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- person_outline Kwon Y.K.
Publication for NetDS
Unraveling a tumor type specific regulatory core underlying E2F1 mediated epithelial mesenchymal transition to predict receptor protein signatures
[…] overall organization of the network (Supplementary Table ; Supplementary Fig. ). (ii) Network motif identification: Feedback loops from the E2F1 interaction map were identified using Cytoscape plugin NetDS (v3.0). For the identification of feedback loops, we set the loop length to three nodes (see “Discussion” section for detail). (iii) Motif ranking: To identify the most important motifs with res […]
Identification of miRNA mRNA Modules in Colorectal Cancer Using Rough Hypercuboid Based Supervised Clustering
[…] sents the extended network.The final version of the network was further analyzed to identify regulatory motifs like feedback (FBLs) and feedforward loops (FFLs), with the help of the Cytoscape plugin NetDS. The transcription factors and miRNAs are responsible for the combinatorial regulation of gene expression at transcription level and post-transcription level, respectively. The network shown in […]
Analysis of microRNA and Gene Expression Profiles in Multiple Sclerosis: Integrating Interaction Data to Uncover Regulatory Mechanisms
[…] eir targets, unless otherwise indicated in TransmiR. The gene-based network was created in a similar fashion. The networks were constructed and visualized using Cytoscape (version 3.2.0). We employed NetDS, a plugin for Cytoscape, to uncover FFLs and FBLs that contribute to the complexity of the regulatory networks in MS. The Cytoscape session files are available from the corresponding authors upo […]
PANET: A GPU Based Tool for Fast Parallel Analysis of Robustness Dynamics and Feed Forward/Feedback Loop Structures in Large Scale Biological Networks
[…] he robustness , and the coherent FFLs can be considered as a design principle of human signaling networks that improve network robustness against update-rule perturbations .Inspired by those studies, NetDS, a Cytoscape plugin, was recently developed to analyze the robustness-related dynamics and FFL/FBL structures of networks . However, there were some significant limitations with regard to fully […]
A Systems' Biology Approach to Study MicroRNA Mediated Gene Regulatory Networks
[…] of a gene regulatory network. The final version of the network can be further analyzed to identify regulatory motifs like feedforward loops (FFLs), for example, with the help of the Cytoscape plugin NetDS . Thereafter, the complete network or parts of it can be converted into a detailed mechanistic model which is described in detail in the following section. (3) Model Construction and Calibra […]
RMOD: A Tool for Regulatory Motif Detection in Signaling Network
[…] toKavosh detect motifs that recur in the network much more often than expected in a random network; NetMatch searches only for network motifs that match a user-defined query graph. In addition, the NetDS , a Cytoscape plugin, was recently developed to analyze a limited size of feedback and feedforward loops. However, it is difficult to identify regulatory motifs in the signaling networks using t […]
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