Any Tools To Plot Or Classify Mitochondrial Genes?

Question

[Dejian]

I have a list of mitochondrial genes which are widely distributed on mitochondria and involved in variously biological processes such as TCA, ETC, fatty acid metabolism. I want to describe these genes in a concise way, for example, coloring these genes on a mitochondrial image or automatically classifying these genes according to their function. I have tried some tools based on GO and KEGG but did not find suitable tools. Any tools? Or other way to summarize the list of genes? Thanks!

Answer 1

[Benm]

I don't know OGDRAW can help you or not, here is the reference:

Lohse M, Drechsel O, Bock R. OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr Genet. 2007 Nov;52(5-6):267-74. Epub 2007 Oct 24.

Answer 2

[Pierre Lindenbaum]

Did you try Reactome.org ? There is a tool named "Pathway Analysis"

Allows you to analyse a list of protein, gene, expression data or compound identifiers and determine how they are likely to affect pathways.

Answer 3

[Chris Evelo]

You could try [?]PathVisio[?]. With the analysis plugin it will evaluate a list of genes for over representation in pathways. It will work with the community curated pathways from [?]WikiPathways[?], which include the Reactome pathways mentioned by Pierre. Community curation might be relevant here since it allows you to add your own genes to existing pathways (either on the wiki or locally for personal use only), you cane even create a dedicated pathway with just your relevant genes. From the PathVisio download page you can also download a zip file with converted KEGG pathways.

Also see the answer to [?]this BioStar question[?]. where a number of other tools are mentioned and where I tried to indicate some limitations of pathway statistics.

Answer 4

[Khader Shameer]

You already have nice answers from Pathway perspective.

I would like to suggest some tools for visualizing your genes using GO terms:

BiNGO(Cytoscape plugin) - You can generate neat plots using GO terms and their relations ships.

If you have GO terms for your genes, you can map the terms to the Directed Acyclic Graph (DAG) structure of the Ontology using tools like Ontologizer etc. Detailed list of GO based visualizations tools with similar capabilities are available here. Another option is to visualize the terms using REViGO.