Results 51 to 60 of about 45,444 (316)

Weighted Correlation Network Analysis (WGCNA) Applied to the Tomato Fruit Metabolome

PLoS ONE, 2011
Advances in "omics" technologies have revolutionized the collection of biological data. A matching revolution in our understanding of biological systems, however, will only be realized when similar advances are made in informatic analysis of the resulting "big data." Here, we compare the capabilities of three conventional and novel statistical ...
Matthew V DiLeo, Gary D Strahan, Meghan den Bakker, Owen A Hoekenga   +3 more
openaire   +4 more sources

Identification of potential biomarkers for endometrial carcinoma based on WGCNA

, 2022
Abstract Background Endometrial carcinoma (EC) is a group of malignant epithelial tumors occurring in the endometrium. With the increasing incidence of recent years, identifying the molecular mechanisms associated with endometrial carcinoma has become particularly important for the early diagnosis and treatment of cancer. Methods RNA-seq data
Lei Wang, Ying Ma, Zhe Liu, Yu Zhang, Xudong Liu, Yafan Wang, Lijun Zhao, Jinke Fan, Tao Peng, Rui Li, Yuxuan Chen, Xinqiang Song   +11 more
openaire   +1 more source

Identification of susceptibility modules and hub genes of osteoarthritis by WGCNA analysis

Frontiers in Genetics, 2022
Osteoarthritis (OA) is a major cause of pain, disability, and social burden in the elderly throughout the world. Although many studies focused on the molecular mechanism of OA, its etiology remains unclear. Therefore, more biomarkers need to be explored to help early diagnosis, clinical outcome measurement, and new therapeutic target development.
Yanchao Wang, Wenjun Zhou, Wenjun Zhou, Wenjun Zhou, Yan Chen, Dong He, Zhen Qin, Zhao Wang, Zhao Wang, Song Liu, Song Liu, Lei Zhou, Lei Zhou, Lei Zhou, Jianwen Su, Jianwen Su, Jianwen Su, Chi Zhang, Chi Zhang, Chi Zhang   +19 more
openaire   +3 more sources

Investigating the cell of origin and novel molecular targets in Merkel cell carcinoma: a historic misnomer

Molecular Oncology, EarlyView.
This study indicates that Merkel cell carcinoma (MCC) does not originate from Merkel cells, and identifies gene, protein & cellular expression of immune‐linked and neuroendocrine markers in primary and metastatic Merkel cell carcinoma (MCC) tumor samples, linked to Merkel cell polyomavirus (MCPyV) status, with enrichment of B‐cell and other immune cell
Richie Jeremian, Sriraam Sivachandran, Melissa Galati, Brandon Ramchatesingh, Hibo Rijal, Johnny Hanna, Elena Netchiporouk, May Chergui, Margaret Redpath, Samy Abou Setah, Ivan V. Litvinov   +10 more
wiley   +1 more source

Integrated genomics and proteomics define huntingtin CAG length-dependent networks in mice. [PDF]

, 2016
To gain insight into how mutant huntingtin (mHtt) CAG repeat length modifies Huntington's disease (HD) pathogenesis, we profiled mRNA in over 600 brain and peripheral tissue samples from HD knock-in mice with increasing CAG repeat lengths.
A Dobin, A Hodges, A Kuhn, A Pal, A Reiner, A Valencia, Andreas Tebbe, B Zhang, B Zhang, BM Bolstad, C Zuccato, CA Ross, Christoph Schaab, Daniel J Lavery, David Howland, DI Shirasaki, Doxa Chatzopoulou, DV Zaykin, EH Aylward, Eliana Marisa Ramos, ES Deneris, ES Lein, Fuying Gao, G Fishell, GA Smith, Giovanni Coppola, HT Orr, I Al-Ramahi, IS Seong, Ismael Al-Ramahi, J Cox, J Cox, J Labbadia, JA Miller, JC Jacobsen, JE Phillips, Jeffrey P Cantle, Jeffrey S Aaronson, JF Gusella, JF Gusella, Jim Rosinski, JM Dowen, JM Van Raamsdonk, JP Vonsattel, Juan Botas, K Becanovic, K Monahan, K Sharma, Karla El-Zein, LB Menalled, LB Menalled, LB Menalled, LS Kaltenbach, M Biagioli, M Heiman, M MACDONALD, M Mann, M Mielcarek, MA Pouladi, MC Oldham, MI Love, MK Lobo, MT Lin, N Wang, Nan Wang, P Giles, P Grange, P Langfelder, P Langfelder, P Langfelder, P Langfelder, P Langfelder, Peter Langfelder, PF Durrenberger, RC Gentleman, S Anders, S Horvath, S Toyoda, Sandeep Deverasetty, Seung Kwak, Steve Horvath, T Geiger, T Lu, WE Johnson, WV Chen, X Gu, X Gu, X William Yang, XH Lu, Xiao-Hong Lu, Y Benjamini, Y Guo, Y Shen, Y Wang, Yining Zhao   +94 more
core   +1 more source

ACT2.6: Global Gene Coexpression Network in Arabidopsis thaliana Using WGCNA

Genes
Background/Objectives: Genes with similar expression patterns across multiple samples are considered coexpressed, and they may participate in similar biological processes or pathways. Gene coexpression networks depict the degree of similarity between the expression profiles of all genes in a set of samples.
Vasileios L. Zogopoulos, Konstantinos Papadopoulos, Apostolos Malatras, Vassiliki A. Iconomidou, Ioannis Michalopoulos   +4 more
openaire   +3 more sources

Transcriptional network analysis of PTEN‐protein‐deficient prostate tumors reveals robust stromal reprogramming and signs of senescent paracrine communication

Molecular Oncology, EarlyView.
Combining PTEN protein assessment and transcriptomic profiling of prostate tumors, we uncovered a network enriched in senescence and extracellular matrix (ECM) programs associated with PTEN loss and conserved in a mouse model. We show that PTEN‐deficient cells trigger paracrine remodeling of the surrounding stroma and this information could help ...
Ivana Rondon‐Lorefice, Jose I. Lopez, Aitziber Ugalde‐Olano, Maite Zufiaurre, Ianire Astobiza, Natalia Martin‐Martin, Laura Bozal‐Basterra, Saioa Garcia‐Longarte, Amaia Zabala‐Letona, Sofia Rey, Aida Santos‐Martin, Miguel Unda, Ana Loizaga‐Iriarte, Mariona Graupera, Paolo Nuciforo, Arkaitz Carracedo, Isabel Mendizabal   +16 more
wiley   +1 more source

Fuzzy Forests: Extending Random Forest Feature Selection for Correlated, High-Dimensional Data

Journal of Statistical Software, 2019
In this paper we introduce fuzzy forests, a novel machine learning algorithm for ranking the importance of features in high-dimensional classification and regression problems. Fuzzy forests is specifically designed to provide relatively unbiased rankings
Daniel Conn, Tuck Ngun, Gang Li, Christina M. Ramirez   +3 more
doaj   +1 more source

ManiNetCluster: a novel manifold learning approach to reveal the functional links between gene networks. [PDF]

, 2019
BACKGROUND:The coordination of genomic functions is a critical and complex process across biological systems such as phenotypes or states (e.g., time, disease, organism, environmental perturbation).
Blaby, Ian K, Nguyen, Nam D, Wang, Daifeng   +2 more
core  

Tricks to translating TB transcriptomics. [PDF]

, 2015
Transcriptomics and other high-throughput methods are increasingly applied to questions relating to tuberculosis (TB) pathogenesis. Whole blood transcriptomics has repeatedly been applied to define correlates of TB risk and has produced new insight into ...
Coussens, AK, Deffur, A, Wilkinson, RJ
core   +1 more source