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  Dear Biostars, Hi I have a list of **zebrafish** TFs (both family and members) upregulated in my...
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  I got some hub genes based on PPI network and then I did promoter analysis based on transcription...
• Finding a way to comparison induced cells and real tissue by Cytoscape!
  Hi, I have some gene expression data from induced cells by some small molecule in vitro (differe...
• Reconstruct principal curves from the results of pathifier package
  Hello. I'm using the pathifier tool, to extract PDSs (Pathway de-regulation scores) from some mi...
• Cytoscape 3.3.0 visualize network with up/down regulated color
  Hello, So, I want to visualize my network with cytoscape. I generate my network using R and it i...
• Co-expression Network on Cytoscape between miRNA-mRNA and mRNA-mRNA
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• How to export a network of a specific module to Cytoscape - Consensus modules / multiExpr
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• Clustering Analysis In Gene Coexpression Network
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• Up-regulated and down-regulated genes in pathway analysis
  Hi, I have expression of genes in two different groups of patients, I want to do pathway analysis...
• Color nodes based on attribute(column in data table) in cytoscape
  I merged to networks (MPK3 and MPK6 regulated proteins) and uploaded this in Cytoscape. Know I ha...
• What if a network is not scale-free?
  I have built a gene coexpression data from RNAseq data sets using the protocol as mentioned in th...
• Different versions of RegulonDB regulatory network - which to use (and how)?
  Hi there, I do a little project where I analyze regulatory networks motifs (such as feedforward/f...
• Could any of you help me to explain the steps in creating backbone network or the steps in validating the same in Cytoscape?
  I am doing my work in protein protein interaction network and I have constructed PPI using STRING...
• How to report differentially expressed transcription factors in scatter plot
  **Dear Biostars Friends, Hi** I want to report transcription factors (TFs) that are expressed di...
• Gene Expression Network Analysis
  Hi I've constructed a network for oxidative stress pathway genes using bisogenet.I need to do net...
• Identifying Interaction Between Tfs As Regulators Or/And Targets
  Hi! I have ChIP seq data of 5 TFs and I want to construct a transcriptional regulatory network b...
• miRWalk and Cytoscape to show microRNA-mRNA interactions
  Hi All, I have about 5 miRNAs and each of them I have some confirmed mRNA target, I want to use...
• How to use Jactivemodule plugin from Cytoscape?
  Hi there, I want to construct a lot of networks to show, what are the effects of different cultu...