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Comparisons of gene coexpression network modules in breast cancer and ovarian cancer

Shuqin Zhang
2018 BMC Systems Biology  
The objective of this study is to compare the coexpression network modules of both cancers, so as to infer the potential cancer-related modules.  ...  Methods: We applied the eigen-decomposition to the matrix that integrates the gene coexpression networks of both breast cancer and ovarian cancer.  ...  Availability of data and materials The level 3 gene expression data for breast cancer (BRCA) and ovarian cancer (OV) were downloaded from The Cancer Genome Atlas (TCGA).  ... 
doi:10.1186/s12918-018-0530-9 pmid:29671401 pmcid:PMC5907153 fatcat:xgb5ths5zzdazg6un6busn6sse

Small Molecule Wnt Pathway Modulators from Natural Sources: History, State of the Art and Perspectives

Artem Blagodatski, Antonina Klimenko, Lee Jia, Vladimir L. Katanaev
2020 Cells  
In this article, we provide an up-to-date overview of existing small molecule modulators of the Wnt pathway derived from natural products.  ...  In each part, we pay specific attention to the mechanisms of action of the natural products, to the models on which they were investigated, and to the potential of different taxa to yield bioactive molecules  ...  Speaking of the sources of NP as drug candidates, it is clear that plants, fungi and bacteria dominate.  ... 
doi:10.3390/cells9030589 pmid:32131438 pmcid:PMC7140537 fatcat:xv3tkfawqnhwfgaowkikrqr5na

Topology-driven analysis of protein-protein interaction networks detects functional genetic modules regulating reproductive capacity [article]

Tarun Kumar, Leo Blondel, Cassandra G. Extavour
2019 bioRxiv   pre-print
These modules predict involvement of previously uncharacterised genes with higher accuracy than the original candidate screen.  ...  Here, we use egg-producing structures of insect ovaries, called ovarioles, to deduce systems-level gene regulatory relationships from quantitative functional genetic analysis.  ...  Comprehensive identification of cell cycle-regulated genes of the 1383 yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol.  ... 
doi:10.1101/852897 fatcat:onytaulak5aodjixa3fl4jhzqq

Bioinformatic identification of key genes and analysis of prognostic values in clear cell renal cell carcinoma

Ting Luo, Xiaoyi Chen, Shufei Zeng, Baozhang Guan, Bo Hu, Yu Meng, Fanna Liu, Taksui Wong, Yongpin Lu, Chen Yun, Berthold Hocher, Lianghong Yin
2018 Oncology Letters  
The present study aimed to identify new key genes as potential biomarkers for the diagnosis, prognosis or targeted therapy of clear cell renal cell carcinoma (ccRCC).  ...  Seventeen hub genes and one significant module were filtered out and selected from the PPI network. The differential expression of hub genes was verified in TCGA patients.  ...  Clear cell renal cell carcinoma (ccRCC) is the most common (~75%), lethal subtype of RCC (3) .  ... 
doi:10.3892/ol.2018.8842 pmid:30008862 pmcid:PMC6036467 fatcat:jjg5ztw5nzg63j6mjd4xcuhzre

Pentraxin 3 is a diagnostic and prognostic marker for ovarian epithelial cancer patients based on comprehensive bioinformatics and experiments

Xiaoying Chang, Dan Li, Chang Liu, Zhe Zhang, Tao Wang
2021 Cancer Cell International  
Further application of WGCNA (weighted gene coexpression network analysis) identified 15 gene modules, with the purple module showing the highest correlation with ovarian epithelial cancer.  ...  Twenty-five genes were shared between the purple module and DEGs, 13 genes were related to the prognosis of ovarian epithelial cancer patients, and the PTX3 gene had the highest hazardous risk (HR) value  ...  In ovarian clear-cell carcinoma cells, KIF20A may significantly promote the proliferation of ovarian clear-cell carcinoma cells [24] .  ... 
doi:10.1186/s12935-021-01854-7 pmid:33952272 fatcat:clnpyglsxrf7jdtu3odm4r26o4

BRCA1 directly modulates gene expression required for estrogen biosynthesis: a possible mechanism of tissue-specific tumor suppression

Y Hu, S Aiyar, W Yue, S Ghosh, Y Lu, R Li
2005 Breast Cancer Research  
cells under control of the MMTV promoter/enhancer increases the incidence of mammary carcinomas.  ...  Again, to accomplish complete knockout of the type II TGF-β receptor gene in mammary stromal cells, FSP1-Cre and Tgfbr2 flox/flox mice were crossed to attain Tgfbr2 fspKO mice.  ...  P6.01 Identification of drug targets for the treatment of To identify potential targets, the gene expression data for approximately 1500 drug targets were examined across a breast tumor data set of 150  ... 
doi:10.1186/bcr1115 fatcat:k4hiwtpgyrhfzn3kqwhfwkvyma

Mast Cell Infiltration in Human Brain Metastases Modulates the Microenvironment and Contributes to the Metastatic Potential

Ananya Roy, Sylwia Libard, Holger Weishaupt, Ida Gustavsson, Lene Uhrbom, Göran Hesselager, Fredrik J. Swartling, Fredrik Pontén, Irina Alafuzoff, Elena Tchougounova
2017 Frontiers in Oncology  
Our findings indicate MCs' capability of modulating gene expression in BM cells and suggest that MCs can serve as a new target for drug development against metastases in the brain.  ...  Gene set enrichment analyses indicate increased expression of signal transduction and transmembrane proteins related genes in the cocultured BM cells.  ...  The authors wish to thank Marianne Kastemar at the Department of Immunology, Genetics and Pathology for technical assistance with cell culturing.  ... 
doi:10.3389/fonc.2017.00115 pmid:28626727 pmcid:PMC5454042 fatcat:bcflezqoofejhn46jsoz6gteuq

Ovarian Cancer: Biomarkers and Targeted Therapy

Mihaela Raluca Radu, Alina Prădatu, Florentina Duică, Romeo Micu, Sanda Maria Creţoiu, Nicolae Suciu, Dragoş Creţoiu, Valentin Nicolae Varlas, Viorica Elena Rădoi
2021 Biomedicines  
the status, progression, and efficacy of the drug therapy in this type of disorder.  ...  Early detection of the disorder is one of the most important steps that facilitate a favorable prognosis and a good response to medical therapy for the patients.  ...  Informed Consent Statement: Not applicable. Data Availability Statement: Not applicable. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/biomedicines9060693 fatcat:qbyxhu6cwbgabe7s5skcgjawm4

Multiple Alternative Splicing Markers for Ovarian Cancer

R. Klinck, A. Bramard, L. Inkel, G. Dufresne-Martin, J. Gervais-Bird, R. Madden, E. R. Paquet, C. Koh, J. P. Venables, P. Prinos, M. Jilaveanu-Pelmus, R. Wellinger (+3 others)
2008 Cancer Research  
High-volume identification of cancer-associated splice forms by the LISA paves the way for the use of alternative splicing profiling to diagnose subtypes of cancer.  ...  Intense efforts are currently being directed toward profiling gene expression in the hope of developing better cancer markers and identifying potential drug targets.  ...  Using this integrated bioinformatics/robotics infrastructure, we have comprehensively analyzed alternative splicing in a set of 600 genes representing many confirmed cancer-associated genes or <4% of the  ... 
doi:10.1158/0008-5472.can-07-2580 pmid:18245464 fatcat:4d56czkfljfkxn5rle3ltcc6wy

The Role of microRNAs in the Tumorigenesis of Ovarian Cancer

Gianpiero Di Leva, Carlo M. Croce
2013 Frontiers in Oncology  
In this review, we discuss the current data concerning the accumulating evidence of the modulated expression of miRNAs in EOC, their role in diagnosis, prognosis, and prediction of response to therapy.  ...  There have been major advances in the understanding of the cellular and molecular biology of this human malignancy, however the survival rate of women with EOC has changed little since platinum-based-treatment  ...  resensitize to the apoptotic role of the drugs the ovarian malignant cells.  ... 
doi:10.3389/fonc.2013.00153 pmid:23785667 pmcid:PMC3682193 fatcat:sp3rcowhbndxhmpeqmidonz4qy

Hereditary Ovarian Cancer: Not OnlyBRCA1 and 2 Genes

Angela Toss, Chiara Tomasello, Elisabetta Razzaboni, Giannina Contu, Giovanni Grandi, Angelo Cagnacci, Russell J. Schilder, Laura Cortesi
2015 BioMed Research International  
The recent development and implementation of next-generation sequencing technologies have provided the opportunity to simultaneously analyze multiple cancer susceptibility genes, reduce the delay and costs  ...  Particularly, the identification of mutations in ovarian cancer susceptibility genes in healthy women may result in a more personalized cancer risk management with tailored clinical and radiological surveillance  ...  Conflict of Interests The authors declare that there is no conflict of interests regarding the publication of this paper.  ... 
doi:10.1155/2015/341723 pmid:26075229 pmcid:PMC4449870 fatcat:vllunaarivekpgvruazqhoj3tm

Therapeutic Perspectives on the Modulation of G-Protein Coupled Estrogen Receptor, GPER, Function

Milad Rouhimoghadam, Anh S. Lu, Aliasger K. Salem, Edward J. Filardo
2020 Frontiers in Endocrinology  
Restoration of estrogen physiology by modulating estrogen bioavailability or receptor activity is an effective approach for treating these pathological conditions.  ...  Here, we review current forms of estrogen therapy and the implications that GPER holds for these therapies.  ...  ACKNOWLEDGMENTS The authors appreciate senior guidance and constructive comments provided by Drs. Ronald Weigel and George Weiner.  ... 
doi:10.3389/fendo.2020.591217 pmid:33329395 pmcid:PMC7719807 fatcat:yxjkbao6t5hbvf33qqffr437ea

Computational analysis of data from a genome-wide screening identifies new PARP1 functional interactors as potential therapeutic targets

Samuele Lodovichi, Alberto Mercatanti, Tiziana Cervelli, Alvaro Galli
2019 OncoTarget  
We identified 12 genes belonging to PARP1related pathways. We decided to further validate RIT1, INCENP and PSTA1 in MCF7 breast cancer cells.  ...  Furthermore, downregulation of RIT1, INCENP and PSAT1 affected olaparib sensitivity of MCF7 cells. Our study identified candidate genes that could have an effect on PARP inhibition therapy.  ...  Moreover, the discovery of different interactors could lead to a more and efficient personalized therapy that may reduce development of resistance and expand therapy application of these drugs.  ... 
doi:10.18632/oncotarget.26812 fatcat:k56zpi5w45bivpctgxphcl7tpe

Ovarian cancer plasticity and epigenomics in the acquisition of a stem-like phenotype

Nicholas B Berry, Sharmila A Bapat
2008 Journal of Ovarian Research  
of bioinformatics to handle the complexity of the cancer epigenome and the various networks that coordinate disease initiation and progression.  ...  The similarity of gene expression between ovarian cancer cells and the stem-like ovarian cancer initiating cells (OCIC) are surprisingly also correlated with epigenetic mechanisms of gene regulation in  ...  Acknowledgements We wish to express our sincere thanks to Dr. G.C. Mishra, Director, National Center for Cell  ... 
doi:10.1186/1757-2215-1-8 pmid:19025622 pmcid:PMC2612659 fatcat:xmgfudjtizehni77udvluws7rm

Deciphering the Long Non-Coding RNAs and MicroRNAs Coregulation Networks in Ovarian Cancer Development: An Overview

César López-Camarillo, Erika Ruíz-García, Yarely M. Salinas-Vera, Macrina B. Silva-Cázares, Olga N. Hernández-de la Cruz, Laurence A. Marchat, Dolores Gallardo-Rincón
2021 Cells  
In particular, microRNAs and long non-coding RNAs (lncRNAs) are a new class of small RNAs transcribed from the genome, which modulate the expression of specific genes at transcriptional and posttranscriptional  ...  In cancer cells, the miRNAs and lncRNAs interactions with its target genes and functional pathways are deregulated as a consequence of epigenetic and genetic alterations occurring during tumorigenesis.  ...  Conflicts of Interest: The authors declare that they have no conflicts of interests.  ... 
doi:10.3390/cells10061407 pmid:34204094 pmcid:PMC8227049 fatcat:duqfufhvg5aybaaxm5fcxc57zq
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