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Gene Expression based Survival Prediction for Cancer Patients: A Topic Modeling Approach [article]

Luke Kumar, Russell Greiner
2019 arXiv   pre-print
As standard survival prediction models have a hard time coping with the high-dimensionality of such gene expression (GE) data, many projects use some dimensionality reduction techniques to overcome this  ...  cancer, we represent each patient (~document) as a mixture over cancer-topics, where each cancer-topic is a mixture over GE values (~words).  ...  We also thank Dream Challenges and Broad Institute for making the METABRIC and KIPAN cancer data sets publicly available.  ... 
arXiv:1903.10536v1 fatcat:scleyjmgxzd67amzitvkdawfhm

Gene expression based survival prediction for cancer patients—A topic modeling approach

Luke Kumar, Russell Greiner, Paweł Pławiak
2019 PLoS ONE  
cancer, we represent each patient (≈ document) as a mixture over cancer-topics, where each cancer-topic is a mixture over gene expression values (≈ words).  ...  As standard survival prediction models have a hard time coping with the high-dimensionality of such gene expression data, many projects use some dimensionality reduction techniques to overcome this hurdle  ...  We also thank Dream Challenges and Broad Institute for making the METABRIC and KIPAN cancer data sets publicly available.  ... 
doi:10.1371/journal.pone.0224446 pmid:31730620 pmcid:PMC6857918 fatcat:xk77bh7pw5g3lcmcsqjc3b4qru

A Novel Approach for Classifying Gene Expression Data using Topic Modeling

Soon Jye Kho, Hima Bindu Yalamanchili, Michael L. Raymer, Amit P. Sheth
2017 Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics - ACM-BCB '17  
Overall, our results project LDA as a promising approach for classification of tissue types based on gene expression data in cancer studies.  ...  Next we developed a novel LDA-based classification approach to classify unknown samples based on similarity of co-expression patterns.  ...  Classification In this section, we propose a novel approach to classification using LDA-based topic modeling, and explore the effectiveness of the proposed method in distinguishing gene expression patterns  ... 
doi:10.1145/3107411.3107483 dblp:conf/bcb/KhoYRS17 fatcat:yrfs56fdtfccpejpnkfqmbayga

E2F1 and KIAA0191 expression predicts breast cancer patient survival

Robin M Hallett, John A Hassell
2011 BMC Research Notes  
This approach led to highly accurate survival predictions in a large cohort of breast cancer patients using only a 2-gene signature.  ...  Hence, there is a need for more practical methods to predict patient survival.  ...  Competing interests The authors have filed a provisional patent on the use of 2-gene signatures for breast cancer patient prognosis.  ... 
doi:10.1186/1756-0500-4-95 pmid:21453498 pmcid:PMC3078871 fatcat:5n7uuueizzd27gzgasx237xaea

PDXGEM: patient-derived tumor xenograft-based gene expression model for predicting clinical response to anticancer therapy in cancer patients

Youngchul Kim, Daewon Kim, Biwei Cao, Rodrigo Carvajal, Minjung Kim
2020 BMC Bioinformatics  
In the present study, we develop a bioinformatics analysis pipeline to build a predictive gene expression model (GEM) for cancer patients' drug responses based on gene expression and drug activity data  ...  Although several attempts have been made to predict the anti-cancer therapeutic responses, there remains a great need to develop highly accurate prediction models of response to the anti-cancer drugs for  ...  Ava Cho for proofreading the article. Editorial assistance was provided by the Moffitt Cancer Center's Scientific Editing Department by Dr. Paul Fletcher & Daley Drucker. Declaration Not applicable.  ... 
doi:10.1186/s12859-020-03633-z pmid:32631229 fatcat:5lza34kp2rckddreft4hnl2zza

A gene-based risk score model for predicting recurrence-free survival in patients with hepatocellular carcinoma

Wenhua Wang, Lingchen Wang, Xinsheng Xie, Yehong Yan, Yue Li, Quqin Lu
2021 BMC Cancer  
A robust likelihood-based survival modeling approach was used to select the best genes for the prognostic model. Then, the GSE76427 dataset was used to evaluate the prognostic model's effectiveness.  ...  The recurrence-free survival (RFS) of HCC patients is a critical factor in devising a personal treatment plan.  ...  Availability of data and materials The gene expression profiles and clinical information datasets downloaded from The Cancer Genome Atlas (TCGA-LIHC)(https://portal.gdc.cancer.gov) and the Gene Expression  ... 
doi:10.1186/s12885-020-07692-6 pmid:33402113 fatcat:5nxyj7o4sfh37c5nbh5spqtk74

An autophagic gene-based signature to predict the survival of patients with low-grade gliomas

Jian Chen, Yuntian Li, Xinghua Han, Yueyin Pan, Xiaojun Qian
2021 Cancer Medicine  
A nomogram was constructed to meet individual needs. With a visualization approach, Sankey diagrams show the relationship of the histological type, IDH status, and predict index.  ...  Univariate Cox analysis and the least absolute shrinkage and selection operator (LASSO) regression model were carried out to identify the differentially expressed prognostic autophagy-related genes.  ...  All autophagy-related genes were obtained from the Human Autophagy Database. ORCID Xiaojun Qian https://orcid.org/0000-0002-0883-0987  ... 
doi:10.1002/cam4.3748 pmid:33591634 fatcat:wqml6krvizbv7iubxistnewi3q

Construction and Validation of a Potent Epigenetic Modification-Related Prognostic Signature for Osteosarcoma Patients

Siyu Liu, Bing Wu, Xiaomin Li, Lulu Zhao, Wen Wu, Songtao Ai, Song Cao
2021 Journal of Oncology  
A risk score model constructed based on four epigenetic modification-related genes (MYC, TERT, EIF4E3, and RBM34) can effectively predict the prognosis of patients with osteosarcoma.  ...  Based on the risk score and clinical features, we constructed a nomogram. Conclusion.  ...  the predicted 1-, 3-, and 5-year survival rates for each patient were obtained based on the total score. 3.8.  ... 
doi:10.1155/2021/2719172 pmid:34853590 pmcid:PMC8629625 fatcat:twr5qe67vzcmllaxunrra6uoiu

Lifelong Machine Learning and root cause analysis for large-scale cancer patient data

Gautam Pal, Xianbin Hong, Zhuo Wang, Hongyi Wu, Gangmin Li, Katie Atkinson
2019 Journal of Big Data  
Also, the current machine learning approaches do the model prediction without providing a comprehensive root cause analysis.  ...  The aim is to prescribe personalized medicine based on the thousands of genotype and phenotype parameters for each patient.  ...  Availability of data and materials The National Cancer Institute's Genomic Data Commons (GDC) unified data repository for the cancer patient is available online at Government website: https ://gdc.cance  ... 
doi:10.1186/s40537-019-0261-9 fatcat:3bosbw7ukfg7lfrgzxss3taveu

Identification and Validation of Autophagy-Related Gene Nomograms to Predict the Prognostic Value of Patients with Cervical Cancer

Jinqun Jiang, HongYan Xu, YiHao Wang, Hai Lu, Quan Cheng
2021 Journal of Oncology  
Our constructed autophagy risk signature may be a prognostic tool for cervical cancer.  ...  In this study, we constructed risk signatures of autophagy-related genes (ARGs) to predict the prognosis of cervical cancer.  ...  Based on the risk score, G, T, M, and N staging, a nomograph was constructed (Figure 10(a) ). e total score based on the above indicators could be predicted for each patient for 1-, 2-, and 5-year survival  ... 
doi:10.1155/2021/5583400 fatcat:pobsiz45bjei5gceyjpj7vokiy

Predictive biomarkers in patients with resected non-small cell lung cancer treated with perioperative chemotherapy

E. Bergot, G. Levallet, K. Campbell, F. Dubois, E. Lechapt, G. Zalcman
2013 European Respiratory Review  
Prediction of survival by RRM1 tumour expression was not confirmed in a prospective phase III trial in 275 patients with stage IV disease, precluding its use in early-stage NSCLC.  ...  Of the several cDNA gene expression studies in early-stage NSCLC with non-overlapping prognostic signatures, few have been replicated in independent cohorts for prognostic value, and none received external  ...  Therefore, methylation assays need to be correlated to gene expression for each specific gene.  ... 
doi:10.1183/09059180.00007113 pmid:24293473 fatcat:oitdqe6d4vhtnldghqhyp7zin4

Construction of a Ferroptosis-Related Gene Signature for Predicting Survival and Immune Microenvironment in Melanoma Patients

Ni Zeng, Liwen Ma, Yuxin Cheng, Qingyue Xia, Yueyue Li, Yihe Chen, Zhiyu Lu, Qian Lu, Feng Jiang, Dan Luo
2021 International Journal of General Medicine  
Our gene signature has shown to be a reliable predictor of OS, reflect the immune microenvironment, and predict the effectiveness of immunotherapy for SKCM patients.  ...  In this research, we studied the genes associated with ferroptosis to develop a prognostic model and find out an association with tumor immune microenvironment in skin cutaneous melanoma (SKCM) patients  ...  To sum up, our research results indicate that a two-gene prognostic model is a reliable tool for predicting the overall survival of SKCM; it may be useful for guiding therapeutic strategies to improve  ... 
doi:10.2147/ijgm.s327348 pmid:34675611 pmcid:PMC8502037 fatcat:rfw5nohedbcmnc4ru4dsvqe3ay

Survival Prediction using Gene Expression Data - A Topic Modeling Approach

Luke N Kumar
2017
Survival prediction is becoming a crucial part of treatment planning for most terminally ill patients.  ...  we represent each patient (document) as a mixture over "(cancer) strains" (topics), where each strain is a mixture over gene expression values (words).  ...  This motivated us to apply a topic modeling approach to gene expression data, for the survival prediction task.  ... 
doi:10.7939/r39883180 fatcat:b2a5fa65xfgbhgizwjm3hu4pqe

An immune-related pseudogene signature to improve prognosis prediction of endometrial carcinoma patients

Shanshan Tang, Yiyi Zhuge
2021 BioMedical Engineering OnLine  
The signature might have important implications for improving the clinical survival of EC patients and provide new strategies for cancer treatment.  ...  Background Pseudogenes show multiple functions in various cancer types, and immunotherapy is a promising cancer treatment.  ...  Acknowledgements The authors sincerely acknowledge the publicly available ImmPort database (https:// immpo rt. niaid. nih. gov) and TCGA (https:// portal. gdc. cancer. gov/) database.  ... 
doi:10.1186/s12938-021-00902-7 pmid:34193185 pmcid:PMC8243762 fatcat:kania2ahezbkzjlwmqrjzcvapq

Development and Validation of a Four Adenosine-to-Inosine RNA Editing Site-Relevant Prognostic Signature for Assessing Survival in Breast Cancer Patients

Jian Wan, Shizhen Chen, Anqin Zhang, Yiting Liu, Yangyang Zhang, Qinghua Li, Ziqi Yu, Yuwei Wan, Lei Yang, Qi Wang
2022 Frontiers in Oncology  
–0.763), and 0.635 (95%CI = 0.566–0.705) for predicting DFS in the three cohorts.ConclusionAIRS nomogram could help to predict OS and DFS of patients with BRCA.  ...  However, no studies have been conducted to identify an ATIRE signature for predicting cancer survival.MethodsBreast cancer (BRCA) samples with ATIRE profiles from The Cancer Genome Atlas were divided into  ...  These prediction models were mostly established by gene expression data recorded by The Cancer Genome Atlas (TCGA) database (https://portal.gdc. cancer.gov/) or Gene Expression Omnibus (GEO) database (  ... 
doi:10.3389/fonc.2022.861439 pmid:35494026 pmcid:PMC9039306 fatcat:l5kg5mkqbvdbvlkvk5f6dixvey
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