genetic aspects | Nucleotide sequencing | Gene expression | DNA sequencing | Breakpoints | Inversions | Genomes | Topology | Boundaries | Embryos | Gene sequencing | Domains | Insects | Fruit flies | Disruption | Chromosomes | Bioinformatics | Deoxyribonucleic acid--DNA | Index Medicus | Life Sciences | chromatin organization | embryogenesis | chromosomal rearrangements | enhancers | transcription | genome topology | allele-specific Hi-C | TADs | gene expression
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5. Full Text Comparison and contrast of genes and biological pathways responding to Marek's disease virus infection using allele-specific expression and differential expression in broiler and layer chickens
by Perumbakkam, Sudeep and Muir, William M and Black-Pyrkosz, Alexis and Okimoto, Ron and Cheng, Hans H
BMC genomics, ISSN 1471-2164, 01/2013, Volume 14, Issue 1, pp. 64 - 64
Biological pathways | RNA-Seq | Marek's disease | Genetic resistance | Allele-specific expression | Genetics & Heredity | Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Science & Technology | Herpesvirus 2, Gallid - physiology | Marek Disease - genetics | Species Specificity | Genomics | Chickens - virology | Gene Expression Profiling | Chickens - immunology | Meat | Marek Disease - immunology | Animals | Sequence Analysis, RNA | Alleles | Chickens - genetics | Oviposition | Polymorphism, Single Nucleotide | Chickens - physiology | Disease Resistance - genetics | RNA sequencing | Allelomorphism | Genes | Vaccines | Genetic transcription | Gene expression | Virus diseases | Infection | Genetic markers | Analysis | Chickens | Genetic research | Single nucleotide polymorphisms | Disease | Poultry | Classification | Birds | Genetics | Binomial distribution | Genomes | Index Medicus | Spleen | RNA | Transcription | Single-nucleotide polymorphism | Progeny | Signal transduction | Inbreeding | genomics | Age
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6. Full Text Discovering single nucleotide polymorphisms regulating human gene expression using allele specific expression from RNA-seq data
by Kang, Eun Yong and Martin, Lisa J and Mangul, Serghei and Isvilanonda, Warin and Zou, Jennifer and Ben-David, Eyal and Han, Buhm and Lusis, Aldons J and Shifman, Sagiv and Eskin, Eleazar
Genetics (Austin), ISSN 0016-6731, 11/2016, Volume 204, Issue 3, pp. 1057 - 1064
Expression quantitative trait loci | Causal variants | Allele specific expression | Life Sciences & Biomedicine | Genetics & Heredity | Science & Technology | Promoter Regions, Genetic | European Continental Ancestry Group - genetics | HapMap Project | Immune System Diseases - genetics | Europe | Humans | Transcriptome | Algorithms | Alleles | Cell Line, Tumor | Polymorphism, Single Nucleotide | Genome-Wide Association Study - methods | Quantitative Trait Loci | Allelomorphism | RNA sequencing | Usage | Research | Gene expression | Genetic variation | Studies | Haplotypes | Genomes | Bias | Quality | Index Medicus | expression quantitative trait loci | Investigations | causal variants
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7. Full Text Evidence for weak selective constraint on human gene expression
by Glassberg, Emily C and Gao, Ziyue and Harpak, Arbel and Lan, Xun and Lan, Xun and Pritchard, Jonathan K and Pritchard, Jonathan K
Genetics (Austin), ISSN 0016-6731, 02/2019, Volume 211, Issue 2, pp. 757 - 772
Heritability | Gene expression | Allele-specific expression | Stabilizing selection | Life Sciences & Biomedicine | Genetics & Heredity | Science & Technology | Gene Frequency | Humans | Alleles | Selection, Genetic | Transcriptome | Models, Genetic | Quantitative Trait Loci | DNA Copy Number Variations | Copy number | Genes | Gene regulation | Genomics | Phenotypic variations | Genomes | Genetic diversity | Consortia | Depletion | Gene frequency | Index Medicus | Investigations
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8. Full Text Impacts of Neanderthal-Introgressed Sequences on the Landscape of Human Gene Expression
by McCoy, Rajiv C and Wakefield, Jon and Akey, Joshua M
Cell (Cambridge), ISSN 0092-8674, 02/2017, Volume 168, Issue 5, pp. 916 - 927.e12
gene flow | archaic hominin | allele-specific expression | RNA-seq | gene regulation | evolution | introgression | Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Science & Technology | Cell Biology | Brain - metabolism | Gene Expression | Testis - metabolism | Animals | Humans | Gene Expression Regulation | Male | Neanderthals - genetics | Polymorphism, Single Nucleotide | Organ Specificity | Quantitative Trait Loci | Evolution, Molecular | RNA | Genes | Genomics | Genomes | Neanderthals | Gene expression | Natural selection | Anopheles | Index Medicus
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9. Full Text Deciphering the genetic regulation of peripheral blood transcriptome in pigs through expression genome-wide association study and allele-specific expression analysis
by Maroilley, T and Lemonnier, G and Lecardonnel, J and Esquerré, D and Ramayo-Caldas, Y and Mercat, M.J and Rogel-Gaillard, C and Estellé, J
BMC genomics, ISSN 1471-2164, 12/2017, Volume 18, Issue 1, pp. 967 - 967
EQTL | RNA-Seq | Transcriptome | EGWAS | Allele-Specific Expression | Blood | Pig | Genetics & Heredity | Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Science & Technology | RNA sequencing | Quantitative genetics | Genetic markers | RNA | Swine | Analysis | Genes | Genomics | Livestock | Genomes | Genetic transcription | Single nucleotide polymorphisms | Transcription | Gene regulation | Single-nucleotide polymorphism | Nucleotides | Disease resistance | Genotype & phenotype | Immunology | Sustainability | Peripheral blood | Physiology | Standard deviation | RNA processing | Chromosomes | Phenotypes | Immune response | Genetic control | Breeding | Chromosome 7 | Genetic diversity | Ribonucleic acid--RNA | Gene expression | Disease control | Biological activity | Quantitative trait loci | Hogs | DNA microarrays | Animals | Major histocompatibility complex | Alleles | Husbandry | Biomarkers | Gene mapping | Polymorphism | Index Medicus | Life Sciences | Animal genetics | Genetics | Computer Science | eQTL | eGWAS
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