disconnected clusters from MCL

Our MCL clusters at high I-values give genes in clusters with disconnected nodes. This is a problem has been discussed before:

http://larsjuhljensen.wordpress.com/2010/03/01/analysis-markov-clustering-and-the-case-of-the-unnatural-clusters/

According to the post, this is not an "error", but a possible though "unexpected" result. Looks like "--force-connected=y" option might solve this problem. I will redo the clustering and then check.

two step ranking

q< 0.2 and p<0.1 (top candidates should often be better than 0.2), chose only consistent clusters.

then sort from low to high by q1*q2

CYP2E1 needs discussion

description of I values needs changes.

methods needs update.

focus on consistent 3 clusters HSPB1, ATP2A1, CYP2E1. 

   1. delete crx
2. add CYP2E1
3. prepare pic for clusters
4. change methodology
5. clustering descriptive statistics. 

Student Jiang, 2013Nov 14

Last time we discussed problems in retrieving genes associated with SNPs that have OMIM IDs. One of the problem is that some OMIM entries in the OmimVarLocusIdSNP table do not have genes listed. I just tried searching the genome database at UCSC using the SNP_id, and got the corresponding gene names.

For example, "188890" is associated with 11 SNPs and the query results are:

rs686           chr5    DRD1
rs4532         chr5    DRD1
rs921451      chr7    DDC
rs1051730    chr15    CHRNA3
rs1451371    chr7    DDC
rs2060762    chr7    DDC
rs3733829    chr19    EGLN2
rs3733829    chr19    RAB4B-EGLN2
rs3735273    chr7    DDC
rs3757472    chr7    DDC
rs4105144    chr19  N/A
rs6474412    chr8    N/A

We got DRD1, DDC, CHRNA3, and EGLN2 (I assume EGLN2 and RAB4B-EGLN2 are the same), and there are no gene returned for SNP rs4105144 and rs6474412.

However, on the webpage of "188890" (http://omim.org/entry/188890):

1. The table "Phenotype Gene Relationships" listed several genes/locus, which do not match with the above results.

2. In the "Mapping" section, rs4105144 and rs6474412 are mentioned, and are associated with CYP2A6, CYP2B6, CHRNB3 and CHRNA6, but I got no results when search on UCSC genome database.
"These 2 loci include genes involved in nicotine metabolism, such as CYP2A6 (122720) and CYP2B6 (123930) on 19q13, and nicotinic acetylcholine receptor subunits on 8p11 (CHRNB3; 118508) and CHRNA6 (606888)."

In this section, EGLN2 gene is also mentioned.

3. In the "Molecular Genetics" section, several genes are described,
Glutamate Transporters: SLC1A2, SLC17A6 and SLC17A7
Dopamine Transporter/Receptors: SLC6A3, DRD2 and DRD1
DOPA Decarboxylase: DDC
Cholinergic Receptors: CHRNA4, CHRNB2, CHRNA2, CHRNB4, NTRK2, CHRNA3, CHRNA5
G Protein-Coupled Receptor-51: GABABR2
Serotonin Transporter: SLC6A4
Taste Receptor Polymorphisms: TAS2R38

I think I am lost on which gene we should choose in our analysis.

Thanks,