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Extracting a low-dimensional description of multiple gene expression datasets reveals a potential driver for tumor-associated stroma in ovarian cancer [article]

Safiye Celik, Benjamin A Logsdon, Stephanie Battle, Charles W Drescher, Mara Rendi, David Hawkins, Su-In Lee
2016 bioRxiv   pre-print
Results: We evaluated INSPIRE on synthetically generated datasets with known underlying network structure among modules, and gene expression datasets from multiple ovarian cancer studies.  ...  Many methods designed for expression data analysis cannot integrate multiple datasets with variable discrepancy to infer a single combined model, whereas INSPIRE can naturally model the dependencies among  ...  He et al. 23 defined an LDR as a set of latent factors, and modeled each latent factor as a linear combination of genes (structured latent factor analysis -SLFA).  ... 
doi:10.1101/048215 fatcat:h4xnqkxelvgvtc2smay247lpny

Extracting a low-dimensional description of multiple gene expression datasets reveals a potential driver for tumor-associated stroma in ovarian cancer

Safiye Celik, Benjamin A. Logsdon, Stephanie Battle, Charles W. Drescher, Mara Rendi, R. David Hawkins, Su-In Lee
2016 Genome Medicine  
We demonstrate that applying INSPIRE to nine ovarian cancer datasets leads to a new marker and potential driver of tumor-associated stroma, HOPX, followed by experimental validation.  ...  We show that INSPIRE infers more accurate models than existing methods to extract low-dimensional representation of expression data.  ...  [22] defined an LDR as a set of latent factors and modeled each latent factor as a linear combination of genes (structured latent factor analysis (SLFA)). While similar to Celik et al.  ... 
doi:10.1186/s13073-016-0319-7 pmid:27287041 pmcid:PMC4902951 fatcat:zpfhax3ddnf6vjsz7xiaiyb3ra

Deep learning in cancer diagnosis, prognosis and treatment selection

Khoa A. Tran, Olga Kondrashova, Andrew Bradley, Elizabeth D. Williams, John V. Pearson, Nicola Waddell
2021 Genome Medicine  
models.  ...  AbstractDeep learning is a subdiscipline of artificial intelligence that uses a machine learning technique called artificial neural networks to extract patterns and make predictions from large data sets  ...  Acknowledgements Khoa Tran was the recipient of the Maureen and Barry Stevenson PhD Scholarship, we are grateful to Maureen Stevenson for her support.  ... 
doi:10.1186/s13073-021-00968-x pmid:34579788 pmcid:PMC8477474 fatcat:y73fumwdazft3pw47gqdcncnue

Contrastive learning-based computational histopathology predict differential expression of cancer driver genes [article]

Haojie Huang, Gongming Zhou, Xuejun Liu, Lei Deng, Chen Wu, Dachuan Zhang, Hui Liu
2022 arXiv   pre-print
In this paper, we propose a self-supervised contrastive learning framework, HistCode, to infer differential gene expressions from whole slide images (WSIs).  ...  We leveraged contrastive learning on large-scale unannotated WSIs to derive slide-level histopathological feature in latent space, and then transfer it to tumor diagnosis and prediction of differentially  ...  Acknowledgments We would like to thank The Cancer Genome Atlas (TCGA) for providing free WSI datasets and RNA-seq data.  ... 
arXiv:2204.11994v2 fatcat:bkuplsykzrds7cgyg4p6y26274

Machine learning analysis of TCGA cancer data

Jose Liñares-Blanco, Alejandro Pazos, Carlos Fernandez-Lozano
2021 PeerJ Computer Science  
That is the reason for which a greater number of works have focused on the BRCA cohort, while specific works for survival, for example, were centred on the GBM cohort, due to its large number of events  ...  Finally, it is intended that this work will serve as a basis for future research in this field of study.  ...  Jose A. Seoane for comments during the preparation of this review. ADDITIONAL INFORMATION AND DECLARATIONS  ... 
doi:10.7717/peerj-cs.584 fatcat:rpqlnnmujbhaxhqota5oz2gtcu

Gynecologic

2008 Laboratory Investigation  
Tissue microarrays (TMAs) representing 87 ovarian carcinomas (including all ovarian carcinoma subtypes and 8 CCs) and 4 of the study cases were evaluated immunohistochemically for HNF expression.  ...  to selected 48 cases of renal carcinomas of various subtypes, 7 oncocytomas and 13 normal kidney.  ...  The significantly more frequent finding of endometriosis and intraepithelial carcinoma in cyst-associated tumors suggests these lesions are precursors in a progression model for this subtype.  ... 
doi:10.1038/sj.labinvest.3700732 fatcat:xp6ii4s7t5hf3bnbq25qqzpvzy

Gynecologic & Obstetrics

2010 Modern Pathology  
From these, 45 slides were selected for this study, with preferential selection of challenging examples.  ...  Design: All cases (slides and reports) of high grade endometrial carcinoma from 1988-2008 were retrieved from the pathology databases of two urban hospitals.  ...  One slide from each round was stained for p53.  ... 
doi:10.1038/modpathol.2010.16 fatcat:ytcbh2sqzzhola73ffg5ohsbbu

Gynecologic & Obstetrics

2010 Laboratory Investigation  
From these, 45 slides were selected for this study, with preferential selection of challenging examples.  ...  Design: All cases (slides and reports) of high grade endometrial carcinoma from 1988-2008 were retrieved from the pathology databases of two urban hospitals.  ...  One slide from each round was stained for p53.  ... 
doi:10.1038/labinvest.2010.19 fatcat:xe2ihujbsbd63gehes2b2pwirm

Disabled-2 Heterozygous Mice Are Predisposed to Endometrial and Ovarian Tumorigenesis and Exhibit Sex-Biased Embryonic Lethality in a p53-Null Background

Dong-Hua Yang, Zia Fazili, Elizabeth R. Smith, Kathy Qi Cai, Andres Klein-Szanto, Cynthia Cohen, Ira R. Horowitz, Xiang-Xi Xu
2006 American Journal of Pathology  
A role for Dab2 in epithelial cell positioning organization was derived from study of knockout mice: homozygous deletion of dab2 results in early embryonic lethality due to the disorganization of the primitive  ...  We now report that dab2 heterozygous mice develop uterine hyperplasia and ovarian preneoplastic morphological changes at a high frequency.  ...  Patricia Bateman for secretarial assistance; Xiang Hua of the Fox Chase Cancer Center transgenic mouse facility for assistance and contribution; Tony Lerro and Jackie Valvardi of the animal facility; Cass  ... 
doi:10.2353/ajpath.2006.060036 pmid:16816378 pmcid:PMC1698752 fatcat:wyd6ncinfnewdgkjdpw6rkk3wm

Abstracts from USCAP 2020: Informatics (1522-1590)

2020 Laboratory Investigation  
Design: Our department serves as a model facility for the primary diagnosis through digital pathology. In 2018 we achieved 100% digital workflow for biopsies, surgicals, and frozen service.  ...  Medicare Part B payments for all medical specialties was $68,889,358,763 in 2017; a 7.8 percent increase from 2012.  ...  Conclusions: We demonstrate the feasibility of applying a DIA workflow for estimating stromal CD8+ TILs in NSCLC.  ... 
doi:10.1038/s41374-020-0393-8 pmid:32139865 fatcat:wecibsafmzhzjjgxqvxalr3xn4

Detection of ovarian cancer (± neo-adjuvant chemotherapy effects) via ATR-FTIR spectroscopy: comparative analysis of blood and urine biofluids in a large patient cohort

Panagiotis Giamougiannis, Camilo L. M. Morais, Brice Rodriguez, Nicholas J. Wood, Pierre L. Martin-Hirsch, Francis L. Martin
2021 Analytical and Bioanalytical Chemistry  
Classification algorithms with blind predictive model validation demonstrated that serum was the best biofluid, achieving 76% sensitivity and 98% specificity for ovarian cancer detection, whereas urine  ...  A drop in sensitivities for the NACT ovarian cancer group in plasma and serum indicates the potential of ATR-FTIR spectroscopy to identify chemotherapy-related spectral changes.  ...  Funding Funding from Rosemere Cancer Foundation at Royal Preston Hospital is gratefully acknowledged.  ... 
doi:10.1007/s00216-021-03472-8 pmid:34195877 pmcid:PMC8405472 fatcat:t3qun2dzongjjltery2f7knona

Expression of Epstein-Barr nuclear antigen 1 in gastric carcinoma cells is associated with enhanced tumorigenicity and reduced cisplatin sensitivity

Sheu
2009 International Journal of Oncology  
However, EBNA1 was able to enhance tumorigenicity, the growth rate and the malignant histopathological grade in a xenograft nude mice test.  ...  Finally, our results suggest that EBV infection with EBNA1 expression in gastric carcinomas provides advantages for host cell survival, growth ability and transformation potential involving escape from  ...  The authors sincerely thank Hsien-Chuan Chin for the excellent statistical analysis.  ... 
doi:10.3892/ijo_00000486 fatcat:fo2ez2njg5fy7occkzdoump7dq

Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer

Allen W. Zhang, Andrew McPherson, Katy Milne, David R. Kroeger, Phineas T. Hamilton, Alex Miranda, Tyler Funnell, Nicole Little, Camila P.E. de Souza, Sonya Laan, Stacey LeDoux, Dawn R. Cochrane (+33 others)
2018 Cell  
All samples were from removed structures during attempts at optimal debulking; hence the majority of samples were from omentum and ovarian sites.  ...  Warp red chromogen was added to the slide for 7 minutes, hematoxylin at a 1/5 dilution was then added for 5 minutes.  ...  Getis-Ord Gi* G Ã i values for each grid square i were computed using localG from spdep.  ... 
doi:10.1016/j.cell.2018.03.073 pmid:29754820 fatcat:fbq26hfn2jdm7lwi2gz6ew6sci

Gynecologic

2006 Laboratory Investigation  
From review of the H&E slides, the subtype and percentage of carcinoma (CA), subtype and percentage of sarcoma (SA), and composition of myoinvasive component as well as the presence/absence of vascular  ...  Background: Ovarian carcinomas are believed to originate from the ovarian surface epithelium, a layer of coelomic mesothelium, in most cases, although for some subtypes, in particular, there is some uncertainty  ...  Does Micropapillarity in Ovarian Serous Borderline Tumors Represent a Transition between Typical Ovarian Serous Borderline Tumors and Low Grade Serous Carcinoma?  ... 
doi:10.1038/sj.labinvest.3700613 fatcat:rnzhkucvyzdmvm6tqkyjcoclfa

Gynecologic

2006 Modern Pathology  
From review of the H&E slides, the subtype and percentage of carcinoma (CA), subtype and percentage of sarcoma (SA), and composition of myoinvasive component as well as the presence/absence of vascular  ...  Background: Ovarian carcinomas are believed to originate from the ovarian surface epithelium, a layer of coelomic mesothelium, in most cases, although for some subtypes, in particular, there is some uncertainty  ...  Does Micropapillarity in Ovarian Serous Borderline Tumors Represent a Transition between Typical Ovarian Serous Borderline Tumors and Low Grade Serous Carcinoma?  ... 
doi:10.1038/sj.modpathol.3800847 fatcat:6uxkcpw52baixdsl3fdaqt2m3m
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