Hello
I am doing gene network analysis using micro array data set for identifying the gene enrichment,pathway and transcription factor analysis. My data set contain 79 sample with different time points( 40 control + 39 infected). Each infected has two GSE files in my data-set. I would like analyze the whole samples individually with cytoscape Mcode. Can you please share how handle the large clusters and analyze the network.
hi
AllegroMCODE for Cytoscape is a high-performance MCODE cluster finder supporting both of CPU and GPU clustering. Clusters in a protein interaction network can be considered as protein complexes and functional modules, which can be identified as highly interconnected subgraphs.
It finds the same clusters as the MCODE does, but to process large complex networks it is totally redesigned for fast analysis, low memory consumption, and interactive cluster exploring without creating a network view. Its GPU analysis usually takes less than a second even for a large complex network.
To address this question let me first say that I have used MCODE for protein cluster (protein complex) identification earlier in PPI networks. where the data set consist of protein interactions. The dataset is a file with three columns ( two column is acceptable) where each row corresponds to an interaction such as ,
column1 column2 column3
Prot1 0.77 Prot2
Pro11 0.41 Prot3
where the middle row indicate the correlation of expression (gene) between the two proteins.
if you can translate your data into such format the rest are simple.
seems like you have a 2-D matrix array kind of data with you.
Also adding to @Noor Edan Jarad's comment above, MCODE on Cytoscape can be time taking if you don't have a powerful system.
I stopped using it after it failed to complete on some big data networks.
- Badges
- Science topic
- Similar topics
- Biological Science
- Genetics
- Gene Expression