Results 121 to 130 of about 474,387 (314)

MultiGNN: A Graph Neural Network Framework for Inferring Gene Regulatory Networks from Single-Cell Multi-Omics Data

Computation
Gene regulatory networks (GRNs) describe the interactions between transcription factors (TFs) and their target genes, playing a crucial role in understanding gene functions and how cells regulate gene expression under different conditions.
Dongbo Liu, Hao Chen, Jianxin Wang, Yeru Wang   +3 more
doaj   +1 more source

Tumour–host interactions in Drosophila: mechanisms in the tumour micro‐ and macroenvironment

Molecular Oncology, EarlyView.
This review examines how tumour–host crosstalk takes place at multiple levels of biological organisation, from local cell competition and immune crosstalk to organism‐wide metabolic and physiological collapse. Here, we integrate findings from Drosophila melanogaster studies that reveal conserved mechanisms through which tumours hijack host systems to ...
José Teles‐Reis, Tor Erik Rusten
wiley   +1 more source

Subtype‐specific enhancer RNAs define transcriptional regulators and prognosis in breast cancers

Molecular Oncology, EarlyView.
This study employed machine learning methodologies to perform the subtype‐specific classification of RNA‐seq data sets, which are mapped on enhancers from TCGA‐derived breast cancer patients. Their integration with gene expression (referred to as ProxCReAM eRNAs) and chromatin accessibility profiles has the potential to identify lineage‐specific and ...
Aamena Y. Patel, Peyman Zarrineh, Nathnael T. Tuffa, Jigar H. Sheth, Sumitra Mohan, Mudassar Iqbal, Sankari Nagarajan   +6 more
wiley   +1 more source

Dynamics of molecular fluctuations in gene regulatory networks

, 2009
The components that are central to cellular processing are proteins, whose production is regulated by other proteins known as transcription factors. Proteins are products of genes that regulate the expression of one another, thereby forming large gene ...
Pakka, Vijayanarasimha Hindupur
core  

Temporal ChIP-on-chip reveals Biniou as a universal regulator of the visceral muscle transcriptional network [PDF]

, 2007
Smooth muscle plays a prominent role in many fundamental processes and diseases, yet our understanding of the transcriptional network regulating its development is very limited.
Astorga (Johansson), Jeanette, Jakobsen, Janus S, Astorga, Jeanette,, Carlsson, Peter,, Furlong, E. E., Furlong, Eileen E M, Carlsson, Peter, Gustafson, E. H., Jakobsen, J. S., Braun, M., Gustafson, E Hilary, Karzynski, M., Karzynski, Michal, Sandmann, T., Sandmann, Thomas, Braun, Martina   +15 more
core   +1 more source

Large-Scale Analysis of Drug Side Effects via Complex Regulatory Modules Composed of microRNAs, Transcription Factors and Gene Sets

Scientific Reports, 2017
Identifying the occurrence mechanism of drug-induced side effects (SEs) is critical for design of drug target and new drug development. The expression of genes in biological processes is regulated by transcription factors(TFs) and/or microRNAs.
Xiaodong Jia, Qing Jin, Xiangqiong Liu, Xiusen Bian, Yunfeng Wang, Lei Liu, Hongzhe Ma, Fujian Tan, Mingliang Gu, Xiujie Chen   +9 more
doaj   +1 more source

Network divergence analysis identifies adaptive gene modules and two orthogonal vulnerability axes in pancreatic cancer

Molecular Oncology, EarlyView.
Tumors contain diverse cellular states whose behavior is shaped by context‐dependent gene coordination. By comparing gene–gene relationships across biological contexts, we identify adaptive transcriptional modules that reorganize into distinct vulnerability axes.
Brian Nelson, Lyanne Delgado‐Coka, Natalia Marchenko, Luisa F. Escobar‐Hoyos, Kenneth R. Shroyer, Alisa Yurovsky, Trey Ideker, Gábor Balázsi, Thomas MacCarthy, Scott Powers   +9 more
wiley   +1 more source

Chaotic Motifs in Gene Regulatory Networks

PLoS ONE, 2012
Chaos should occur often in gene regulatory networks (GRNs) which have been widely described by nonlinear coupled ordinary differential equations, if their dimensions are no less than 3. It is therefore puzzling that chaos has never been reported in GRNs in nature and is also extremely rare in models of GRNs.
Zhaoyang Zhang, Weiming Ye, Yu Qian, Zhigang Zheng, Xuhui Huang, Gang Hu   +5 more
openaire   +4 more sources

Feedback control of pluripotency in embryonic stem cells: Signaling, transcription and epigenetics

Stem Cell Research, 2018
Embryonic stem cells (ESCs) can proliferate and self-renew, maintaining their pluripotency status in vitro for a long period of time. Pluripotent states of ESCs in vitro are supported by a network of signaling, transcriptional and epigenetic regulatory ...
Dmitri Papatsenko, Avinash Waghray, Ihor R. Lemischka   +2 more
doaj   +1 more source

EDNRB‐dependent endothelin signaling reduces proliferation and promotes proneural‐to‐mesenchymal transition in gliomas

Molecular Oncology, EarlyView.
Glioma cells mainly express the endothelin receptor EDNRB, while EDNRA is restricted to a perivascular tumor subpopulation. Endothelin signaling reduces glioma cell proliferation while promoting migration and a proneural‐to‐mesenchymal transition associated with poor prognosis. This pathway activates Ca2+, K+, ERK, and STAT3 signalings and is regulated
Donovan Pineau, Leonor Garcia, Hugo Arnold, Antonija Hanžek, Maialen Arrieta, Laurent R Gauthier, Christine Granotier‐Beckers, François D Boussin, Amaury Herbet, Marie Hautière, Valentin Asei‐Ceschino, Clémentin Jacques, Laura Brard, Thomas Harnois, Valérie Coronas, Bruno Constantin, Aurélien Chatelier, Jean Chemin, Serge Urbach, Martial Seveno, Szimonetta Hideg, Chantal Ripoll, Kasandra Aguilar‐Cázarez, Min Zheng, Guo‐Hao Huang, Sheng‐Qing Lv, Lei Zhang, Philippe Rondard, Laurent Prezeau, Jean‐Philippe Pin, Hugues Duffau, Luc Bauchet, Valérie Rigau, Franck Denat, Charles Truillet, Didier Boquet, Jean‐Philippe Hugnot   +36 more
wiley   +1 more source