Biostatistical approaches for the reconstruction of gene co-expression networks based on transcriptomic data

L López-Kleine, L Leal, C López - Briefings in functional …, 2013 - academic.oup.com
Techniques in molecular biology have permitted the gathering of an extremely large amount
of information relating organisms and their genes. The current challenge is assigning a …

A survey and comparative study of statistical tests for identifying differential expression from microarray data

S Bandyopadhyay, S Mallik… - … /ACM transactions on …, 2013 - ieeexplore.ieee.org
DNA microarray is a powerful technology that can simultaneously determine the levels of
thousands of transcripts (generated, for example, from genes/miRNAs) across different …

A novel fuzzy similarity measure and prevalence estimation approach for similarity profiled temporal association pattern mining

V Radhakrishna, SA Aljawarneh, PV Kumar… - Future generation …, 2018 - Elsevier
Abstract Data generated from Sensors, IoT environment and many real time applications is
mainly spatial, temporal, or spatio-temporal. Some of them include data generated from …

Natural cubic spline regression modeling followed by dynamic network reconstruction for the identification of radiation-sensitivity gene association networks from time …

A Michna, H Braselmann, M Selmansberger, A Dietz… - PloS one, 2016 - journals.plos.org
Gene expression time-course experiments allow to study the dynamics of transcriptomic
changes in cells exposed to different stimuli. However, most approaches for the …

Functional clustering of time series gene expression data by Granger causality

A Fujita, P Severino, K Kojima, JR Sato, AG Patriota… - BMC systems …, 2012 - Springer
Background A common approach for time series gene expression data analysis includes the
clustering of genes with similar expression patterns throughout time. Clustered gene …

Shifting-and-scaling correlation based biclustering algorithm

HA Ahmed, P Mahanta… - … /ACM transactions on …, 2014 - ieeexplore.ieee.org
The existence of various types of correlations among the expressions of a group of
biologically significant genes poses challenges in developing effective methods of gene …

Comprehensive analysis of microrna–messenger rna from white yak testis reveals the differentially expressed molecules involved in development and reproduction

Q Zhang, Q Wang, Y Zhang, S Cheng, J Hu… - International journal of …, 2018 - mdpi.com
Testis development is a vital and tightly regulated process in mammals. Understanding the
biological mechanisms underlying testis development will benefit the animal reproduction …

Construction and comparison of gene co-expression networks shows complex plant immune responses

LG Leal, C Lopez, L Lopez-Kleine - PeerJ, 2014 - peerj.com
Gene co-expression networks (GCNs) are graphic representations that depict the
coordinated transcription of genes in response to certain stimuli. GCNs provide functional …

Studying the differential co-expression of microRNAs reveals significant role of white matter in early Alzheimer's progression

M Bhattacharyya, S Bandyopadhyay - Molecular BioSystems, 2013 - pubs.rsc.org
MicroRNAs (miRNAs) are a class of short non-coding RNAs, which show tissue-specific
regulatory activity on genes. Expression profiling of miRNAs is an important step for …

DTFP-Growth: Dynamic Threshold-Based FP-Growth Rule Mining Algorithm Through Integrating Gene Expression, Methylation, and Protein–Protein Interaction …

S Mallik, T Bhadra, A Mukherji - IEEE transactions on …, 2018 - ieeexplore.ieee.org
Association rule mining is an important technique for identifying interesting relationships
between gene pairs in a biological data set. Earlier methods basically work for a single …