Home
Home Page for the UCSD SNP Discovery programs
PPG
Program
PPG program aims, organization,
projects, personnel, flow
chart
PPG
Program Data
Public Data and UCSD Account Data
PPG
SNP Data
Excel Workbooks, SNP ID Names, Public Domain and Proprietary Data
Human
Chromosomes
Human Genome info
Candidate
Loci
Mouse
Chromosomes
Mouse Genome info
Cand
Loci Homologues
SNPs
and Haplotypes
Single Nucleotide Polymorphism and Haplotype info
Usage
Usage and help for Program software
Biological
Protocols
Protocols used in laboratory
research by the PPG program
Recent
Changes
Changes in Web Site Data
DNASYSTEM
Web pages with Links to other Bioinformatic Sites
Purpose of this Site
This is the Web site for a 5 year NIH sponsored Program Grant (PPG) to investigate physiological, pharmocological, genetic, biochemical, and molecular biological aspects underlying human human essential hypertension.
The sympathetic branch of the autonomic system is a key regulator ,,, more
Recent Changes in Data Files
31
Oct 2006: Complete Renewal and Update of SNP ID Names
SNP ID Names have now been assigned to all SNPs known to be of interest
to Hypertension personnel as of May, 2006, including those analysed by
Sequenom, UCSD resequencing, TGCA, and Weber. Names are provided based
on CAP site (transcription start), on AUG site (translation start), or
on Mature Peptide start site for nonCDS SNPs, or on Protein or Mature
Peptide protein start sites for CDS SNPs. Locus information provided includes
four coordinate systems (Locus start site, 5000 bp upstream of locus start
site, NT start site (NCBI SNP coordinates, NC start site, with comparison
to UCSC chromosomal coordinates), structure coordinates, locus cartoon,
and summary of locus function. Complete data are provided for each transcriptional
Variant and protein Isoform having data at NCBI. Flanking sequence is
provided for all SNPs. For two loci of interest (CHGA and TH), complete
data is also provided in spreadsheet "SNPnames-dbSNPall" for
all SNPs present in dbSNP at NCBI as of Sept, 2006, including 5000 bp
into the promoter (upstream) and 2000 bp 3' (downstream) of the locus.
TH with its 3 transcriptional variants is used as an example for comparison
of SNP ID names between the 3 variants. More information is available
here.
7
Sept 2005: CHI-square Analysis of Select Subgroup Pairs
CHI-square analyses of Sequenom data for pairs of subgroups of the nnnn.Unrelated
population are now available. CHI-sq values were calculated in two ways,
with identical results. The pairs of subgroups are:
- Ethnicity: White vs Black
- Gender: Male vs Female
- Blood Pressure Status: Normotensive vs Hypertensive
- Normotensive and Hypertensive subgroups of Black, White, Male, and Female subgroups
13
July 2005: Biological Protocols of the PPG Program
Biological or laboratory protocols or "standard operating procedures"
(SOPs) have been documented and recorded here, to assist in maintaining
a consistent and stable operating environment.
3
June 2005: Subgroup Analyses of Sequenom Resequencing Data
We have begun analyses of subgroups of the resequencing data
received from Sequenom. Initial analyses are for the nnnn.Unrelated population,
and include data analysis of the following subgroups of the total data
(data received Nov, 2003, Jan, 2004, and Feb, 2004):
- All data
- Ethnicity: White, Black, Hispanic, Asian
- Gender: Male, Female
- Blood Pressure Status: Normotensive, Hypertensive
- Normotensive and Hypertensive subgroups of each of the 4 Ethnicity subgroups
- Normotensive and Hypertensive subgroups of each of the 2 Gender subgroups
Results for each subgroup are presented in Excel worksheets having the same columnar format as developed for analysis of the UCSD Data Workbooks described below. In addition to these worksheets of complete information, worksheets containing major comparative data columns from each subgroup are developed. These worksheets present 8 columns of data for each subgroup in side-by-side style, permitting relatively easy direct comparison between different subgroups; for example, comparison of SNP data for black normotensives vs black hypertensives, or for white hypertensives vs black hypertensives. These types of subgroup analyses can be readily extended to other populations and to data obtained from other sources. Data from different sources can also be combined, and new subgroups can be analysed. Note that these subgroups are of zero order (all data), first order (ethnicity, gender, BP status), and second order (Ethnicity-BP, Gender-BP); others can be developed as desired. For more information see Subgroup Data Workbooks.
10
May 2005: Presentation to Nik Schork Group on"Primary Analysis of
new SNP Genotype Data"
A Powerpoint presentation was given to the Nik Schork group in
May, 2005, on the rationale, analysis methodology, quality control (QC)
methodology, format of resulting SNP data analysis workbooks, and usage
of the analysis and data files available for downloading from this Web
site. The presentation emphasized the following topics: standard format
of raw genotype data, a format independent of sequencing source; format
of the analysis worksheets (one row per SNP, issues of unique SNP ID name);
QC analyses; additional data present in analysis worksheets; types of
SNP ID names; analysis of subsets or subgroups, eg specific gender or
ethnic group, from within a total population. More information is available
here.
... more
Latest modification: October,
2006
If you have comments or queries, send email to Doug Smith
PPG Program Features
CHI-square Analysis of SubGroups