User: benjyrolls

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benjyrolls40
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Posts by benjyrolls

<prev • 18 results • page 1 of 2 • next >
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Finding Primary Motif from Genomic DNA data
... Hello I have a genomic DNA data in fasta format which I have exported to MEME CHIP suite to find the motifs in this data. This has presented me with the p-values and E-values for the known Motifs and have come up with https://ibb.co/conksa, I would like to plot or come out with a plot of Bits and Z ...
chip-seq written 1 day ago by benjyrolls40 • updated 22 hours ago by kennethcondon2007480
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Interpreting Differentially Expressed Genes(DEGs) from RNA Seq experiment
... I have a list of Differentially Expressed Genes(DEGs) from an experiment which involved a mouse model with Sox2 and another model with Sox2 Knock Out( Sox2 WT vs Sox2 KO). What conclusions can I make from these DEGs and what can I say of these genes in terms of Sox2 ? thanks Benjy ...
rna-seq written 2 days ago by benjyrolls40 • updated 2 days ago by igor4.1k
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Answer: A: Cancer expression data sets
... Have a look at this , might help http://biogps.org/dataset/tag/cancer/ ...
written 27 days ago by benjyrolls40
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Interpreting Chip Seq Results
... Hello I performed a ChIP Seq experiment and performed these steps MACS, CEAS, Gene Ontology Enrichment with GREAT . I have some enriched terms as well as enriched pathways such as PTEN Signalling pathway, WNT pathway etc. From my information how can I find the genes which are up or down regulated ...
macs2 chip-seq ceas great written 27 days ago by benjyrolls40 • updated 27 days ago by Devon Ryan65k
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Comment: C: Upstream Regulator Gene Differential expression
... As per you statement "Checking for known binding sites in the majority of the DE genes should reasonably suffice for this." I have performed a check on the binding sites and this is what I [found][1] Sox2 seems to be regulating some genes in conjunction with others? [1]: http://159.149.160.88 ...
written 4 weeks ago by benjyrolls40
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Comment: C: Upstream Regulator Gene Differential expression
... There are 3 replicates. Well, I was trying to reproduce the results in [this experiment][1] using the RNA-Seq data however am not confident in the differentially expressed genes and its role to Sox2 in terms of RNA-Seq. However in the ChIp-Seq experiment, Centrimo motif analysis, using the Chip-Se ...
written 4 weeks ago by benjyrolls40
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Comment: C: Upstream Regulator Gene Differential expression
... Well am very new to RNA Seq because I have a wild type mouse with Sox2 injected(condition 1) and other with SoX2 removed(condition 2) I was thinking the differentially expressed gene will be as a result of Sox2? Can I say that Sox2 presence is driving the response and the DE genes are as a result o ...
written 4 weeks ago by benjyrolls40
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Upstream Regulator Gene Differential expression
... Hi I performed an RNA Seq on two conditions SOX2 WT mouse and SOX2 KO mouse to find the genes which were differentiallly expressed through an RNA Seq pipeline and eventually obtained the differentially expresses DE genes by Cuffdiff To find the upstream regulators these differentially observed ge ...
rna-seq written 4 weeks ago by benjyrolls40
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Empty Cuffdiif Output except Gene Differential expression testing
... Hello I am running a Cuffdiff on two separate conditions of a file. all outputs seem to be empty except the gene differential expression output which shows the deferentially expressed genes. does it mean this output is wrong. i have followed other similar outputs on the forum but cant get this t ...
galaxy cuffdiff rna-seq written 4 weeks ago by benjyrolls40
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Finding Gene names from chromosome positions whilst maintaining fold change and p and q values
... hi I have a peaks interval output from MACS2.1 which is attached below. How do I find the gene names using the start and end positions, whilst maintaining the fold change values in Galaxy in my file attached below? I have followed other posts on the forum such as [this one][1] but this does retur ...
macs galaxy chip-seq written 6 weeks ago by benjyrolls40 • updated 5 weeks ago by Devon Ryan65k

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