slide1 n.
Download
Skip this Video
Loading SlideShow in 5 Seconds..
Gene Expression And Regulation PowerPoint Presentation
Download Presentation
Gene Expression And Regulation

Loading in 2 Seconds...

play fullscreen
1 / 24

Gene Expression And Regulation - PowerPoint PPT Presentation


  • 148 Views
  • Uploaded on

Gene Expression And Regulation. Bioinformatics January 11, 2006 D. A. McClellan (david_mcclellan@byu.edu). Gene Expression. Expressed in the transcriptome Every eukaryotic genome contains between 5000-60,000 protein-coding genes Only a small subset of those genes are transcribed.

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about 'Gene Expression And Regulation' - benita


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
slide1

Gene Expression

And Regulation

Bioinformatics

January 11, 2006

D. A. McClellan (david_mcclellan@byu.edu)

gene expression
Gene Expression
  • Expressed in the transcriptome
  • Every eukaryotic genome contains between 5000-60,000 protein-coding genes
  • Only a small subset of those genes are transcribed
slide3

Gene expression is regulated

in several basic ways

  • • by region (e.g. brain versus kidney)
  • • in development (e.g. fetal versus adult tissue)
  • • in dynamicresponse to environmental signals
  • (e.g. immediate-early response genes)
  • in disease states
  • by gene activity

Page 157

central dogma of molecular biology
Central Dogma of Molecular Biology

DNA

RNA

protein

phenotype

cDNA

Page 159

slide5

protein

protein

DNA

RNA

DNA

RNA

cDNA

cDNA

UniGene

SAGE

microarray

Fig. 6.2

Page 159

expression databases analyses
Expression Databases & Analyses
  • UniGene: for the comparison of cDNA libraries
    • Goals: (1) create one unique entry for each gene, (2) collect all the ESTs associated with each gene
  • SAGE: Serial Analysis of Gene Expression library
  • DNA microarrays
slide7

5’

3’

exon 1

intron

exon 2

intron

exon 3

3’

5’

transcription

5’

3’

RNA splicing (remove introns)

3’

5’

polyadenylation

5’

AAAAA 3’

Export to cytoplasm

Fig. 6.3

Page 161

slide9

Analysis of gene expression in cDNA libraries

  • A fundamental approach to studying gene expression
  • is through cDNA libraries.
  • Isolate RNA (always from a specific
  • organism, region, and time point)
  • Convert RNA to complementary DNA
  • Subclone into a vector
  • Sequence the cDNA inserts.
  • These are Expressed Sequence Tags

insert

vector

Page 162-163

slide10

UniGene: unique genes via ESTs

  • • Find UniGene at NCBI:
  • www.ncbi.nlm.nih.gov/UniGene
  • UniGene clusters contain many ESTs
  • • UniGene data come from many cDNA libraries.
  • Thus, when you look up a gene in UniGene
  • you get information on its abundance
  • and its regional distribution.

Page 164

slide11

Cluster sizes in UniGene

This is a gene with

1 EST associated;

the cluster size is 1

Page 164

& Fig. 2.3,

Page 23

slide12

Cluster sizes in UniGene

This is a gene with

10 ESTs associated;

the cluster size is 10

Page 164

slide13

Cluster sizes in UniGene (human)

Cluster size Number of clusters

1 10,400

2 7,100

3-4 6,800

5-8 5,300

9-16 3,800

17-32 3,100

500-1000 1,500

2000-4000 130

8000-16,000 12

16,000-30,000 3

Page 164

UniGene build 186, 9/05

slide14

Ten largest human UniGene clusters

Cluster

size Gene

22,925 eukary. translation EF (Hs. 522463)

22,320 eukary. translation EF (Hs. 4395522)

16,562 actin, gamma 1 (Hs.514581)

16,309 GAPDH (Hs.169476)

16,231 actin, beta (Hs.520640)

11,076 ribosomal prot. L3 (Hs.119598)

10,517 dehydrin (Hs.524390)

10,087 enolase 1 (alpha)(Hs.517145)

9,973 ferritin (Hs.433670)

8,966 metastasis associated (Hs.187199)

Table 6.2

Page 165

UniGene build 186, 9/05

slide15

UniGene brain

libraries

slide16

UniGene lung

libraries

slide17

Fig. 6.7

Page 167

slide18

Brain

Lung

Fig. 6.7

Page 167

slide19

CamKII

up-regulated

in brain

n-sec1 up-regulated

in brain

surfactant up-

regulated in lung

Page 167

slide20

Fisher’s exact test provides a p value

Digital differential display (DDD) results in UniGene

are assessed for significance using Fisher’s exact test

to generate a p value.

p =

The null hypothesis (that gene 1 is not differentially

regulated in a comparison of two libraries) is rejected

when p is < 0.05/G (where G = the number of UniGene

clusters analyzed).

NA! NB! c! C!

(NA + NB)! g1A! g1B! (NA – g1A)!(NB – g1B)!

Pages 165

slide21

Pitfalls in interpreting cDNA library data

  • • bias in library construction
  • • variable depth of sequencing
  • • library normalization
  • error rate in sequencing
  • contamination (chimeric sequences)

Pages 166-168

slide22

http://mgc.nci.nih.gov

Fig. 6.8

p. 168-169

slide23

Serial analysis of gene expression (SAGE)

• 9 to 11 base “tags” correspond to genes

• measure of gene expression in different

biological samples

• SAGE tags can be compared electronically

Page 169

slide24

SAGE tags are mapped to UniGene clusters

Cluster 1

Cluster 2

Cluster 3

Tag 1

Tag 1

Tag 2

Tag n

Cluster 1

Page 169