I am currently designing qPCR array to investigate the effect of my gene of interest (CSMD1) on the expression of a number of genes. My cell culture studies showed that CSMD1 affects cell shape, cell proliferation and migration. I need to choose only 200 genes to be tested. Does anybody has a good idea about the best way of choosing genes to be included in the array? Help is very much appreciated.
SABioscience does a wide range of focused gene arrays covering genes used in adhesions, proliferation etc. take a look at website
Many thanks Val and Leon, I have contacted Lonza for that. But I still need to custom design my array. My gene is involved in a number of cell processes. I need to find a useful and accessible algorithm to help me choosing functionally and structurally relevant genes.
Acces to Ingenuity will help. Or else, MSKCC has good online software . This is link to the paper that describes the software packages http://cbio.mskcc.org/~enright/papers/networks.pdf It will provide you with all the networks in which your protein may be active. From there, you could select what you think is relevant in your cell system.
Very good suggestions. I can use this information for my work in gene studies
I concur with Valerie's suggestion for using SA biosciences qPCR arrays as a starting point. The question is, are you looking at specific pathways or gene functions? CSMD1 does not seem to fall into any specific pathways nor has it been listed in the gene ontology list. If you know of other genes that correlate with CSMD1, look for pathways that include the other gene(s) and then start looking at mutual relations. If the gene is known to affect cell shape, proliferation and motility, follow the KEGG pathway link (http://www.genome.jp/kegg/pathway.html) download gene lists in the related pathways and start from there. Section 3.2, 3.3, 4.2 (Cell motility), 4.3 and 4.4 may be of interest to you.
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