scholarly journals MGV: a generic graph viewer for comparative omics data

2011 ◽  
Vol 27 (16) ◽  
pp. 2248-2255 ◽  
Author(s):  
Stephan Symons ◽  
Kay Nieselt
Keyword(s):  
Omics Data ◽  
Graph Viewer

Integrative Analysis of Multi-omics Data Reveals AP-1 Is a Key Regulator in Intrahepatic Cholangiocarcinoma

2020 ◽  
Author(s):  
Ke He ◽  
Yuliang Feng ◽  
Sanqi An ◽  
Jianguo Xu ◽  
Fei Liu ◽  
...  
Keyword(s):  
Intrahepatic Cholangiocarcinoma ◽  
Integrative Analysis ◽  
Omics Data

scholarly journals Comparison between instrumental variable and mediation-based approaches for reconstructing causal gene networks in yeast

2021 ◽  
Author(s):  
Adriaan-Alexander Ludl ◽  
Tom Michoel
Keyword(s):  
Instrumental Variable ◽  
Gene Networks ◽  
Omics Data ◽  
Causal Gene ◽  
Causal Networks ◽  
Transcriptomics Data ◽  
A Cell ◽  
Flow Of Information

Causal gene networks model the flow of information within a cell. Reconstructing causal networks from omics data is challenging because correlation does not imply causation. When genomics and transcriptomics data...

scholarly journals Integrating Multi–Omics Data for Gene-Environment Interactions

BioTech ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 3
Author(s):  
Yinhao Du ◽  
Kun Fan ◽  
Xi Lu ◽  
Cen Wu
Keyword(s):  
Variable Selection ◽  
Complex Disease ◽  
Level Structure ◽  
Alternative Methods ◽  
Integrative Model ◽  
Omics Data ◽  
Promising Alternative ◽  
Disease Outcomes ◽  
Interaction Studies ◽  
Gene Environment

Gene-environment (G×E) interaction is critical for understanding the genetic basis of complex disease beyond genetic and environment main effects. In addition to existing tools for interaction studies, penalized variable selection emerges as a promising alternative for dissecting G×E interactions. Despite the success, variable selection is limited in terms of accounting for multidimensional measurements. Published variable selection methods cannot accommodate structured sparsity in the framework of integrating multiomics data for disease outcomes. In this paper, we have developed a novel variable selection method in order to integrate multi-omics measurements in G×E interaction studies. Extensive studies have already revealed that analyzing omics data across multi-platforms is not only sensible biologically, but also resulting in improved identification and prediction performance. Our integrative model can efficiently pinpoint important regulators of gene expressions through sparse dimensionality reduction, and link the disease outcomes to multiple effects in the integrative G×E studies through accommodating a sparse bi-level structure. The simulation studies show the integrative model leads to better identification of G×E interactions and regulators than alternative methods. In two G×E lung cancer studies with high dimensional multi-omics data, the integrative model leads to an improved prediction and findings with important biological implications.

scholarly journals Multi-omics data integration reveals correlated regulatory features of triple negative breast cancer

2021 ◽  
Author(s):  
Kevin Chappell ◽  
Kanishka Manna ◽  
Charity L. Washam ◽  
Stefan Graw ◽  
Duah Alkam ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Data Integration ◽  
Triple Negative Breast Cancer ◽  
Triple Negative ◽  
Biological Pathways ◽  
Omics Data ◽  
Insight Into ◽  
Omics Data Integration

Multi-omics data integration of triple negative breast cancer (TNBC) provides insight into biological pathways.

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