Search found 8 matches

by ermis
Wed Oct 11, 2006 7:37 am
Forum: Bioinformatics
Topic: SNPs and promoter polymorphisms
Replies: 16
Views: 16600

Tutorial

G-Do wrote:It sounds like you need a primer on how to use these databases. I would recommend that you find yourself a tutorial online on (i) how to use UCSC efficiently and (ii) how to use dbSNP efficiently before asking any more questions.


Any good suggestions?
by ermis
Tue Oct 10, 2006 1:12 pm
Forum: Molecular Biology
Topic: Antioxidant Status molecules
Replies: 0
Views: 870

Antioxidant Status molecules

Can anyone tell me which of these molecules (or genes that encode them) are associated with antioxidant status? Thanks in advance. ADD1 ADRA1A ADRB1 ADRB2 ADRB3 AGT AGTR1 ALAP ALOX5AP APOA4 APOH CCR2 CLU CPT1B CPT2 CYP11B2 CYP4A11 EDNRA F2 F5 F7 F12 F13B FGB GNB3 GRK4 HSD11B2 HTR2A ICAM1 IL1B IL6 IR...
by ermis
Mon Oct 09, 2006 8:10 pm
Forum: Bioinformatics
Topic: SNPs and promoter polymorphisms
Replies: 16
Views: 16600

The color-coding is annotated function; it tells you what the minor allele of the SNP is believed to do in terms of gene structure. 1) The promoter for TGFB1 overlaps another gene, so be careful - SNPs in this region may have been annotated with the other gene's function. 2) As for the SNPs you cou...
by ermis
Sun Oct 08, 2006 11:28 am
Forum: Bioinformatics
Topic: SNPs and promoter polymorphisms
Replies: 16
Views: 16600

VWF is on the (-) strand and the numbers UCSC gives are for the (+) strand. You can tell that this is the case because when you look at VWF in the UCSC Genome Browser, the arrow notches point from right to left and not left to right. Therefore, you have to think about the whole thing backwards. Tra...
by ermis
Thu Oct 05, 2006 8:21 pm
Forum: Bioinformatics
Topic: SNPs and promoter polymorphisms
Replies: 16
Views: 16600

Hi ermis, 1) No. This list gives you all SNPs within 2kb of the VWF gene, but that includes downstream, too. So not all of these SNPs are promoter SNPs. The gene of the particular example, VWF, starts at 5928301 and ends at 6104097 of the minus strand. Does this means that the promoter snips locate...
by ermis
Wed Oct 04, 2006 2:41 pm
Forum: Bioinformatics
Topic: SNPs and promoter polymorphisms
Replies: 16
Views: 16600

Re: Well, that didn't work.

1) How about this method: I went here: w and I have chosen the GENE database. Let's say I was interested at the VWF promoter gene polymorphisms. I typed VWF itno the search box and it gave me the VWF gene information for several organisms. I chose HOMO SAPIENS, but not the gene itself but the word l...
by ermis
Tue Aug 22, 2006 12:00 pm
Forum: Bioinformatics
Topic: SNPs and promoter polymorphisms
Replies: 16
Views: 16600

there is no database where you can just look up the promoter sequence of any random gene (as far as I know, if you can show me otherwise I'd be really interested). I think you just have to work yourself through this database 1) So, I guess that I will first look at the references for each gene and ...
by ermis
Mon Aug 21, 2006 3:08 pm
Forum: Bioinformatics
Topic: SNPs and promoter polymorphisms
Replies: 16
Views: 16600

SNPs and promoter polymorphisms

Here is the thing: I search here m for SNPs that concern the promoter of several genes. My question is: 1) Am I searching at the right place, or should I try here: m ? 2) If this is the right place (m) which option should I use from the "limits" section in order to take as results only the...