A multiomics project

Assignment 2: NAR database

by xien low

“critically and collaboratively inquiring into the dimensions associated with creating and sustaining safe, healthy, equitable, inclusive, accepting and engaging learning environments.”

by celine singh

Teaching in the Inclusion Classroom

by mila rowe

Nucleic Acid Research Database

by MUHAMMAD HAFIZUDDIN BIN YUSOF

case study

MS

Asthma

SLE

VitD

Gaps

OBJECTIVES

2. Proteomics expression of Vit D deficiency

1. Identify genetic mechanism of Vit D defiency

CASE STUDY: VITAMIN D & CALCIUM

Step 5: Check X levels in lab results, questionnaires, EMR - HM

get baseline characteristics

Step3: Check SNPs in the protein statistically diff - RZ

identify impact status

Moderate

affecting effectiveness

High

affects prot structure

Step2: Perform proteomics diff expression - RZ

Step1: Categorize groups - HM

Vit D def & normal lipid

463

Vit D def & Dyslepidimia def

114

Vit D normal & dyslepedimia

199

Vit D normal & normal lipid

851

lipid threshold

HDL

LDL

triglycerides

cholesterol

WORKFLOW 2: From 14k, we segregate samples into

previous work by others

3 dominant gene variants

CYP2R1

rs10741657

NADSYN1

rs12785878

rs2282679

~1223 samples

>12ng/ml, < 20 ng/ml

normal/sufficient

~1049 samples

>=20 ng/ml

~576 samples

how many of these 4205 samples have proteomics data

get the genetic variants profile

filter proteomics using "HDL associated proteins" ~ 100 types

low APO-X

high APO-X

proteomics expression analysis

find statistically sig protein expression

compared genetics w protein exp

MODIFIER

gtex

MODERATE

HIGH

match w n=270

compare the proteins

Subtopic

genetic variants that causes X to the proteins in previous studies

<12 ng/ml

WORKFLOW 1: get list of proteins enriched in vitD deficiency from our proteomics study (n=270)

find the genetic variants associated w them

indirect

non-coding region

coding but modifier

it regulates the expression of the protein

direct

coding region

moderate impact

it reduces the effectiveness of a protein

high impact

it affects protein structure formation

certain genes linking vitD defeciency with

some ppl have higher rate of deciciency compared to others

this means there might be genetic/inherited factors

Preliminary work

n=270

control

~90

case

~180

previously we look at

its molecular pathways associated with vitamin D deficiency and dyslipidemia

its anti-inflammatory potential

effects of vitamin D on HDL production

AIM

xxxxxx

Objectives

OBJ4

OBJ3

OBJ2

OBJ1

DATA

Metabolomics

Proteomics

#samples

orig 3000

inclusion/exclusion

exc = anyone with pregnancy

incl = do not suffer from chronic diseases

2000

sufficient

>20

655

insufficient

>=12,<20

821

deficient

<12

399

Genomics