When is hub gene selection better than standard meta-analysis?

P Langfelder, PS Mischel, S Horvath - PloS one, 2013 - journals.plos.org
Since hub nodes have been found to play important roles in many networks, highly
connected hub genes are expected to play an important role in biology as well. However …

Enhanced construction of gene regulatory networks using hub gene information

D Yu, J Lim, X Wang, F Liang, G Xiao - BMC bioinformatics, 2017 - Springer
Background Gene regulatory networks reveal how genes work together to carry out their
biological functions. Reconstructions of gene networks from gene expression data greatly …

Feature selection with the Fisher score followed by the Maximal Clique Centrality algorithm can accurately identify the hub genes of hepatocellular carcinoma

C Li, J Xu - Scientific reports, 2019 - nature.com
This study aimed to select the feature genes of hepatocellular carcinoma (HCC) with the
Fisher score algorithm and to identify hub genes with the Maximal Clique Centrality (MCC) …

Hubba: hub objects analyzer—a framework of interactome hubs identification for network biology

CY Lin, CH Chin, HH Wu, SH Chen… - Nucleic acids …, 2008 - academic.oup.com
One major task in the post-genome era is to reconstruct proteomic and genomic interacting
networks using high-throughput experiment data. To identify essential nodes/hubs in these …

Screening hub genes as prognostic biomarkers of hepatocellular carcinoma by bioinformatics analysis

Z Zhou, Y Li, H Hao, Y Wang, Z Zhou… - Cell …, 2019 - journals.sagepub.com
Hepatocellular carcinoma (HCC) is a widespread, common type of cancer in Asian
countries, and the need for biomarker-matched molecularly targeted therapy for HCC has …

RefFinder: a web-based tool for comprehensively analyzing and identifying reference genes

F Xie, J Wang, B Zhang - Functional & Integrative Genomics, 2023 - Springer
Although many genes may serve as reference genes, they may cause different expression
patterns by selecting different reference genes because no single gene is expressed …

A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide

JD Wren - Bioinformatics, 2009 - academic.oup.com
Abstract Motivation: Approximately 9334 (37%) of Human genes have no publications
documenting their function and, for those that are published, the number of publications per …

Predicting hub genes associated with cervical cancer through gene co-expression networks

SP Deng, L Zhu, DS Huang - IEEE/ACM Transactions on …, 2015 - ieeexplore.ieee.org
Cervical cancer is the third most common malignancy in women worldwide. It remains a
leading cause of cancer-related death for women in developing countries. In order to …

SWIM: a computational tool to unveiling crucial nodes in complex biological networks

P Paci, T Colombo, G Fiscon, A Gurtner, G Pavesi… - Scientific reports, 2017 - nature.com
SWItchMiner (SWIM) is a wizard-like software implementation of a procedure, previously
described, able to extract information contained in complex networks. Specifically, SWIM …

A comprehensive evaluation of module detection methods for gene expression data

W Saelens, R Cannoodt, Y Saeys - Nature communications, 2018 - nature.com
A critical step in the analysis of large genome-wide gene expression datasets is the use of
module detection methods to group genes into co-expression modules. Because of …