Moderator: Jean-Karim Heriche
Jean-Karim Heriche ♦ 17k
- Reputation:
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- Location:
- EMBL Heidelberg, Germany
- Website:
- http://jkh1.github.io/
- Last seen:
- 2 hours ago
- Joined:
- 7 years, 4 months ago
- Email:
- h******@embl.de
Posts by Jean-Karim Heriche
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... Also, as a complement, check out this [tutorial on network visualization with R][1].
[1]: http://kateto.net/network-visualization ...
written 4 days ago by
Jean-Karim Heriche ♦ 17k
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... In addition to previous suggestions of looking for relevant protein domains and GO annotations, you could also check which of the proteins in your list are known or putative cell surface proteins in the following databases:
- [cell surface protein atlas][1]
- [extracellular matrix interaction d ...
written 4 days ago by
Jean-Karim Heriche ♦ 17k
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... A hub is a node that has a higher degree than other nodes in the graph. How this translates in practice seems to vary between papers. Some just use an arbitrary threshold either as a fixed number or as a percentage, others choose a threshold based on some statistical argument e.g. outliers in the di ...
written 5 days ago by
Jean-Karim Heriche ♦ 17k
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... You can do it in RStudio as long as your computer does have enough RAM. The main issue will probably be the time it takes to read the file. ...
written 5 days ago by
Jean-Karim Heriche ♦ 17k
1
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... The correlation ranks have to be calculated relative to each gene separately. Try something like this:
R <- matrix(NA, nrow = number.of.genes, ncol = number.of.genes)
# Compute correlation ranks for each gene
for(i in 1:number.of.genes) {
# Rank all genes relative to gene ...
written 6 days ago by
Jean-Karim Heriche ♦ 17k
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... The future is in data integration. Sequences are not going to be highly valuable on their own for very long but will be just one piece of data to use among others. From my perspective, sequencing, and other omics technologies, are moving to the microscope. Now that you can get sequence information f ...
written 6 days ago by
Jean-Karim Heriche ♦ 17k
3
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... A gene regulatory network, as the name implies, is a network (i.e. a directed graph) in which the nodes are genes and the edges represent some form of regulatory action of one gene on another (usually activation or repression). A protein-protein interaction graph is typically an undirected graph whe ...
written 6 days ago by
Jean-Karim Heriche ♦ 17k
1
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75
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... Today and tomorrow don't define time points very precisely. I can imagine that today, you take a sample two hours after the patient has taken their medication but tomorrow, you'll take the sample just before. This is also without taking into account the effect that taking the first sample can have o ...
written 7 days ago by
Jean-Karim Heriche ♦ 17k
1
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75
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... You can almost never be sure a single measurement is representative because of all sources of variation such as biological and measurement noises. This is why there are replicates in a study.
You should define what a time point is because how precisely/reproducibly you sample from a "time point" can ...
written 8 days ago by
Jean-Karim Heriche ♦ 17k
1
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Answer:
C: secretome P error
... Missing features could indicate that some features couldn't be computed. One possible reason is that you didn't install software required to compute them. See the docs for secretomeP.
One another note, it seems that using secretome P (that has been trained with mammalian proteins) for non-mammalian ...
written 8 days ago by
Jean-Karim Heriche ♦ 17k
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