User: The Last Word

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The Last Word170
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Posts by The Last Word

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Comment: C: Significance in gene ontology terms
... I am just getting a list of all the gene ontology terms given out by DAVID above a certain significance threshold. Of course comparing between significance values is not what I want to do or plan to do but this question just struck me when I saw the list of ontology significance terms. ...
written 10 days ago by The Last Word170
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Significance in gene ontology terms
... When we do gene ontology analysis, we get a list of Biological processes, cellular components and molecular functions with different significant values. What does these significant values exactly mean. I did gene ontology analysis with a set of genes and I got the CC cytoplasm more significant when ...
ontology written 10 days ago by The Last Word170 • updated 9 days ago by jared.andrews071.7k
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Comment: C: Compare the degree distribution of a real networks and multiple random networks
... basically check and prove that the degree distribution of my network is different from a random one and state that its just not a random collection of nodes but potentially have underlying functional properties ...
written 10 days ago by The Last Word170
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Compare the degree distribution of a real networks and multiple random networks
... Before the paper real world networks are rarely scale free, studies used to (still do) check for the slope in degree distribution graphs and if the slope fell between 2 and 3, discern that the network is a real world network. The slope of my networks are not between 2 and 3, and so I decided to cond ...
network kolmogorov-smirnov written 10 days ago by The Last Word170
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Check the significance for the number of genes in a cluster
... This is more of a statistical question. I have 8 gene clusters and a list of gene names. All the clusters are of varying lengths. I have a list of 200 gene names and I found that 60 out genes out of the list fall in the third cluster. How do I statistically check if a significant number of genes fro ...
statistics written 6 weeks ago by The Last Word170 • updated 6 weeks ago by Kevin Blighe33k
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Comparing between different groups of clusters after network clustering
... I have a set of eight gene clusters which I obtained from clustering a network. However, I had to update the genes in the network at a later stage which lead to certain deletions (genes not present in the new gene list). I did the clustering again and this time there were a total of 9 clusters. Is t ...
network written 7 weeks ago by The Last Word170
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Less number of motifs found in the real network when compared to the random network
... I know that motif detection is usually done by comparing the number of motifs of a particular type in a real world network again a random network generated. If a significant more number of that particular motif is present in the real world network when compared to the random, then that motif is said ...
network motif written 7 weeks ago by The Last Word170
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Comment: C: Network Analyzer in Cytoscape
... Hi Jean, just to clarify, the correlation refers to the correlation coefficient right? It just says correlation and I am confused as to if that stands for something else. ...
written 7 weeks ago by The Last Word170
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Network Analyzer in Cytoscape
... Hi, Anyone who has used Cytoscape might be familiar with the Network Analyzer tool in Cytoscape which is used to calculate the degree distribution of the network. I did the same, plot the degree distribution and fit a power law y = ax(squared b) where b is the slope. Cytoscape gives the R-squared a ...
cytoscape written 8 weeks ago by The Last Word170 • updated 8 weeks ago by Jean-Karim Heriche17k
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Motifs in bipartite networks
... Hi, I was looking to check if SIM (simple input motifs) motifs were over expressed in my directed bipartite network (transcription factors and genes).Since it is a directed network, I was only expecting to find motifs of transcription factors regulating genes. ![enter image description here][1] ...
bipartite network written 8 weeks ago by The Last Word170

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