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Old 07-30-2013, 06:46 AM   #1
jmwhitha
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Default Excel List of Locus Tags and Pathways

Hello SeqAnswers Community,

I am working with Clostridium ljungdahlii (a bacteria that can be found in the KEGG) and am interested in generating a two column excel spreadsheet; first column- all of CLJU's locus_tags (CLJU_c00000) and the second- a list of all the pathways the product of the gene may be a part of separated by commas or semicolons (Glycolysis,Gluconeogenesis,Pentose Phosphate Pathway).

Besides that, I'd like to use my cuff_diff output to create a beautiful visual of up-regulated and down-regulated pathways.

Any help is much appreciated.

God bless,
Jason
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Old 07-30-2013, 07:48 AM   #2
rhinoceros
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For what it's worth, I don't see what you need excel for. Without a doubt, the best tool for this is the command line..
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Old 07-30-2013, 09:13 AM   #3
jmwhitha
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I can do command line. How do I use the command line to achieve my goals?
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Old 07-30-2013, 11:08 AM   #4
swbarnes2
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Look, coming on a board, asking people to do your work for you...no one is going to do that.

You ask a specific question, demonstrate that you have spent some time trying to do it on your own, ask a question that matches the subject of the board (hint: do not ask about how to format things in Excel) , you might get some feedback.

For instance, "I am looking for a list of GO or KEGG annotations for the genes of my organism, does anyone have any ideas? I already checked NCBI's entry, and a bunch of papers in PubMed" might get a response. Because that question shows that you put in a little effort, and it is a small, specific question.
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Old 07-30-2013, 12:14 PM   #5
jmwhitha
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My apologies swbarnes2 and anyone else bothered by my questions.

I have looked around the KEGG website to see if I could download a file containing a list of pathways that correspond to locus_tags (KEGG annotations), but I was unsuccessful in finding a file containing these two fields. I am hoping that I have overlooked this option since this is the first time I have used the KEGG in my research, and such a file would make my analysis a lot easier.

After reading some papers in PubMed, I found that GOseq was a good option for my first question, except that I have to define categories (pathways) for each geneID since my bacteria's genome is not in the UCSC genome browser (according to the manual), thus defeating my purpose.

As for my second question, I apologize. I know that KEGG has tools for this (maybe KEGG Map - Color Pathway), and I will research them further for more specific questions.

Thank you,
Jason
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Old 07-31-2013, 08:55 AM   #6
jmwhitha
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Hello SeqAnswers Community,

In case you would like I excel spreadsheet with one column containing locus tags and another containing corresponding pathways, I have discovered one method that will get you such a list and additional columns for EC and KO numbers.

1. Go to http://www.kegg.jp/kegg/kegg2.html and search for your organism.
2. Select your organism, and on the page starting with "http://www.kegg.jp/kegg-bin/show_organism", click the "Brite hierarchy" tab.
3. Click the first link in the Brite functional heirarchy; should be "00001 KEGG Orthology (KO) "
4. Click "download htext" at the top of the page, and open with Excel; you might need to browse to open it in Excel.
5. Write a VBA script to separate the locus tag, gene_long_name, pathway, EC and KO numbers. Have VBA search for multiple instances of the same tag and then concatenate the pathway to the first instance; delete the subsequent instances.

Thank you and God bless,
Jason
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Old 08-07-2013, 02:14 AM   #7
jp.
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how can we do pathway analysis ? I got some diff genes and some without name from cuffdiff. where is the way to go for pathway analysis ?
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Old 08-07-2013, 04:30 AM   #8
jmwhitha
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What's your organism? Feel free to message me if you don't want to divulge that online. There are many options if you are working with human or mouse or yeast, but there are very few if you are working with bacteria/ archaea.
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