EE 434

BIOMEDICAL SIGNAL PROCESSING

FINAL PRESENTATION

on

SAM Analysis of Microarrays of

Mycrobacterium Tuberculosis and Capreomycn

Başak Esin Köktürk

120206021

WHAT IS TUBERCULOSIS?

Tyberculosis or TB, is an

infectious bacterial disease

caused by Mycrobacterium

tuberculosis.

It affacts commonly lungs but

also it affects the central

nervous system,lymphatic

system, circulatory

system, genitourinary system

and gastrointestinal system Source :

http://upload.wikimedia.org/wikipedia/commons/thumb/4/49/

Extrapulmonary_tuberculosis_symptoms.png/180px-

Extrapulmonary_tuberculosis_symptoms.png

SYMPTOMS OF TUBERCULOSIS

Coughing up blood

Cheast pain

Weakness

Weight loss

Night sweats

TREATMENT OF TUBERCULOSIS

Active tuberculosis will kill about two of every three

people affected if left untreated. Treated

tuberculosis has a mortality rate of less than 5%.

Tuberculosis is treatable with a six-month course of

antibiotics.

One of this antibiotics is Capreomycin .

WHAT IS CAPREOMYCIN?

Capreoycin is an peptide

antibiotic against to tuberculosis.

The importance of capreomycin is

reflected by its potential to deal

with multi-drug resistance and

latent infection together.

Capreomycin inhibits protein

translation by intefering with the

function of ribosomes.Source :

http://upload.wikimedia.org/wikipedia/commons/thumb/6/

62/Capreomycin_IB.svg/800px-Capreomycin_IB.svg.png

GSD 2677 DATASET EXAMINATION

Title : Capreomycin effect on Mycobacterium tuberculosis

Summary : Analysis of Mycobacterium tuberculosis cultures after treatment withcapreomycin. Capreomycin is a drug used to treat multi-drug resistanttuberculosis (TB), and possesses bactericidal activity against non-replicatingTB bacilli. Results provide insight into the spectrum of action of capreomycin.

Platform organism: Mycobacterium tuberculosis H37Rv

Sample organism : Mycobacterium tuberculosis

Platform : GPL4519: [TB-All-Antisense] Affymetrix M. tuberculosis AntisenseArray

Cititation : Fu LM, Shinnick TM. Genome-wide exploration of the drug action of capreomycin on Mycobacterium tuberculosis using Affymetrix oligonucleotideGeneChips. J Infect 2007 Mar;54(3):277-84.

Sample Count : 4

Sample Subsets :

GSM183531 untreated M. tuberculosis_H37Rv_log-phase_rep1

GSM183633 untreated M. tuberculosis_H37Rv_log-phase_rep2

GSM183632 capreomycin M. tuberculosis_capreomycin_4h_rep1

GSM183634 capreomycin M. tuberculosis_capreomycin_4h_rep2

A GLANCE TO REFERENCE STUDY

Using microarray technology action of capreomycin

on the mechanism is investigated.

Microarray approach is chosen because , it is

useful for unveiling genes physiologically or

relevant to the drug’s mode action.

As a result in this work , gene expression patterns

are reported when response M. tuberculosis

bacteria on capreomycin.

METARIALS AND METHODS

Drug-treatment of M. tuberculosis

RNA isolation

Tatol RNA was converted to cDNA

cDNA is used in PCR analysis

Gene expression data analysis with GCOSv1.4

SAM ANALYSIS

Microarrays can measure the expression of thousands

of genes to identify changes in expression between

different biological states.

Significance Analysis of Microarrays (SAM), that assigns

a score to each gene on the basis of change in gene

expression relative to the standard deviation of repeated

measurements.

For genes with scores greater than an adjustable

threshold, SAM uses permutations of the repeated

measurements to estimate the percentage of genes

identified by chance, the false discovery rate (FDR).

Source : Virginia Goss Tusher, Robert Tibshirani, Gilbert Chu,”Significance analysis of

microarrays applied to the ionizing radiation response” , Departments of Medicine and

Biochemistry, Stanford University,2001

SAM ANALYSIS PROCEDURE WITH MEV

Loading dataset SOFT file

Choosing affymetrix matrix with platform

information

Normalization of dataset

Begining SAM analyse

Determining number of non-significant genes

Adjust the delta value

Determine the most expressed gene

SAM ANALYSIS RESULTS FOR GSD2677

POSITIVE SIGNIFICANT GENES

The gene with identifier lppS is fadD35

fadD35