User: kevluv93

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kevluv93150
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Posts by kevluv93

<prev • 39 results • page 1 of 4 • next >
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Visualize location of genes on Chromosomes
... I'm trying to create a figure which visualizes the locations of NBS-LRR genes on chromosome 1 on the watermelon genome based on the watermelon sequencing genome paper here. Essentially, I want to create a chromosome map of locations of specified genes for a figure. I've tried to set up the watermel ...
genome alignment rna-seq blast written 3.2 years ago by kevluv93150 • updated 3.2 years ago by Alex Reynolds27k
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Comment: C: Summarizing long list of GO terms
... Sorry, was away. I've already ran GO term enrichment analysis and it's produced a list of 300+ GO terms which are considered "enriched" for certain categories. I need a way to make this list smaller by getting rid of redundant terms to a certain level. Also if possible, generate a figure which shows ...
written 3.4 years ago by kevluv93150
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Comment: C: Taking out transcription factors from a tomato transcriptome
... I think I wrote the question improperly. I have a list of gene IDs that represent my differentially expressed genes. It's not a list of sequences. I meant to say that I wanted to find which genes made transcription factors. Not which areas on my sequences take promoters. I'm sorry about that, I'll ...
written 3.4 years ago by kevluv93150
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Answer: A: Taking out transcription factors from a tomato transcriptome
... I actually found what I was looking for. If you need a database of transcription factors and their sequences for Solanum Lycopersicum,  there is a database from Cornell that has this info: http://bioinfo.bti.cornell.edu/cgi-bin/itak/db_browse.cgi ...
written 3.4 years ago by kevluv93150
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Taking out transcription factors from a tomato transcriptome
... I have a list of differentially expressed genes from an experiment where we compared the transcriptome of two different Solanum lycopersicum plants. I want to take out all of the transcription factors from this list of differentially expressed genes. Right now the only method I've been trying is so ...
transcription factors rna-seq written 3.4 years ago by kevluv93150
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Comment: C: Turning GO Terms to GO IDs
... If there's a text file available with GO terms to GO IDs, I can just do it in excel. Not ideal, but it'll work. I'm going to have to learn R at some point, but right now I can deal with this. ...
written 3.6 years ago by kevluv93150
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Comment: C: Turning GO Terms to GO IDs
... Wait, is GO.db an R package or a textfile with conversions? I've never used R before, I just type in library(GO.db) and R knows where to get that package? example GO terms: Nucleotide binding, nucleic acid binding, RNA Binding, DNA Binding   ...
written 3.6 years ago by kevluv93150
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Turning GO Terms to GO IDs
... I recently ran gene enrichment on a transcriptome set using Plant MetGenMap. The outputs gave me a list of GO terms that are enriched and their p-values, but many of the GO terms are redundant (like binding is enriched and nucleotide binding is enriched). I'm planning on plugging this dataset into r ...
gene ontology written 3.6 years ago by kevluv93150 • updated 3.6 years ago by Sukhdeep Singh9.6k
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Comment: C: Functional Annotation of Tomato Transcriptome
... I used the ITAG2.4 Loci IDs from the sol genomics database for my tomato transcriptome. (ex solyc12g011350). I ended up using blast2go, AgriGO, and Plant MetGenMap. I can't get PANTHER's statistical gene enrichment function to work for some reason, idk why. I used these three programs and the output ...
written 3.6 years ago by kevluv93150
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Extracting certain gene sets from RNA data
... I have a list of genes from a transcriptome, their GO IDs, and their annotations. I want to take out all the putative defense related genes from this dataset and put it into another graph for a figure. Does anyone know a good bioinformatics way of taking out genes with certain functions from a datas ...
rna-seq ontology written 3.6 years ago by kevluv93150 • updated 3.5 years ago by mark.ziemann1.1k

Latest awards to kevluv93

Scholar 3.6 years ago, created an answer that has been accepted. For A: Convert Gene IDs of Tomato Sol Database

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