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Fuzzy logic based approaches for gene regulatory network inference [article]

Khalid Raza
2018 arXiv   pre-print
Gene regulatory network (GRN) is a gene-gene interaction network which plays pivotal role in understanding gene regulation process and disease studies.  ...  In this paper, we present a consolidated review on fuzzy logic and its hybrid approaches for GRNI developed during last two decades.  ...  Brock et al. (2009b) stated that fuzzy logic and related techniques can be applied as a screening tool for GRN detection.  ... 
arXiv:1804.10775v1 fatcat:ct4yxzdq45ebdobxdsuwb3zlmy

A Knowledge-guided Mechanistic Model of Synthetic Lethality in the HCT116 Vorinostat-resistant Colon Cancer Xenograft Model Cell-line [article]

Paul Aiyetan
2021 bioRxiv   pre-print
We employed a knowledege-guided fuzzy logic regulatory inference method to elucidate mechanistic relationships. We validated inferred regulatory models in independent datasets.  ...  Reasoning that significant regulatory network genes are likely implicated in the clinical course of colorectal cancer, we show that the identified key regulatory network genes' expression profile are able  ...  Acknowledgements A special thanks to Dr. Iosif Vaisman, Dr. Dmitri Klimov, and Dr. Saleet Jafri for their advises on the greater body of work presented here.  ... 
doi:10.1101/2021.06.22.449530 fatcat:adcanrahajcpzpstgso4enqax4

Computational Modeling and Reverse Engineering to Reveal Dominant Regulatory Interactions Controlling Osteochondral Differentiation: Potential for Regenerative Medicine

Raphaelle Lesage, Johan Kerkhofs, Liesbet Geris
2018 Frontiers in Bioengineering and Biotechnology  
Particular attention is paid to an in-house developed example of gene regulatory network modeling of growth plate chondrocyte differentiation as all the aforementioned steps can be illustrated.  ...  Computer modeling provides a tool to simulate this intricate interplay from a network perspective.  ...  For explicit cases of application see sections Current Computational Models as Predictive Tools for Cell Differentiation and Intracellular Regulatory Network Models of Growth Plate Cells.  ... 
doi:10.3389/fbioe.2018.00165 pmid:30483498 pmcid:PMC6243751 fatcat:6mcrreicojewdk4nyr6pljmimy

Pathway Retrieval for Transcriptome Analysis using Fuzzy Filtering Technique andWeb Service

Kyung-Mi Lee, Keon-Myung Lee
2012 International Journal of Fuzzy Logic and Intelligent Systems  
The tool accepts a transcriptome data set, and then selects and categorizes some of genes into four classes using a fuzzy filtering technique where classes are defined by membership functions.  ...  It collects and edits the pathway maps related to those selected genes without analyst' intervention.  ...  International Journal of Fuzzy Logic and Intelligent Systems, vol. 12, no. 2, June 2012 This paper presents a bioinformatics tool developed to take care of all the burdensome tasks mentioned above for  ... 
doi:10.5391/ijfis.2012.12.2.167 fatcat:pzntxxvjzfgqxasx7jvmtwt7eu

Pathway and network analysis of cancer genomes

2015 Nature Methods  
This was extended to fuzzy logic 61 that relaxes the rules of gene interactions and allows for biological noise and uncertainty.  ...  Other methods integrate gene expression and CNA data to identify cancer driver genes and downstream regulatory networks.  ...  competinG Financial interests The authors declare no competing financial interests. reprints and permissions information is available online at http://www.nature. com/reprints/index.html.  ... 
doi:10.1038/nmeth.3440 pmid:26125594 pmcid:PMC4717906 fatcat:qxeg5bsmufdubboiqdp2bfn2eu

Utilizing logical relationships in genomic data to decipher cellular processes

Peter M. Bowers, Brian D. O'Connor, Shawn J. Cokus, Einat Sprinzak, Todd O. Yeates, David Eisenberg
2005 The FEBS Journal  
Utilizing logical relationships in genomic data FEBS Journal 272 (2005) 5110-5118 ª 2005 FEBS 5117 Utilizing logical relationships in genomic data P. M. Bowers et al.  ...  Utilizing logical relationships in genomic data FEBS Journal 272 (2005) 5110-5118 ª 2005 FEBS P. M. Bowers et al.  ...  Fig. 2 . 2 Microarray experiments for 85 glioma samples were used in the logic analysis method to detect relationships in triplets of genes and phenotypes combined with one of eight logical operators.  ... 
doi:10.1111/j.1742-4658.2005.04946.x pmid:16218945 fatcat:dxk6obh5jjahfjvmqhxm7hmpve

Building with a scaffold: emerging strategies for high- to low-level cellular modeling

Trey Ideker, Douglas Lauffenburger
2003 Trends in Biotechnology  
An important new paradigm for cellular modeling involves building a comprehensive scaffold of molecular interactions and then mining this scaffold to reveal a hierarchy of signaling, regulatory and metabolic  ...  Pathway maps can be extracted from the scaffold using 'high-level' computational models, which identify the key components, interactions and influences required for more detailed 'low-level' models.  ...  Doyle and O. Ozier for inspiring discussions and for very helpful comments on the manuscript.  ... 
doi:10.1016/s0167-7799(03)00115-x pmid:12788545 fatcat:anguqrphzfa7pkbfvn5mf6mf7q

Breast Cancer Statistics and Prediction Methodology: A Systematic Review and Analysis

Ashutosh Kumar Dubey, Umesh Gupta, Sonal Jain
2015 Asian Pacific Journal of Cancer Prevention  
Breast cancer is a menacing cancer, primarily affecting women. Continuous research is going on for detecting breast cancer in the early stage as the possibility of cure in early stages is bright.  ...  It provides a strong bridge in improving the classification and detection accuracy of breast cancer data.  ...  The garner logic were go by trained network. It is 0.9 for malignant, 0.5 for benign and 0.1 for normal images.  ... 
doi:10.7314/apjcp.2015.16.10.4237 fatcat:n3iddqbtsverhikvu4betrixaa

Network Medicine: New Paradigm in the -Omics Era

Nancy Lan Guo
2011 Anatomy & Physiology  
The synchronous dynamics of a Boolean network can be captured by a Petri net [152] , which is a non-deterministic model widely used for detecting active pathways and state cycles [153] and for analyzing  ...  Another model, module networks, infers the regulation logic of gene modules as a decision tree, given gene expression data [159] . The Boolean implication networks presented by Sahoo et al.  ... 
doi:10.4172/2161-0940.1000e106 pmid:24634802 pmcid:PMC3951174 fatcat:q5zyxa4rizchzpxe7i6kzlfj5e

TeaCoN: a database of gene co-expression network for tea plant (Camellia sinensis)

Rui Zhang, Yong Ma, Xiaoyi Hu, Ying Chen, Xiaolong He, Ping Wang, Qi Chen, Chi-Tang Ho, Xiaochun Wan, Youhua Zhang, Shihua Zhang
2020 BMC Genomics  
The TeaCoN project can serve as a beneficial platform for candidate gene screening and functional exploration of important agronomical traits in tea plant.  ...  However, only a small fraction of tea genes (especially for those metabolite-related genes) have been functionally characterized to date.  ...  QC, CH, and XW provided scientific suggestions and criticisms for improving the manuscript and website. YZ and SZ supervised the whole project and wrote the manuscript.  ... 
doi:10.1186/s12864-020-06839-w pmid:32620074 fatcat:khbplk22wfcehfe7r5w2ovrqhy

WGCNA: an R package for weighted correlation network analysis

Peter Langfelder, Steve Horvath
2008 BMC Bioinformatics  
For example, weighted gene co-expression network analysis is a systems biology method for describing the correlation patterns among genes across microarray samples.  ...  Correlation networks facilitate network based gene screening methods that can be used to identify candidate biomarkers or therapeutic targets.  ...  Lin Wang for helpful discussions and suggestions.  ... 
doi:10.1186/1471-2105-9-559 pmid:19114008 pmcid:PMC2631488 fatcat:wbkhvqxm2napppgmaxin66upgm

Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis

Yingshu Li, Yongjie Liu, Hang Yang, Ting Zhang, Kiyoshi Naruse, Qiang Tu
2020 Genome Research  
A high-quality genome sequence and a variety of genetic tools are available for this model organism.  ...  With the expression dynamics of genes and accessibility dynamics of cis-regulatory elements, we investigated isoform switching, regulatory logic between accessible elements and genes during embryogenesis  ...  Yunhao Wang and Xiu-Jie Wang (Institute of Genetics and Developmental Biology) for helpful suggestions regarding the PacBio data analysis, Ms. Hui Hu and Dr.  ... 
doi:10.1101/gr.258871.119 pmid:32591361 pmcid:PMC7370878 fatcat:hy4vphjqxrfmtc5gkodypkgw7q

Bioinformatics Accelerates the Major Tetrad: A Real Boost for the Pharmaceutical Industry

Tapan Behl, Ishnoor Kaur, Aayush Sehgal, Sukhbir Singh, Saurabh Bhatia, Ahmed Al-Harrasi, Gokhan Zengin, Elena Emilia Babes, Ciprian Brisc, Manuela Stoicescu, Mirela Marioara Toma, Cristian Sava (+1 others)
2021 International Journal of Molecular Sciences  
dimensions of healthcare and integrating computing tools in drug innovation, facilitating prevention, detection/more accurate diagnosis, and treatment of disorders, while saving time and money.  ...  , a personalized approach, and drug repositioning were considered together with translational medicine.  ...  Acknowledgments: The authors would like to thank Chitkara College of Pharmacy, Chitkara University, Punjab, India for providing the various resources for completion of the article and University of Oradea  ... 
doi:10.3390/ijms22126184 pmid:34201152 pmcid:PMC8227524 fatcat:foyvjk4asjfozhj2khewmnwf5q

Formal concept analysis for knowledge discovery from biological data

Khalid Raza
2017 International Journal of Data Mining and Bioinformatics  
, gene expression clustering, finding genes in gene regulatory networks, enzyme/protein classifications, binding site classifications, and so on.  ...  It also presents a list of FCA-based software tools applied in biological domain and covers the challenges faced so far.  ...  Identifying genes of gene regulatory networks Gene regulatory networks (GRNs) are the systematic biological networks describing interaction among set of genes in the form of a graph, where node represents  ... 
doi:10.1504/ijdmb.2017.10009312 fatcat:wdopyvkr4jh63loxlsv6z6dmie

The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation

E. Wingender
2008 Briefings in Bioinformatics  
Since its beginning as a data collection more than 20 years ago, the TRANSFAC project underwent an evolution to become the basis for a complex platform for the description and analysis of gene regulatory  ...  events and networks.  ...  We, therefore, offer this database as a platform for related data that have emerged from systematic screening studies.  ... 
doi:10.1093/bib/bbn016 pmid:18436575 fatcat:5umimjlklvfx3nuuchv5gpkuoa
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