User: Zara

gravatar for Zara
Zara20
Reputation:
20
Status:
New User
Location:
Germany
Last seen:
3 years, 1 month ago
Joined:
6 years, 2 months ago
Email:
z*********@gmail.com

Posts by Zara

<prev • 21 results • page 1 of 3 • next >
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Comment: C: cluster Yeast ORFs based on GO biological process term
... You mean I find the differentially expressed genes under each condition and then run the inference only on that subset? ...
written 3.7 years ago by Zara20
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Comment: C: cluster Yeast ORFs based on GO biological process term
... Thank you for your reply. I want to run gene regulatory inference algorithms on yeast gene expression data. In some papers the authors claim that before inference they do clustering. I want to do the same. Clustering genes based on biological process, then run network inference on each cluster. ...
written 3.7 years ago by Zara20
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cluster Yeast ORFs based on GO biological process term
... Hi, I have a gene expression file for Yeast. I want to cluster Yeast genes based on GO biological process. So I need to generate a file containing genes and their relative GO terms (this is not an enrichment analysis, I have just a search over all genes). I was thinking I may download the complete ...
yeast go biological process written 3.7 years ago by Zara20 • updated 3.7 years ago by a.zielezinski9.2k
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area under ROC or PR curve for assessing gene regulatory network inference methods
... Hi I'm trying to test some network inference methods. When I run each method, I get a Precision and Recall. Some methods have parameters for which I get different precision-recall values and in some I don't find special parameters. Now I need to assess area under ROC or PR curves. I have no idea h ...
gene regulatory network inference assessment written 4.5 years ago by Zara20
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filter genes with no significant change in expression value
... Hi Everybody, I'm trying to run a gene regulatory inference method. In the first step I need to remove genes with no specific change in their expression values. I don't know how to specify if a gene has "significant" change. What does it mean? My second question: Should I just remove these genes ( ...
gene expression significant change written 4.5 years ago by Zara20 • updated 4.5 years ago by WouterDeCoster44k
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Inferring gene regulatory networks - evaluation
... Hi everyone, I'm using DREAM  4 challenge data in order to evaluate my gene regulatory inference method. I have a couple of questions: 1- How should I use the perturbation data. I don't know what does G1(-/-) or G1(+/-) mean. Does this plus and minus signs represent mutations? How come we have tw ...
gene regulatory dataset dream dream 4.0 written 4.6 years ago by Zara20 • updated 4.4 years ago by Biostar ♦♦ 20
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Is there any difference between methods for analyzing gene expression profiles of Eukaryote and Prokaryotes?
... Hello everybody My question is :  Is there any difference between methods for analyzing gene expression profiles of Eukaryote and Prokaryotes?  Is the answer the same if we have microarray expression profiles or RNA-Seq profiles?   Thank you in advance :) ...
eurkaryote microarray rna-seq prokaryote written 5.0 years ago by Zara20 • updated 5.0 years ago by Being Bioinformatician180
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Comment: C: Computing fold change values for RT-PCR
... Thank you Devon ^_^   ...
written 5.3 years ago by Zara20
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Comment: C: Computing fold change values for RT-PCR
... I have another question: Now I have a fold-change value for each sample. Suppose I have three groups (control, treated-1, treated-2). For each group I have several samples. How can I get a single fold-change value for each group? I saw for example R package HTqPCR that also reports a p-value for t ...
written 5.3 years ago by Zara20
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Comment: C: Computing fold change values for RT-PCR
... Thanks a lot Devon. So it doesnt matter for which sampl which control to pick? Or it's better to average over all controls... Thank you :) ...
written 5.3 years ago by Zara20

Latest awards to Zara

Popular Question 3.7 years ago, created a question with more than 1,000 views. For Computing fold change values for RT-PCR
Great Question 4.5 years ago, created a question with more than 5,000 views. For Computing fold change values for RT-PCR
Epic Question 4.5 years ago, created a question with more than 10,000 views. For Computing fold change values for RT-PCR
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Computing fold change values for RT-PCR
Popular Question 4.5 years ago, created a question with more than 1,000 views. For simulating time series data for Biomodels model with Copasi
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Computing fold change values for RT-PCR

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