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INTEGRATIVE NETWORK ANALYSIS TO IDENTIFY ABERRANT PATHWAY NETWORKS IN OVARIAN CANCER

LI CHEN, JIANHUA XUAN, JINGHUA GU, YUE WANG, ZHEN ZHANG, TIAN-LI WANG, IE-MING SHIH
2011 Biocomputing 2012  
pathways related to ovarian cancer.  ...  We propose an integrative framework to identify pathway related networks based on large-scale TCGA copy number data and gene expression profiles.  ...  Acknowledgments This research was supported in part by NIH Grants (CA139246, CA149653, CA149147, and NS29525-18A1) and a DoD/CDMRP grant (BC030280).  ... 
doi:10.1142/9789814366496_0004 fatcat:qnefyqaaejgbjgihaheg4ouikq

Identifying candidate drivers of drug response in heterogeneous cancer by mining high throughput genomics data

Sheida Nabavi
2016 BMC Genomics  
In this method, an integrative method based on module network analysis is applied to identify potential driver genes.  ...  We applied this method to the ovarian cancer data from the cancer genome atlas.  ...  It has been shown that the module network analysis, which is a non-linear approach, performs well in identifying driver genes in cancer [1] .  ... 
doi:10.1186/s12864-016-2942-5 pmid:27526849 pmcid:PMC4986197 fatcat:d5ehriukmrbt5k7l4xvh4ktuom

A New Mutational aktivation in the PI3K Pathway

Joan Brugge, Mien-Chie Hung, Gordon B. Mills
2007 Cancer Cell  
This analysis of 500 gliomas, ovarian cancers, and lung cancers is designed to detect events that occur with at least 5% frequency.  ...  A systems biology approach to development of robust PI3K network computational models in normal cells integrating the effect of aberrations present in cancer patients will be required for efficient implementation  ... 
doi:10.1016/j.ccr.2007.07.014 pmid:17692802 fatcat:5nx2nldp7few5gs4xlvc3rhwdm

Integrated Genomic Analysis of Ovarian Carcinoma

2011 Cancer Discovery  
Gene expression analysis identified 4 distinct subtypes of ovarian cancer.  ...  Impact: Up to half of these cancers may have aberrations in genes involved in homologous recombination and thus benefit from PARP inhibitors.  ...  Integrated Genomic Analysis of Ovarian Carcinoma  ... 
doi:10.1158/2159-8290.cd-rw042711-14 fatcat:yzekuxfsgzh7ppff2mnrwb4iem

IDENTIFYING MASTER REGULATORS OF CANCER AND THEIR DOWNSTREAM TARGETS BY INTEGRATING GENOMIC AND EPIGENOMIC FEATURES

OLIVIER GEVAERT, SYLVIA PLEVRITIS
2012 Biocomputing 2013  
As a proof-of-concept, we show that the GBM and ovarian cancer module networks recapitulate known processes in these cancers.  ...  We applied our biocomputational algorithm to identify master regulators and their targets in glioblastoma multiforme (GBM) and serous ovarian cancer.  ...  The master regulators in both the glioblastoma and ovarian cancer network belong to known pathways affected in these cancers.  ... 
doi:10.1142/9789814447973_0013 fatcat:w2xrqyswrvgatiy22fqjyo3rkm

Identifying master regulators of cancer and their downstream targets by integrating genomic and epigenomic features

Olivier Gevaert, Sylvia Plevritis
2013 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
As a proof-of-concept, we show that the GBM and ovarian cancer module networks recapitulate known processes in these cancers.  ...  We applied our biocomputational algorithm to identify master regulators and their targets in glioblastoma multiforme (GBM) and serous ovarian cancer.  ...  Acknowledgments This research was supported by the Center for Cancer Systems Biology (CCSB) at Stanford (U54 CA149145).  ... 
pmid:23424118 pmcid:PMC3911770 fatcat:gyzs5jidevffdpac5jmt6nuvuy

Driver Pattern Identification Over The Gene Co-Expression Of Drug Response In Ovarian Cancer By Integrating High Throughput Genomics Data [article]

Xinguo Lu, Jibo Lu, Bo Liao, Keqin Li
2017 bioRxiv   pre-print
are hidden in drug response dataset of ovarian cancer.  ...  The multiple types of high throughput genomics data create a potential opportunity to identify driver pattern in ovarian cancer, which will acquire some novel and clinical biomarkers for appropriate diagnosis  ...  Acknowledgements The authors are grateful to Peter Langfelder's team who provided the weighted correlation network analysis method with WGCNA package, Prof Ripley B.  ... 
doi:10.1101/145268 fatcat:zqcp7z5iufhrfberoa2xezjj6a

An Integrative Computational Approach Based on Expression Similarity Signatures to Identify Protein–Protein Interaction Networks in Female-Specific Cancers

Katia Pane, Ornella Affinito, Mario Zanfardino, Rossana Castaldo, Mariarosaria Incoronato, Marco Salvatore, Monica Franzese
2020 Frontiers in Genetics  
Secondly, we investigated the signaling pathways and co-regulatory protein–protein interaction networks underlying these three cancers by leveraging the Ingenuity Pathway Analysis software.  ...  Breast, ovarian, and endometrial cancers have a major impact on mortality in women.  ...  In this study, we carried out a computational analysis by integrating three hormone-sensitive female cancer datasets, i.e., breast, ovarian, and endometrial TCGA cohorts.  ... 
doi:10.3389/fgene.2020.612521 pmid:33424936 pmcid:PMC7793872 fatcat:s7otgjzwgzefzdl5adir6cpzyi

Pathway Crosstalk Analysis Based on Protein-protein Network Analysis in Ovarian Cancer

Xiao-Hua Pan
2012 Asian Pacific Journal of Cancer Prevention  
In this study, we constructed a crosstalk network among ovarian cancer related pathways by integrating protein-protein interactions and KEGG pathway information.  ...  Several significant pathways were identified to crosstalk with each other in ovarian cancer, such as the chemokine, Notch, Wnt and NOD-like receptor signaling pathways.  ...  To identify the relevant pathways changed in ovarian cancer, we used a statistical approach Pathway Crosstalk Analysis Based on Protein-protein Network Analysis in Ovarian Cancer The lines indicate that  ... 
doi:10.7314/apjcp.2012.13.8.3905 fatcat:b5drab4kh5fynot7yfkrfh4ayi

InFlo: a novel systems biology framework identifies cAMP-CREB1 axis as a key modulator of platinum resistance in ovarian cancer

N Dimitrova, A B Nagaraj, A Razi, S Singh, S Kamalakaran, N Banerjee, P Joseph, A Mankovich, P Mittal, A DiFeo, V Varadan
2016 Oncogene  
Published approaches to decipher driver mechanisms do not explicitly model tissue-specific changes in pathway networks and the regulatory disruptions related to genomic aberrations in cancers.  ...  Using large-scale multi-omics cancer datasets, we show that InFlo exhibits higher sensitivity and specificity in detecting pathway networks associated with specific disease states when compared to published  ...  The data were used in accordance to the TCGA's informed consent and data access policies (http://cancergenome.nih.gov/abouttcga/ policies).  ... 
doi:10.1038/onc.2016.398 pmid:27819677 pmcid:PMC5415943 fatcat:5vtgp4kvxfcsxk63celxlspykq

Gene-gene interaction network analysis of ovarian cancer using TCGA data

Huanchun Ying, Jing Lv, Tianshu Ying, Shanshan Jin, Jingru Shao, Lili Wang, Hongying Xu, Bin Yuan, Qing Yang
2013 Journal of Ovarian Research  
Methods: Microarray data of ovarian cancer were downloaded from TCGA database, and Limma package in R language was used to identify the differentially expressed genes (DEGs) between ovarian cancer and  ...  Conclusion: our data provides a comprehensive bioinformatics analysis of genes, functions, and pathways which may be involved in the pathogenesis of ovarian cancer.  ...  Bioinformatics analysis provides a first large scale integrative view of the aberrations in high grade serous ovarian cancer, with surprisingly simple mutational spectrum [3] .  ... 
doi:10.1186/1757-2215-6-88 pmid:24314048 pmcid:PMC4029308 fatcat:q6yq3fq4gzc5fg4zcccmwqv4dy

Combined Radiotherapy and Androgen-deprivation Therapy

2011 Cancer Discovery  
Gene expression analysis identified 4 distinct subtypes of ovarian cancer.  ...  Impact: Up to half of these cancers may have aberrations in genes involved in homologous recombination and thus benefit from PARP inhibitors.  ... 
doi:10.1158/2159-8290.cd-rw042711-13 fatcat:d6qltzw3avb4ln4psyuoph4zlu

Identification of ovarian cancer subtype-specific network modules and candidate drivers through an integrative genomics approach

Di Zhang, Peng Chen, Chun-Hou Zheng, Junfeng Xia
2015 OncoTarget  
In this study, we introduced a simple but efficient multistep procedure to define ovarian cancer types and identify core networks/pathways and driver genes for each subtype by integrating multiple data  ...  Applying similarity network fusion approach to a patient cohort with 379 ovarian cancer samples, we found two distinct integrated cancer subtypes with different survival profiles.  ...  We then used an integrated network-based approach [6] to identify frequently altered network modules and candidate drivers in each ovarian cancer subtype.  ... 
doi:10.18632/oncotarget.6774 pmid:26735889 pmcid:PMC4826206 fatcat:54shmew2ojer3l6zlbz3o4wxr4

Proteogenomic convergence for understanding cancer pathways and networks

Emily S Boja, Henry Rodriguez
2014 Clinical Proteomics  
changes in proteins and their interacting partners, isoforms, and post-translational modifications (PTMs) in response to stimuli in the context of signaling pathways and protein networks.  ...  proteomic assays to measure panels of proteins involved in biologically relevant pathways have made significant progress in understanding cancer at the molecular level.  ...  Acknowledgement We would like to thank Dr. Robert Clay Rivers for his critical reading of this review.  ... 
doi:10.1186/1559-0275-11-22 pmid:24994965 pmcid:PMC4067069 fatcat:6so4o3yqzbg6rau4z53xnneu4q

Prioritizing cancer-related genes with aberrant methylation based on a weighted protein-protein interaction network

Hui Liu, Jianzhong Su, Junhua Li, Hongbo Liu, Jie Lv, Boyan Li, Hong Qiao, Yan Zhang
2011 BMC Systems Biology  
Conclusions: Here we have shown that network theory combined with epigenetic characteristics provides a favorable platform from which to identify cancer-related genes.  ...  By examining the PubMed co-citations, we found 43 optimized genes were related with cancers and aberrant methylation, and 10 genes were validated to be methylated aberrantly in cancers.  ...  The optimized genes were also annotated to cancer pathways, and to the Notch signaling pathway and the cell cycle in KEGG.  ... 
doi:10.1186/1752-0509-5-158 pmid:21985575 pmcid:PMC3224234 fatcat:rhchman6snb2tn3hmsi3zvtkuy
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