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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
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