Moderator: Larry_Parnell
Larry_Parnell ♦ 16k
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Computational biologist
Posts by Larry_Parnell
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A: Common target genes
... KEGG and REACTOME are indeed good places to begin to identify the genes encoding proteins that reside in pathways just upstream or downstream of your set of 50 genes, with regard to information flow. The word "target" could imply transcription factor (TF) binding, or your gene encodes a TF. If this ...
written 5.5 years ago by
Larry_Parnell ♦ 16k
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C: Identifying Motifs In A Geneset
... It is a general rule of thumb, but I use genome length and gene density. Some knowledge of the literature helps, too, in determining how often near, middle distance and far upstream gene control elements have been identified.
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written 5.5 years ago by
Larry_Parnell ♦ 16k
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A: GWAS SNPs LD Clumping
... We use 1000 Genomes data for populations with ancestry relevant to the populations we study, e.g. CEU for pops of European ancestry. We use Haploview and routinely use r^2 cutoffs of 0.8. This will need to be done as one moves from one population to another because LD blocks are different in differe ...
written 5.5 years ago by
Larry_Parnell ♦ 16k
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A: DNA methylation analysis
... Use MeDIPs or Batman for this type of dataset. These are standard tools, ones we've used here for our analysis of such data that we generated ourselves.
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written 5.6 years ago by
Larry_Parnell ♦ 16k
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A: Pathway Analysis Tool
... Yet another option is to use MetaboAnalyst. Colleagues on a metabolomics-microbiome project have used this via the downloads available at the link provided. Other researchers at our university use this, but by running it through MatLab, which gives them more control over parameters that may be speci ...
written 5.6 years ago by
Larry_Parnell ♦ 16k
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... Thanks, I knew that. What is not free is my time for such an endeavor that is really quite beyond my main research focus. If this could be done in a few minutes, say by looking at the Ötzi viewer that once existed - fine. But that is not the case and so I must shelve this idea for another time, or f ...
written 5.6 years ago by
Larry_Parnell ♦ 16k
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Answer:
A: Isoforms' unique loci
... Try the fly genome browser @ Ensembl http://www.ensembl.org/Drosophila_melanogaster/Info/Index
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written 5.6 years ago by
Larry_Parnell ♦ 16k
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... Indeed! More often journals have illustrated abstracts or the public relationships dept wishes to use something visual. So, once it is written and written well, consider artistic expression.
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written 5.6 years ago by
Larry_Parnell ♦ 16k
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Answer:
A: Pathway Analysis Tool
... We've used and liked PAPi. Pathway Activity Profiling (PAPi) compares metabolic pathway activities from metabolite profiles. PAPi is an R package.
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written 5.6 years ago by
Larry_Parnell ♦ 16k
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... EcoCyc is something that you should look into. It's focus is E. coli, but can be useful for other bacterial species. A partner database is BioCyc, a collection of 3563 Pathway/Genome Databases (PGDBs), with tools for understanding their data.
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written 5.6 years ago by
Larry_Parnell ♦ 16k
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For Tools For Pathway/Gene Set Analysis Of Gwas (Genome-Wide Association Study) Data
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