Opinions
From Variome
association study is feasible? 2007/04/15 Areum Han
splice [splais] 2007/02/08 Areum Han
━verb (spliced, splicing)
1. to join (two pieces of rope) by weaving the strands of one into the other.
2. to join (two pieces of timber, etc) by overlapping and securing the ends.
3. to join the neatened ends of (two pieces of film, magnetic tape, wire, etc) using solder, adhesive, etc.
reference : yahoo dictionay
NCBI launched dbGaP (Genotype and Phenotype) dabase! 2007/01/25 Areum Han
They are dealing with information from the subject selections to genotype results.
Pretty interesting..but not well organized yet.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gap
Does SNP within non-functional region have effects? 2006/07/25 Areum Han
It is very interesting paper about intronic SNPs which is related with efficiency of mRNA splicing.
http://www.nature.com/ng/journal/v30/n1/full/ng809.html
The list of genes affected by positive selection of recent human
| Gene | Function Category | Function |
| HBB | Host–pathogen interations | beta globin |
| Duffy blood group | Host–pathogen interations | Duffy blood group |
| G6PD | Host–pathogen interations | Glucose-6-phosphate dehydrogenase |
| Glycophorin A | Host–pathogen interations | Glycophorin A |
| Pyrin | Host–pathogen interations | |
| TNFSF5 | Host–pathogen interations | Tumor necrosis factor ligand superfamily, member 5 |
| ALDH2 | Dietary adaptation | Aldehyde dehydrogenase 2 |
| LCT | Dietary adaptation | Lactase |
| MC1R | Appearance | Melanocortin 1 receptor |
| TAS2R38 | Sensory systems | Taste receptor type 2 member 38 |
The list of genes detected from Fst analysis 2006/07/13 Areum Han
| Gene | Function | Type of selection |
| ABCC1 | one of family of organic anion transporters, can protect cell against drugs, also linked to Strep pneumo resistance in mouse models | Positive |
| ABO | A & B code for glycosyltransferases, O null allele | Balancing |
| ADH | alcohol metabolism, associated with alcoholism | Positive |
| ALDH2 | alcohol metabolism, associated with alcoholism | Positive |
| APCS | serum amyloid P component gene | Positive |
| ASPM | controls human brain size, mutations lead to primary microcephaly | Positive |
| C6 | membranolytic activity important for defense against invading microorganisms | Balancing |
| CAPN10 | associated with type 2 diabetes | Positive,Balancing |
| CYP3A4 | involved in metabolism of exogenous substances | Positive |
| CYP3A5 | involved in metabolism of exogenous substances, mutation associated with increased blood pressure | Positive |
| DMD | mutation causes Duschenne's Muscular Dystrophy | Positive |
| FUT2 | encodes a protein responsible for determing an individual's A, B, and O blood protein secretor status | Balancing |
| FY | protection from P. vivax malaria | Positive |
| GRK4 | involved in blood pressure regulation, associated with hypertension | Positive |
| HFE | decreased risk of anemia in pregnancy vs. hemochromatosis | Positive |
| IL13 | believed to play important role in the pathogenesis of atopy and allergic asthma | Positive |
| IL4 | cytokine, stimulates: T cells to take TH2 phenotype, B cell type switching, and IgE secretion | Positive |
| KIR3DL1 | expressed by cells of the immune system and regulates their function | Positive |
| KIR3DL3 | expressed by cells of the immune system and regulates their function | Balancing |
| LDLR | cell surface glycoprotein, plays a role in plasma and cholesterol maintenance | Balancing |
| LILRA3 | expressed by cells of the immune system and regulates their function | Positive |
| MC1R | phenotypic variation in skin and hair pigmentation | Positive, purifying |
| MMP3 | associated with risk of coronary artery disease | Positive |
| PTC/ TAS2R38 | bitter taste receptor, population differentiation | Balancing |
| VAV3 | a hemopoetic cell specific guanine nucleotid exchange factor involved in actin rearrangement | Positive |
| KIR gene family | cell-surface receptors expressed on natural killer cells (killer inhibitory receptor) | Positive, Balancing |
I extracted this information from a brand new paper from sabati's group (2006, science)
DNA - RNA - Protein 2006/06/12 Areum Han
I found the expression from Dr. Eva's paper (Cancer letters, 2006, 1-12)
The mRNA as an intermeidate between DNA (with 'coding' potential) and protein (with 'executive' fuction').
What are “the most effective/strong SNPs" in view of their category 2006/06/07 Areum Han
Today, in KOBIC Dr.Hahn from NIH had a talk about the human specific mutations.
He focused on frameshift and nonsense(prem-stop) mutations since he assumed that they
make 'strong' differences on protiens. And I agree with that.
Where are “favorite loci of SNPs”? 2006/06/01 Areum Han
Where are “favorite loci of SNPs”?
I believe the genetic loci for SNPs might be determined following function f.
f = p * i
p = population of gene products where a SNP is located
(e.g., number of transcripts, durability of transcripts)
i = impact of a SNP to a host gene and neighbor genes
(e.g., closeness to critical sites such as protein interaction sites)
The value of f function should not be too large to be eliminated nor too small to make no difference.
