scholarly journals Tissue Specificity and Sex-Specific Regulatory Variation Permit the Evolution of Sex-Biased Gene Expression

2016 ◽  
Vol 188 (3) ◽  
pp. E74-E84 ◽  
Author(s):  
Rebecca Dean ◽  
Judith E. Mank
Keyword(s):  
Gene Expression ◽  
Tissue Specificity ◽  
Evolution Of Sex ◽  
Regulatory Variation

scholarly journals Analyzing cancer gene expression data through the lens of normal tissue-specificity

2021 ◽  
Author(s):  
H. Robert Frost
Keyword(s):  
Gene Expression ◽  
Normal Tissue ◽  
Tissue Specificity ◽  
Cancer Genomics ◽  
Expression Profiles ◽  
Genetic Alterations ◽  
Cancer Type ◽  
Tissue Specific ◽  
Normal Tissues ◽  
Cancer Types

AbstractThe genetic alterations that underlie cancer development are highly tissue-specific with the majority of driving alterations occurring in only a few cancer types and with alterations common to multiple cancer types often showing a tissue-specific functional impact. This tissue-specificity means that the biology of normal tissues carries important information regarding the pathophysiology of the associated cancers, information that can be leveraged to improve the power and accuracy of cancer genomic analyses. Research exploring the use of normal tissue data for the analysis of cancer genomics has primarily focused on the paired analysis of tumor and adjacent normal samples. Efforts to leverage the general characteristics of normal tissue for cancer analysis has received less attention with most investigations focusing on understanding the tissue-specific factors that lead to individual genomic alterations or dysregulated pathways within a single cancer type. To address this gap and support scenarios where adjacent normal tissue samples are not available, we explored the genome-wide association between the transcriptomes of 21 solid human cancers and their associated normal tissues as profiled in healthy individuals. While the average gene expression profiles of normal and cancerous tissue may appear distinct, with normal tissues more similar to other normal tissues than to the associated cancer types, when transformed into relative expression values, i.e., the ratio of expression in one tissue or cancer relative to the mean in other tissues or cancers, the close association between gene activity in normal tissues and related cancers is revealed. As we demonstrate through an analysis of tumor data from The Cancer Genome Atlas and normal tissue data from the Human Protein Atlas, this association between tissue-specific and cancer-specific expression values can be leveraged to improve the prognostic modeling of cancer, the comparative analysis of different cancer types, and the analysis of cancer and normal tissue pairs.

scholarly journals A novel nonsymbiotic hemoglobin from oak: cellular and tissue specificity of gene expression

2007 ◽  
Vol 0 (0) ◽  
pp. 071106233614004-??? ◽  
Author(s):  
Claire Parent ◽  
Audrey Berger ◽  
Hélène Folzer ◽  
James Dat ◽  
Michèle Crevècoeur ◽  
...  
Keyword(s):  
Gene Expression ◽  
Tissue Specificity

Tissue Specificity of Gene Expression

2016 ◽  
Vol 4 (4) ◽  
pp. 163-169 ◽  
Author(s):  
François Aguet ◽  
Kristin G. Ardlie
Keyword(s):  
Gene Expression ◽  
Tissue Specificity

Quantitative neurogenetics: applications in understanding disease

2021 ◽  
Author(s):  
Ali Afrasiabi ◽  
Jeremy T. Keane ◽  
Julian Ik-Tsen Heng ◽  
Elizabeth E. Palmer ◽  
Nigel H. Lovell ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Risk ◽  
Tissue Specificity ◽  
High Throughput Sequencing ◽  
Molecular Genetic ◽  
Brain Dysfunction ◽  
Neural Cells ◽  
Expression Index ◽  
The Central Nervous System ◽  
The Brain

Neurodevelopmental and neurodegenerative disorders (NNDs) are a group of conditions with a broad range of core and co-morbidities, associated with dysfunction of the central nervous system. Improvements in high throughput sequencing have led to the detection of putative risk genetic loci for NNDs, however, quantitative neurogenetic approaches need to be further developed in order to establish causality and underlying molecular genetic mechanisms of pathogenesis. Here, we discuss an approach for prioritizing the contribution of genetic risk loci to complex-NND pathogenesis by estimating the possible impacts of these loci on gene regulation. Furthermore, we highlight the use of a tissue-specificity gene expression index and the application of artificial intelligence (AI) to improve the interpretation of the role of genetic risk elements in NND pathogenesis. Given that NND symptoms are associated with brain dysfunction, risk loci with direct, causative actions would comprise genes with essential functions in neural cells that are highly expressed in the brain. Indeed, NND risk genes implicated in brain dysfunction are disproportionately enriched in the brain compared with other tissues, which we refer to as brain-specific expressed genes. In addition, the tissue-specificity gene expression index can be used as a handle to identify non-brain contexts that are involved in NND pathogenesis. Lastly, we discuss how using an AI approach provides the opportunity to integrate the biological impacts of risk loci to identify those putative combinations of causative relationships through which genetic factors contribute to NND pathogenesis.

scholarly journals A comprehensive gene expression atlas of sex- and tissue-specificity in the malaria vector, Anopheles gambiae

BMC Genomics ◽  
2011 ◽  
Vol 12 (1) ◽  
Author(s):  
Dean A Baker ◽  
Tony Nolan ◽  
Bettina Fischer ◽  
Alex Pinder ◽  
Andrea Crisanti ◽  
...  
Keyword(s):  
Gene Expression ◽  
Anopheles Gambiae ◽  
Malaria Vector ◽  
Tissue Specificity ◽  
Gene Expression Atlas ◽  
Expression Atlas

scholarly journals The genetic basis of evolutionary change in gene expression levels

2010 ◽  
Vol 365 (1552) ◽  
pp. 2581-2590 ◽  
Author(s):  
J. J. Emerson ◽  
Wen-Hsiung Li
Keyword(s):  
Gene Expression ◽  
Genetic Basis ◽  
Regulation Of Gene Expression ◽  
Specific Expression ◽  
Genetic Changes ◽  
Expression Variation ◽  
Regulatory Variation ◽  
Global Mapping ◽  
History Of ◽  
Trait Locus

The regulation of gene expression is an important determinant of organismal phenotype and evolution. However, the widespread recognition of this fact occurred long after the synthesis of evolution and genetics. Here, we give a brief sketch of thoughts regarding gene regulation in the history of evolution and genetics. We then review the development of genome-wide studies of gene regulatory variation in the context of the location and mode of action of the causative genetic changes. In particular, we review mapping of the genetic basis of expression variation through expression quantitative trait locus studies and measuring the cis / trans component of expression variation in allele-specific expression studies. We conclude by proposing a systematic integration of ideas that combines global mapping studies, cis / trans tests and modern population genetics methodologies, in order to directly estimate the forces acting on regulatory variation within and between species.

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