scholarly journals Efficiently Enumerating All Connected Induced Subgraphs of a Large Molecular Network

2014 ◽  
pp. 171-182 ◽  
Author(s):  
Sean Maxwell ◽  
Mark R. Chance ◽  
Mehmet Koyutürk
Keyword(s):  
Molecular Network ◽  
Induced Subgraphs

scholarly journals Inhibitory effect of sodium butyrate on colorectal cancer cells and construction of the related molecular network

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yang Xi ◽  
Zhuang Jing ◽  
Wu Wei ◽  
Zhang Chun ◽  
Qi Quan ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Sodium Butyrate ◽  
Molecular Network ◽  
Differentially Expressed ◽  
Cell Counting ◽  
Molecular Networks ◽  
Ppi Network ◽  
Invasion And Metastasis ◽  
Cerna Network ◽  
Proliferation Ability

Abstract Background Sodium butyrate (NaB) is produced through the fermentation of dietary fiber that is not absorbed and digested by the small intestine. Purpose Here, we aimed to investigate the effects of NaB on the proliferation, invasion, and metastasis of CRC cells and their potential underlying molecular mechanism(s). Methods The cell counting kit-8 (CCK-8) assay and EdU assay were used to detect cell proliferation ability, flow cytometry was used to investigate the induction of apoptosis and cell cycle progression, and the scratch-wound healing and transwell assays were used to evaluate cell migration and invasion, respectively. The human CRC genome information for tissues and CRC cells treated with NaB obtained from the NCBI GEO database was reannotated and used for differential RNA analysis. Functional and pathway enrichment analyses were performed for differentially expressed lncRNAs and mRNAs. A protein-protein interaction (PPI) network for the hub genes was constructed using the Cytoscape software. Targeted miRNAs were predicted based on the lnCeDB database, and a ceRNA network was constructed using the Cytoscape software. The Kaplan-Meier method was used to analyze patient prognosis using the clinical information and exon-seq data for CRC obtained from the Broad Institute’s GDAC Firehose platform. Results NaB decreased the proliferation ability of CRC cells in a dose- and time-dependent manner. The number of apoptotic CRC cells increased with the increase in NaB concentrations, and NaB induced a G1 phase block in CRC cells. Moreover, NaB suppressed the migratory and invasive capabilities of CRC cells. There were 666 differentially expressed mRNAs and 30 differentially expressed lncRNAs involved in the CRC inhibition by NaB. The PPI network and ceRNA network were constructed based on the differentially expressed mRNAs and lncRNAs. Three differentially expressed mRNAs, including HMGA2, LOXL2, and ST7, were significantly correlated with the prognosis of CRC. Conclusion NaB induces the apoptosis and inhibition of CRC cell proliferation, invasion, and metastasis by modulating complex molecular networks. RNA prediction and molecular network construction need to be the focus of further research in this direction.

scholarly journals Minimal classes of graphs of unbounded clique-width defined by finitely many forbidden induced subgraphs

2021 ◽  
Vol 295 ◽  
pp. 57-69
Author(s):  
A. Atminas ◽  
R. Brignall ◽  
V. Lozin ◽  
J. Stacho
Keyword(s):  
Induced Subgraphs ◽  
Forbidden Induced Subgraphs

scholarly journals Constituents of Chamaecrista diphylla (L.) Greene Leaves with Potent Antioxidant Capacity: A Feature-Based Molecular Network Dereplication Approach

Pharmaceutics ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 681
Author(s):  
Paulo Gomes ◽  
Luis Quirós-Guerrero ◽  
Abraão Muribeca ◽  
José Reis ◽  
Sônia Pamplona ◽  
...  
Keyword(s):  
Antioxidant Capacity ◽  
Ethanolic Extract ◽  
Oxygen Radical ◽  
Molecular Network ◽  
Antioxidant Compounds ◽  
Herbaceous Plant ◽  
Network Approach ◽  
Feature Based ◽  
Promising Source ◽  
First Time

Chamaecrista diphylla (L.) Greene (Fabaceae/Caesalpiniaceae) is a herbaceous plant that is widely distributed throughout the Americas. Plants from this genus have been used in traditional medicine as a laxative, to heal wounds, and to treat ulcers, snake and scorpion bites. In the present study, we investigated the chemical composition of Chamaecrista diphylla leaves through a mass spectrometry molecular network approach. The oxygen radical absorbance capacity (ORAC) for the ethanolic extract, enriched fractions and isolated compounds was assessed. Overall, thirty-five compounds were annotated for the first time in C. diphylla. Thirty-two of them were reported for the first time in the genus. The isolated compounds 9, 12, 24 and 33 showed an excellent antioxidant capacity, superior to the extract and enriched fractions. Bond dissociation energy calculations were performed to explain and sustain the antioxidant capacity found. According to our results, the leaves of C. diphylla represent a promising source of potent antioxidant compounds.

Excluding induced subgraphs: Critical graphs

2010 ◽  
Vol 38 (1-2) ◽  
pp. 100-120 ◽  
Author(s):  
József Balogh ◽  
Jane Butterfield
Keyword(s):  
Induced Subgraphs ◽  
Critical Graphs

Fungi population metabolomics and molecular network study reveal novel biomarkers for early detection of aflatoxigenic Aspergillus species

2022 ◽  
Vol 424 ◽  
pp. 127173
Author(s):  
Huali Xie ◽  
Xiupin Wang ◽  
Justin JJ van der Hooft ◽  
Marnix H. Medema ◽  
Zhi-Yuan Chen ◽  
...  
Keyword(s):  
Early Detection ◽  
Molecular Network ◽  
Aspergillus Species ◽  
Novel Biomarkers

scholarly journals Bifurcation and Singularity Analysis of a Molecular Network for the Induction of Long-Term Memory

2006 ◽  
Vol 90 (7) ◽  
pp. 2309-2325 ◽  
Author(s):  
Hao Song ◽  
Paul Smolen ◽  
Evyatar Av-Ron ◽  
Douglas A. Baxter ◽  
John H. Byrne
Keyword(s):  
Singularity Analysis ◽  
Molecular Network ◽  
Long Term Memory ◽  
Term Memory

scholarly journals Degree and neighborhood intersection conditions restricted to induced subgraphs ensuring Hamiltonicity of graphs

2014 ◽  
Vol 06 (03) ◽  
pp. 1450043
Author(s):  
Bo Ning ◽  
Shenggui Zhang ◽  
Bing Chen
Keyword(s):  
Hamilton Cycles ◽  
Induced Subgraphs ◽  
Degree Sum ◽  
Degree Condition

Let claw be the graph K1,3. A graph G on n ≥ 3 vertices is called o-heavy if each induced claw of G has a pair of end-vertices with degree sum at least n, and called 1-heavy if at least one end-vertex of each induced claw of G has degree at least n/2. In this note, we show that every 2-connected o-heavy or 3-connected 1-heavy graph is Hamiltonian if we restrict Fan-type degree condition or neighborhood intersection condition to certain pairs of vertices in some small induced subgraphs of the graph. Our results improve or extend previous results of Broersma et al., Chen et al., Fan, Goodman and Hedetniemi, Gould and Jacobson, and Shi on the existence of Hamilton cycles in graphs.

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