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Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE)

Evan O. Paull, Daniel E. Carlin, Mario Niepel, Peter K. Sorger, David Haussler, Joshua M. Stuart
2013 Bioinformatics  
We have developed a method called Tied Diffusion Through Interacting Events (TieDIE) that uses a network diffusion approach to connect genomic perturbations to gene expression changes characteristic of  ...  Results: Application of TieDIE to The Cancer Genome Atlas and a breast cancer cell line dataset identified key signaling pathways, with examples impinging on MYC activity.  ...  The Tied Diffusion of Interacting Events (TieDIE) method described here extends on the heat diffusion strategies by leveraging different types of genomic inputs to find relevant genes on a background network  ... 
doi:10.1093/bioinformatics/btt471 pmid:23986566 pmcid:PMC3799471 fatcat:phkdt5hqsfcnveamhsbq4d6xy4

Integrative landscape of dysregulated signaling pathways of clinically distinct pancreatic cancer subtypes

Musalula Sinkala, Nicola Mulder, Darren Patrick Martin
2018 OncoTarget  
Here we use publicly available transcriptomic, copy number alteration and mutation profiling datasets from pancreatic cancer patients together with data on disease outcomes to show that the three major  ...  Besides being highly metastatic, pancreatic cancer is challenging to treat because it is caused by a heterogeneous array of somatic mutations that impact a variety of signaling pathways and cellular regulatory  ...  Connectivity of genomic alterations to transcription factors and their pathway activities in pancreatic cancer To link genomic changes to transcriptional events, we applied the Tied Diffusion Through Interacting  ... 
doi:10.18632/oncotarget.25632 pmid:30018740 pmcid:PMC6044387 fatcat:zxzzesismfcxtfjzoz6w6l5sqa

Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers

Ruth Nussinov, Hyunbum Jang, Chung-Jung Tsai, Feixiong Cheng, Anna R R Panchenko
2019 PLoS Computational Biology  
As noted by Tsang and colleagues, various terms have been used to relate to precision genomic oncology, including simply precision oncology [22], genomics-driven oncology [23], genomic oncology, and personalized  ...  cellular signaling pathways.  ... [435] TieDIE Predicting cancer mutated subnetworks using a network-based diffusion algorithm.  ... 
doi:10.1371/journal.pcbi.1006658 fatcat:ii47m4bybraz7edark3m6axcby

Unsupervised Multi-Omics Data Integration Methods: A Comprehensive Review

Nasim Vahabi, George Michailidis
2022 Frontiers in Genetics  
Through the developments of Omics technologies and dissemination of large-scale datasets, such as those from The Cancer Genome Atlas, Alzheimer's Disease Neuroimaging Initiative, and Genotype-Tissue Expression  ...  discovery, disease subtyping, module discovery, and network/pathway analysis.  ...  GE, PPIs Gene-prioritizing • - walk-, and Network Restart on Multigraphs) Fusion-based • TieDIE (Tied Diffusion through ModE Paull et al. (2013) GE, TF, PPIs Module/sub- • Python code (https://sysbiowiki  ... 
doi:10.3389/fgene.2022.854752 pmid:35391796 pmcid:PMC8981526 fatcat:ijmwfu264rbgtaen66tkbr4sgu

A Network Propagation Approach to Prioritize Long Tail Genes in Cancer [article]

Hussein Mohsen, Vignesh Gunasekharan, Tao Qing, Sahand Negahban, Zoltan Szallasi, Lajos Pusztai, Mark B. Gerstein
2021 bioRxiv   pre-print
We validate UMGs' role in cancer cell survival in vitro using genome-wide RNAi and CRISPR databases and report new cancer-pathway associations based on UMGs that were not previously identified using driver  ...  Network propagation methods have demonstrated high efficacy in uncovering genomic patterns underlying cancer using biological interaction networks.  ...  Paull EO, Carlin DE, Niepel M, Sorger PK, Haussler D, Stuart JM: Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE).  ... 
doi:10.1101/2021.02.05.429983 fatcat:oum4y7g2wbfdvof3mbjfavlzfm

Jones_columbia_0054D_16642.pdf [article]

A fuller understanding of the mechanistic connections between the aberrant genomics leading to the transcriptional dysregulation of tumors is key to both improving our knowledge of cancer biology as well  ...  This thesis explores the development and application of a network based multi-omic master regulator framework designed to elucidate these pathways.  ...  Acknowledgments We acknowledge the genomic and small animal imaging shared resources of the Herbert Irving Comprehensive Cancer Center, supported in part by P30CA013696.  ... 
doi:10.7916/d8-vbgc-f549 fatcat:edi5y3uwbjhcdnl45agkpkm3oy