User: The Last Word

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The Last Word190
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India
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7 months, 3 weeks ago
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6 years ago
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Posts by The Last Word

<prev • 97 results • page 1 of 10 • next >
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Clustering in directed gene networks
... Hi, I have a directed transcriptional regulatory network. I would like to partition it, but most of the clustering algorithm do clustering assuming that the network is undirected. Would it be an issue partitioning a directed, bipartite network as undirected? Kindly advice. ...
network written 7 months ago by The Last Word190 • updated 7 months ago by Jean-Karim Heriche23k
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Homology in EMBL Biomart
... Hi, I am wondering what software determines homologous genes in Ensembl. Biomart,. Is it just a normal BLAST? I also have a second question. A paper which was published 7 years ago was able to find homologous genes for a set of 300 genes. However, I was able to find homologous genes for 215 genes f ...
biomart homology written 12 months ago by The Last Word190 • updated 12 months ago by Ben_Ensembl1.5k
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Comment: C: Compare the degree distribution of a real networks and multiple random networks
... I do understand that biological networks are incomplete and I am comparing just this one instance. My network was computationally generated and can't I use this methodology to test just this one instance. ...
written 19 months ago by The Last Word190
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Modularity score comparion between different algorithms in network analysis
... I used different algorithms for splitting my large gene network into different sub-networks using Cytoscape. I compared the modularity scores and decided that the algorithm with the best modularity score will be used for clustering the network. My colleague came up with the argument that modularity ...
network analysis written 19 months ago by The Last Word190 • updated 19 months ago by Jean-Karim Heriche23k
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Comparing between gene networks of two species
... Hi, I have a gene network of honey bee. Since most of the genes in the network were uncharacterized, I found homologous genes in the fly genome using Biomart, created a network using STRING, did a functional analysis of the genes in the network using ClueGO and suggested a conclusion that since the ...
homologues networks written 20 months ago by The Last Word190
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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 20 months ago by The Last Word190
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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 20 months ago by The Last Word190 • updated 20 months ago by jared.andrews076.4k
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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 20 months ago by The Last Word190
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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 20 months ago by The Last Word190
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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 21 months ago by The Last Word190 • updated 21 months ago by Kevin Blighe63k

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Epic Question 12 months ago, created a question with more than 10,000 views. For PAML input file format
Popular Question 12 months ago, created a question with more than 1,000 views. For Selectively downloading sequences from miRBase
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Popular Question 19 months ago, created a question with more than 1,000 views. For Selectively downloading sequences from miRBase
Popular Question 19 months ago, created a question with more than 1,000 views. For Structure prediction on DNA folding form or RNA folding form
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Great Question 3.5 years ago, created a question with more than 5,000 views. For PAML input file format
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Structure prediction on DNA folding form or RNA folding form
Student 3.5 years ago, asked a question with at least 3 up-votes. For RepeatMasker library out of date.
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