GENE EXPRESSION

CVVCVV

LEAF ROOT

Measuring global gene expression

• OPEN SYSTEM• Serial analysis of gene

expression• potential to detect

every gene expressed

• Potential for use as a gene discovery tool

• CLOSED SYSTEM• Microarrays• limited to detecting

genes that are already identified (spotted on microarray)

• Limited to global gene expression analysis

SAGE - mRNA binding

TTTTTTTUCGAUUCUACUCUGACUCUAAUCUAAUCGUCCGUCAUCUUAACUGACAAAAAAA

TTTTTTTAUCCUAUACGUACUACUAUAUACUGCUAGCUUUCUAUACUAAAAAAA

TTTTTTTUAUCCUAUACGUAACUGUACUGGCUGGUACUGCUGUCUAUAUCUACUGUAAAAAAA

TTTTTTTACUGGUAUCUAGUCGUACGUCGAUCGUAAGUAUGCGCUACUACAAAAAAA

SASAGE - cDNA synthesis

TTTTTTTUCGAUUCUACUCUGACUCUAAUCUAAUCGUCCGUCAUCUUAACUGACAAAAAAAAGCTAAGATGAGACTGAGATTTGATTAGCAGGCAGTAGAATTGACTG

TTTTTTTAUCCUAUACGUACUACUAUAUACUGCUAGCUUUCUAUACUAAAAAAATAGGATATGCATGATGATATATGACGATCGAAAGATATGA

TTTTTTTUAUCCUAUACGUAACUGUACUGGCUGGUACUGCUGUCUAUAUCUACUGUAAAAAAAATAGGATATGCATTGACATGACCGACCATGACGACAGATATAGATGACA

TTTTTTTACUGGUAUCUAGUCGUACGUCGAUCGUAAGUAUGCGCUACTACAAAAAAATGACCATAGATCAGCATGCAGCTAGCATTCATACGCGATGATG

SAGE - cDNA synthesis

TTTTTTTTCGATTCTACTCTGACTCTAATCTAATCGTCCGTCATCTTAACTGACAAAAAAAAGCTAAGATGAGACTGAGATTTGATTAGCAGGCAGTAGAATTGACTG

TTTTTTTATCCTATACGTACTACTATATACTGCTAGCTTTCTATACTAAAAAAATAGGATATGCATGATGATATATGACGATCGAAAGATATGA

TTTTTTTTATCCTATACGTAACTGTACTGGCTGGTACTGCTGTCTATATCTACTGTAAAAAAAATAGGATATGCATTGACATGACCGACCATGACGACAGATATAGATGACA

TTTTTTTACTGGTATCTAGTCGTACGTCGATCGTAAGTATGCGCTACTACAAAAAAATGACCATAGATCAGCATGCAGCTAGCATTCATACGCGATGATG

TTTTTTTTCGATTC TCATCTTAACTGACAAAAAAAAGCTAAG CAGGCAGTAGAATTGACTG

CATGCTGACTCTAATCTAATCGTCCGGTACGACTGAGATTTGATTAG

TTTTTTTATCC GCTTTCTATACTAAAAAAATAGG

CATGCGTACTACTATATACTGCTAGTACGCATGATGATATATGACGATCGAAAGATATGA

TTTTTTTTATCC TGTCTATATCTACTGTAAAAAAAATAGG TGACGACAGATATAGATGACA

CATGCGTAACTGTACTGGCTGGTACTGCGTACGCATTGACATGACCGACCA

TTTTTTTACTGGCATGTAGTCGTACGTCGATCGTAAGTATGCGCTACTACAAAAAAATGACCGTACATCAGCATGCAGCTAGCATTCATACGCGATGATG

TTTTTTTCTGACTCTAATCTAATCGTCCGTCATCTTAACTGACAAAAAAA

GTACGACTGAGATTTGATTAGCAGGCAGTAGAATTGACTG

TTTTTTTCGTACTACTATATACTGCTAGCTTTCTATACTAAAAAAA

GTACGCATGATGATATATGACGATCGAAAGATATGA

TTTTTTTCGTAACTGTACTGGCTGGTACTGCTGTCTATATCTACTGTAAAAAAA

GTACGCATTGACATGACCGACCATGACGACAGATATAGATGACA

TTTTTTTTAGTCGTACGTCGATCGTAAGTATGCGCTACTACAAAAAAA

GTACATCAGCATGCAGCTAGCATTCATACGCGATGATG

TTTTTTTGGGACCATGCTGACTCTAATCTAATCGTCCGTCATCTTAACTGACAAAAAAACCCTGGTACGACTGAGATTTGATTAGCAGGCAGTAGAATTGACTG

TTTTTTTGGGACCATGCGTACTACTATATACTGCTAGCTTTCTATACTAAAAAAACCCTGGTACGCATGATGATATATGACGATCGAAAGATATGA

TTTTTTTGGGACCATGCGTAACTGTACTGGCTGGTACTGCTGTCTATATCTACTGTAAAAAAACCCTGGTACGCATTGACATGACCGACCATGACGACAGATATAGATGACA

TTTTTTTGGGACCATGTAGTCGTACGTCGATCGTAAGTATGCGCTACTACAAAAAAACCCTGGTACATCAGCATGCAGCTAGCATTCATACGCGATGATG

TTTTTTT

TTTTTTT

TTTTTTT

GGGACCATGCTGACTCTAATCTAATCGTCCGTCATCTTAACTGACAAAAAAA

GGGACCATGCGTACTACTATATACTGCTAGCTTTCTATACTAAAAAAA

GGGACCATGCGTAACTGTACTGGCTGGTACTGCTGTCTATATCTACTGTAAAAAAA

CCCTGGTACGACTGAGATTTGATTAGCAGGCAGTAGAATTGACTG

CCCTGGTACGCATGATGATATATGACGATCGAAAGATATGA

CCCTGGTACGCATTGACATGACCGACCATGACGACAGATATAGATGACA

TTTTTTTGGGACCATGTAGTCGTACGTCGATCGTAAGTATGCGCTACTACAAAAAAACCCTGGTACATCAGCATGCAGCTAGCATTCATACGCGATGATG

TTTTTTT

TTTTTTT

TTTTTTT

GGGACCATGCTGACTCTAATCTA ATCGTCCGTCATCTTAACTGACAAAAAAA

GGGACCATGCGTACTACTATATA CTGCTAGCTTTCTATACTAAAAAAA

GGGACCATGCGTAACTGTACTGG CTGGTACTGCTGTCTATATCTACTGTAAAAAAA

CCCTGGTACGACTGAGATTTGAT TAGCAGGCAGTAGAATTGACTG

CCCTGGTACGCATGATGATATAT GACGATCGAAAGATATGA

CCCTGGTACGCATTGACATGACC GACCATGACGACAGATATAGATGACA

TTTTTTTGGGACCATGTAGTCGTACGTCGA TCGTAAGTATGCGCTACTACAAAAAAACCCTGGTACATCAGCATGCAGCT AGCATTCATACGCGATGATG

TTTTTTTGGGACCATGCTGACTCTAATCTA ATCGTCCGTCATCTTAACTGACAAAAAAACCCTGGTACGACTGAGATTTGAT TAGCAGGCAGTAGAATTGACTG

TTTTTTTGGGACCATGCGTACTACTATATA CTGCTAGCTTTCTATACTAAAAAAACCCTGGTACGCATGATGATATAT GACGATCGAAAGATATGA

TTTTTTTGGGACCATGCGTAACTGTACTGG CTGGTACTGCTGTCTATATCTACTGTAAAAAAACCCTGGTACGCATTGACATGACC GACCATGACGACAGATATAGATGACA

TTTTTTTGGGACCATGTAGTCGTACGTCGA TCGTAAGTATGCGCTACTACAAAAAAACCCTGGTACATCAGCATGCAGCT AGCATTCATACGCGATGATG

1

2 33

4

5

5

1

1

11

75 1

155

1 1 5

565

1 7

Gene expression in sample 1

0123456789

10

SEQ

1

SEQ

2

SEQ

3

SEQ

4

SEQ

5

SEQ

6

SEQ

7

Gene expression in sample 1 and 2

0123456789

10

SEQ

1

SEQ

2

SEQ

3

SEQ

4

SEQ

5

SEQ

6

SEQ

7

Microarrays

ACGTATACGA

TATTATCGATCTG

GGACTAGCTAGCTA

GACTACGTAGTACGT

TGATGCTAGTCTA

GCGATGCTATGACGC

Microarrays

• Tissue/condition 1– Isolate mRNA, produce cDNA and label red

• Tissue/condition 2– Isolate mRNA, produce cDNA and label green

Microarrays

ACGTATACGA

TATTATCGATCTG

GGACTAGCTAGCTA

GACTACGTAGTACGT

TGATGCTAGTCTA

GCGATGCTATGACGC

TGCATATGCT

ATAATAGCTAGAC

ATAATAGCTAGAC

ACTACGATCAGAT

Microarrays

Gene expression in sample 1 and 2

0123456789

10

SEQ

1

SEQ

2

SEQ

3

SEQ

4

SEQ

5

SEQ

6

SEQ

7

Differential gene expression in the Arabidopsis hypocotylfrom Microarray or SAGE experiments

-15 -10 -5 0 5 10 15

wildtypeein4

CAUSE?

CONSEQUENCE?

Measuring global gene expression

• OPEN SYSTEM• Serial analysis of gene

expression• potential to detect

every gene expressed

• Potential for use as a gene discovery tool

• CLOSED SYSTEM• Microarrays• limited to detecting

genes that are already identified (spotted on microarray)

• Limited to global gene expression analysis