User: JJ

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JJ300
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Posts by JJ

<prev • 113 results • page 1 of 12 • next >
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Comment: C: How can I compute if the co-occurrence of two TFBSs within a certain width in al
... Thank you for the links to those tools! They provide a different way of approaching the problem. However, if I have evaluated only the promoter regions for TFBSs wouldn't they automatically produce a positive result since all hits are at least as close as the length of the promoter region I have ev ...
written 11 days ago by JJ300
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Comment: C: How can I compute if the co-occurrence of two TFBSs within a certain width in al
... Thanks for your input. So how do I go about the multiple sets of random combinations of TFs? I have the set I am interested in and n number of random combinations of TFs - for each combination I have a set and subset. Do I average the values for set and subset beforehand and then do one Fisher Exac ...
written 11 days ago by JJ300
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How can I compute if the co-occurrence of two TFBSs within a certain width in all promoters is larger than by chance?
... Hi, I have computed the number of co-occurrences of two TFBSs in all promoters in the human genome. [Previously][1], we have discussed how to calculate if the co-occurring of two TFBSs is higher than one would expect by chance, which can be done with a hypergeometric distribution using the princi ...
genome sequence written 12 days ago by JJ300 • updated 11 days ago by dariober9.1k
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Comment: C: Calculate if the co-occurring of two TFBSs is higher than one would expect by ch
... Yes, of course these are two completely different questions - both interesting A third question I am interested in would be if co-occurrence within a certain width is higher than chance. So let's say within 100 bp of one another in all promoters (or even genome). So these are then a subset of the c ...
written 17 days ago by JJ300
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Comment: C: Calculate if the co-occurring of two TFBSs is higher than one would expect by ch
... Thank you very much for your input!!! ...
written 18 days ago by JJ300
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Comment: C: Calculate if the co-occurring of two TFBSs is higher than one would expect by ch
... Thanks, I think so too... ...
written 18 days ago by JJ300
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Comment: C: Calculate if the co-occurring of two TFBSs is higher than one would expect by ch
... On another note, would overlapping bins screw up the statistics? ...
written 18 days ago by JJ300
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Comment: C: Calculate if the co-occurring of two TFBSs is higher than one would expect by ch
... Thank you Alex Reynolds, genome vs. promoter region is also in interesting way of looking at it. I will do that too. And also ejm32 - thank you for the link to the post. Based on this link, I searched some more and I found this [explanation][1], which also describes it very well! Thanks. The only ...
written 18 days ago by JJ300
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Comment: C: Are maps of regulatory regions available for hg38?
... Thanks - I figured this would be the only solutions if nothing else more updated is out there. What tool would you recommend for liftover of a bed file? ...
written 19 days ago by JJ300
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Calculate if the co-occurring of two TFBSs is higher than one would expect by chance within 1000bp of each other
... Hi, How could I calculate if the co-occurring of two TFBSs is higher than one would expect by chance? And this in either all promoters (1000 bp) or even in the complete genome within 1000bp of one another. I thought about this statistical problem but I am not an expert in probability ... and got s ...
genome sequence written 19 days ago by JJ300 • updated 18 days ago by Alex Reynolds24k

Latest awards to JJ

Centurion 23 days ago, created 100 posts.
Student 4 weeks ago, asked a question with at least 3 up-votes. For Scanning for TFBSs of known motifs in all human promoters
Scholar 4 weeks ago, created an answer that has been accepted. For A: Gene Expression data and variants from the same fastqc raw file
Supporter 6 months ago, voted at least 25 times.
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Help in writing NGS pipeline (or: the road from fasta to vcf)

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