User: salvatore.raieli2

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Posts by salvatore.raieli2

<prev • 27 results • page 1 of 3 • next >
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Comment: C: Accessing ENCODE data through R
... thank you, I downloaded the bed file for the TF I needed ...
written 4 months ago by salvatore.raieli260
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Accessing ENCODE data through R
... Hi everyone, I would like to download some ENCODE data. I want to download which genes present in their promoter the binding of particular Transcription Factor. Starting from a trasncription factor I would like an easy way to retrieve a gene list (not sequences, but more processed data) where they ...
R encode written 4 months ago by salvatore.raieli260 • updated 4 months ago by ATpoint25k
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Comment: C: Find Transcription factor binding site for a gene list
... I was thinking something similar if I am not finding a good database ...
written 13 months ago by salvatore.raieli260
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Comment: C: Find Transcription factor binding site for a gene list
... how I can generate a BED file just for the promoter regions of a list of genes? ...
written 14 months ago by salvatore.raieli260
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Comment: C: Find Transcription factor binding site for a gene list
... If I understood well, I get the genomic coordinates for my list of genes and with bedtools getfasta I obtain the fasta, I take all the fasta in one multifasta that I feed to FIMO, right? ...
written 14 months ago by salvatore.raieli260
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Comment: C: Find Transcription factor binding site for a gene list
... thank you, I will give a look to FIMO. I am not sure it is what I need. If I understand well I have to provide the FASTA for each gene I want to scan, right? Meaning that I have to manually download 100 genes and their promoters in the FASTA format. With FIMO can I automize this process? ...
written 14 months ago by salvatore.raieli260
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Find Transcription factor binding site for a gene list
... Hi everyone, I have a list of genes that are different expressed between tumor and normal tissue. I have two drugs that block two different transcriptional factor (let's say TF1 and TF2). What I want to do is to find which of these genes have in their promoter a TF binding site for TF1, for TF2 an ...
R tfbs promoter written 14 months ago by salvatore.raieli260 • updated 12 months ago by Praneet Chaturvedi120
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TF binding site in the Mitochondrial DNA
... Hi everyone, I used TFBStools and I retrieved the sequence and frequence matrix for a TF. for example: library(JASPAR2014) library(TFBSTools) opts <- list() opts[["species"]] <- 9606 opts[["name"]] <- "RUNX1" opts[["type"]] <- "SELEX" opts[["all_versions" ...
tfbs tf written 16 months ago by salvatore.raieli260 • updated 15 months ago by Biostar ♦♦ 20
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Comment: C: how to evaluate a gene signature is present in each patient of a dataset
... arbitrary? there is not the hazard of many false positive and false negative? I was also reading some papers, for instance gene set analysis where they do a rank of the signature genes in the patient sample to evaluate if the signature is enriched or not. what do you think about? ...
written 17 months ago by salvatore.raieli260
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Comment: C: how to evaluate a gene signature is present in each patient of a dataset
... I was thinking about this point, How I can binarize it? I assume one gene in pazient X is 1 if the value is above a theresold? or you would use another system? ...
written 17 months ago by salvatore.raieli260

Latest awards to salvatore.raieli2

Popular Question 13 months ago, created a question with more than 1,000 views. For how to normalize two microarray dataset coming from different platform
Popular Question 13 months ago, created a question with more than 1,000 views. For Find Transcription factor binding site for a gene list
Popular Question 13 months ago, created a question with more than 1,000 views. For performing a PCA on a gene set in R

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