Modeling Species Specific Gene Expression Across Multiple Regions in the Brain

2020 ◽  
pp. 3-22
Author(s):  
Liyang Diao ◽  
Ying Zhu ◽  
Nenad Sestan ◽  
Hongyu Zhao
Keyword(s):  
Gene Expression ◽  
Specific Gene ◽  
Specific Gene Expression ◽  
Multiple Regions ◽  
Species Specific ◽  
The Brain

scholarly journals The Functions of Mediator in Candida albicans Support a Role in Shaping Species-Specific Gene Expression

PLoS Genetics ◽  
2012 ◽  
Vol 8 (4) ◽  
pp. e1002613 ◽  
Author(s):  
Nathalie Uwamahoro ◽  
Yue Qu ◽  
Branka Jelicic ◽  
Tricia L. Lo ◽  
Cecile Beaurepaire ◽  
...  
Keyword(s):  
Gene Expression ◽  
Candida Albicans ◽  
Specific Gene ◽  
Specific Gene Expression ◽  
Species Specific

Melanin-Concentrating Hormone Receptor Subtypes 1 and 2: Species-Specific Gene Expression

Genomics ◽  
2002 ◽  
Vol 79 (6) ◽  
pp. 785-792 ◽  
Author(s):  
Carina P. Tan ◽  
Hideki Sano ◽  
Hisashi Iwaasa ◽  
Jie Pan ◽  
Andreas W. Sailer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hormone Receptor ◽  
Specific Gene ◽  
Receptor Subtypes ◽  
Specific Gene Expression ◽  
Melanin Concentrating Hormone ◽  
Species Specific

scholarly journals Human and Murine Kidneys Show Gender- and Species-Specific Gene Expression Differences in Response to Injury

PLoS ONE ◽  
2009 ◽  
Vol 4 (3) ◽  
pp. e4802 ◽  
Author(s):  
Han Si ◽  
Ramandeep S. Banga ◽  
Pinelopi Kapitsinou ◽  
Manjunath Ramaiah ◽  
Janis Lawrence ◽  
...  
Keyword(s):  
Gene Expression ◽  
Specific Gene ◽  
Specific Gene Expression ◽  
Species Specific

scholarly journals Species specific gene expression dynamics during harmful algal blooms

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Gabriel Metegnier ◽  
Sauvann Paulino ◽  
Pierre Ramond ◽  
Raffaele Siano ◽  
Marc Sourisseau ◽  
...  
Keyword(s):  
Gene Expression ◽  
Harmful Algal Blooms ◽  
Algal Blooms ◽  
Specific Gene ◽  
Specific Gene Expression ◽  
Gene Expression Dynamics ◽  
Species Specific

scholarly journals BrainGENIE: The Brain Gene Expression and Network Imputation Engine

2020 ◽  
Author(s):  
Jonathan L. Hess ◽  
Samuel Chen ◽  
Thomas P. Quinn ◽  
Sek Won Kong ◽  
Murray Cairns ◽  
...  
Keyword(s):  
Gene Expression ◽  
Peripheral Blood ◽  
Brain Region ◽  
Ex Vivo ◽  
Specific Gene ◽  
Expression Levels ◽  
Specific Gene Expression ◽  
Brain Gene Expression ◽  
The Brain ◽  
Gene Expression Levels

AbstractEx vivo molecular analysis of the human brain is virtually impossible given major risks and ethical concerns. Transcriptome imputation offers a promising and non-invasive alternative for developing models (albeit imperfect) of brain gene expression in lieu of biopsying brain tissue. Popular tools such as FUSION (Gusev et al., 2016) and PrediXcan (Gamazon et al., 2015) use genotypes at common cis-expression quantitative trait loci (eQTLs) to predict tissue-specific gene expression levels. However, those tools cannot reliably predict expression levels for a majority of genes in the brain. This raises the question of whether an alternative modeling approach should be evaluated to capture greater variance in more genes in the brain that are not yet imputable with existing cis-eQTL imputation tools. To address this problem, we developed a novel transcriptome-imputation method called the Brain Gene Expression and Network Imputation Engine (BrainGENIE) that imputes brain-region-specific gene expression levels from peripheral blood gene expression. BrainGENIE predicted brain-region-specific expression levels for 1,733 – 11,569 genes (cross-validation R2≥0.01, false-discovery rate-adjusted p<0.05), few of which are imputable by PrediXcan. Disease-related transcriptome signals detected by BrainGENIE showed stronger agreement with known transcriptome signatures from postmortem brain when compared with findings from analyses of peripheral blood or S-PrediXcan. BrainGENIE complements and outperforms existing transcriptome-imputation tools, provides biologically meaningful predictions, and opens avenues for studying brain transcriptomes longitudinally. BrainGENIE was developed using R (v.3.6.3, tested in 4.0.2) and is freely available at: https://github.com/hessJ/BrainGENIE.

scholarly journals Evolutionary re-wiring of p63 and the epigenomic regulatory landscape in keratinocytes and its potential implications on species-specific gene expression and phenotypes

2017 ◽  
Vol 45 (14) ◽  
pp. 8208-8224 ◽  
Author(s):  
Isha Sethi ◽  
Christian Gluck ◽  
Huiqing Zhou ◽  
Michael J. Buck ◽  
Satrajit Sinha
Keyword(s):  
Gene Expression ◽  
Specific Gene ◽  
Specific Gene Expression ◽  
Species Specific ◽  
Regulatory Landscape
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