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• Cytoscape network of upregulate and downregulate transcription factors: how to draw?
  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...
• How to export a network of a specific module to Cytoscape
  Hi I constructed a consensus network based on six data sets of gene expression profiles. To cons...
• Clustering Analysis In Gene Coexpression Network
  Hello! I have a gene coexpression network and i want to analyse and visualize the clusters of th...
• 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...
• 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...
• 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...
• 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...
• Hypergeometric GO analysis? and network diagram of generated GO terms
  Hi, I have a sequencing panel of approx. 1100 genes for 100 or so patients. We found that approx...
• Heatmap: how to just show significantly differentially expressed transcripts in it ?
  **Dear Biostars, Hi** I have about 8000 transcripts that has hit with Transcription Factors (TFs...
• Bipartite network analysis using cytoscape
  Hi, I have a bipartite network of transcription factors and genes. I used network analyzer in Cy...
• Transcription factor discovery from RNA-seq data; Is it practical ?
  Dear Biostars, Hi (*'m not native in English*) I have seen in some papers that via blasting the ...
• Library / Module For Network Analysis
  I would like to know what libraries/modules are used by BioStar members for large scale analysis ...
• Scale-free networks are rare
  I recently read the paper titled "Scale free networks are rare" [(reference)][1]. This gives me h...
• How to draw PPI modules with Cytoscape
  Hi, I am in a project of PPI and need to summarize a long list of statistically significant modul...