User: Calangoa

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Calangoa30
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3 years, 5 months ago
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Posts by Calangoa

<prev • 43 results • page 1 of 5 • next >
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which positions of upstream or downstream sequences would be considered for motif discovery?
... Hi there, For discovery of motifs associated with regulatory region of set of genes in mouse, which positions of upstream or downstream sequences would be considered? Forexample from 2000 sequence upstream of genes to 0( strat codon ) or 400 sequence upstream of gened to 0 for transcription activat ...
motif discovery genes written 8 months ago by Calangoa30
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motif discovery for small set of genes
... Hi there, I am not familiar with motif discovery and I have a question, I have a small set of genes extracted from microarray data and I want to know transcription factors binding site and finding motifs for these small number(27 genes) with [Opossum][1]. the first question is that is motif discover ...
gene expression motif written 9 months ago by Calangoa30
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(Closed) TF finding from motif discovery
... I want to find what transcription factor related to each motif(For example ATACGAG) What website do you suggest? I used RSAT but it doesnt work that good. My imput data is gene symbol and I want to know motif from up stream of the genes then finding TF for that region. ...
motif tf written 10 months ago by Calangoa30 • updated 10 months ago by Benn8.0k
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Comment: C: Which transcriptin factor bind to specific motif in mouse
... I have search my sequence in TomTOm unfortunatly there is no resemblance with any known TF!! ...
written 11 months ago by Calangoa30
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Comment: C: Which transcriptin factor bind to specific motif in mouse
... Thanks ATpoint. I look at TomTom but I have found motif by RSAT. for now I want to know which TF ( by name forexample EGR1) match to this motif Or a name for this motif. Any suggestion? ...
written 11 months ago by Calangoa30
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Which transcriptin factor bind to specific motif in mouse
... Hi there, How to know which transcription factor bind to a specific motif from RSAT website? I extracted cgccgcc/ggcggcg over represented up stream of a set of genes from [RSAT][1] but it seems there is no way to find TF targeted this motif in this website. [1]: http://rsat.sb-roscoff.fr/ind ...
motif written 11 months ago by Calangoa30 • updated 11 months ago by RamRS27k
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How to compare differentially expressed genes among different affymatrix dataset
... I asked a question previuosly but I think the answers were not matched with my goal. And I completely confused! I have a set of data from some microarray dataset that they utilize 2 kind of affymatrix platform for mouse. The data have nearlly the same biological background and only one variable cha ...
R microarray batch effect written 11 months ago by Calangoa30
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Comment: C: Problem in hierarchical clustering
... No I dont know, I just want to. After clustring I found that different daraset from one study stand close together in one cluster but it is not correct when they compared with CM data. How can I do metaanalysis and normilize microarray data from different study? ...
written 11 months ago by Calangoa30
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Comment: C: Problem in hierarchical clustering
... I know, but I want to normalize them to compensate batch effect and to find which data is close to CM without considering what dataset is belong to which study. Any way?! ...
written 11 months ago by Calangoa30
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Comment: A: Problem in hierarchical clustering
... Here is the photo of heirarchical clustring ![][1] I think my mistake is I dont consider the batch effect. I normiliza each study separetly then I clustered them together. How can I compensate batch effect? In what way? Would it a good idea to normiliza all datasets together? But I dont know how c ...
written 11 months ago by Calangoa30 • updated 11 months ago by RamRS27k

Latest awards to Calangoa

Popular Question 12 months ago, created a question with more than 1,000 views. For the best combine score for enrichment analysis from Enrichr
Popular Question 16 months ago, created a question with more than 1,000 views. For how to calculate the log FC for -1.5 fold change?
Scholar 23 months ago, created an answer that has been accepted. For A: What is the meaning of normalize signal intencity in microarray and how to extra

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