Moderator: Jean-Karim Heriche

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EMBL Heidelberg, Germany
Website:
http://jkh1.github.io/
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7 hours ago
Joined:
7 years, 7 months ago
Email:
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Posts by Jean-Karim Heriche

<prev • 2,189 results • page 2 of 219 • next >
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Answer: A: Network statistics on Protein Interaction Networks
... What you want is the solution to a problem called subgraph extraction. For example, given a protein-protein interaction graph, find the subgraph that contains a given list of proteins/genes. There are many algorithms for this depending on what you want from the subgraph. In the past I've used [limit ...
written 5 days ago by Jean-Karim Heriche18k
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Answer: A: Three network comparison using cytoscape
... You can do it by assigning each node an attribute corresponding to each group or combination of groups and then apply a discrete mapping. Have a look at this [post][1]. For a more fancy representation in which a node would have more than one color if if belongs to more than one group, have a look at ...
written 5 days ago by Jean-Karim Heriche18k
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Comment: C: Statistical Tests for Two Data Tables
... At the moment you're comparing the average correlation of the two groups which is simple but may be not entirely satisfying because for large sample sizes even small differences become significant. So unless there is a large difference, the p-value is, in my view, meaningless in terms of biological ...
written 9 days ago by Jean-Karim Heriche18k
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Answer: C: Statistical Tests for Two Data Tables
... The t-test is applicable if your data's distribution is reasonably close to normal. It doesn't make any assumption based on sample size, only on variance. If you think variances are different between the two groups then use Welch's version of the t-test (in R, set var.equal = F which actually is the ...
written 9 days ago by Jean-Karim Heriche18k
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Comment: C: Estimating gene set enrichment using Fishers exact test
... This would be genes expressed in the tumor since only these have a chance of being detected as for the target genes, you'll have to read the paper if you want to know how they defined lncRNA target genes. ...
written 10 days ago by Jean-Karim Heriche18k
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Comment: C: Estimating gene set enrichment using Fishers exact test
... Assuming that in tumor A, 1000 genes are expressed and we're interested in lncRNA X for which we found 80 target genes and pathway P that comprises 13 genes, the contingency table would look like this: | A | Not A | ---------------------------| Targets of X| 10 | 70 ...
written 10 days ago by Jean-Karim Heriche18k
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Comment: C: Estimating gene set enrichment using Fishers exact test
... Without reading the paper but based on your citation, it seems clear (to me) that they take as the universe/background set all genes expressed in a given tumor and test whether genes identified as target of a given lncRNA are enriched in genes for a given pathway and consider significant only pathwa ...
written 10 days ago by Jean-Karim Heriche18k
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Comment: C: Negative dataset selection
... You still haven't told what it is you're trying to do, i.e. what are you trying to predict and what question is this suppose to answer ? If you're trying to detect a motif in sequences, you should try standard approaches first e.g. HMM-based. Just because deep learning is fashionable and applicable ...
written 11 days ago by Jean-Karim Heriche18k
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Comment: C: Silhouette Plots for Clustering Quality (Multiple Algorithm)
... To get the SNN, the distance matrix had to be computed so it should be available somewhere. The SNN matrix is a similarity matrix (it is based on the Jaccard index) so it may need to be converted to a distance. ...
written 12 days ago by Jean-Karim Heriche18k
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Comment: C: Negative dataset selection
... I don't think you're giving enough information for anyone to help you. It seems that you're not convinced that you're taking the right approach so what is the biological question you're trying to address ? What is the data ? How is it represented (i.e. what kind of features do you use) ? Which class ...
written 12 days ago by Jean-Karim Heriche18k

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Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Scholar 5 days ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
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