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Lecture 7
Tuesday, Jan. 27, 2015
Part 1:
C1
Correlation between protein and
mRNA abundance in yeast.
Gygi SP, Rochon Y, Franza BR, & Aebersold R.
Microarray
s1
Affymetrix2
ORF
control
R/G ratios
R, G values
quality indicators
ORF
Averaged PM-MM
presence
PM
MM
feature statistics
25-mers
SAGE3
concatamers
Counts of SAGE
14-mers sequence
tags for each ORF
DeRisi, et.al., Science 278:680-686 (1997); 2 Lockhart, et.al., Nat Biotech 14:1675-1680 (1996)
3
Velculescu, et.al, Serial Analysis of Gene Expression, Science 270:484-487 (1995)
1
Codon
Bias
CAI score of 0:
The gene uses different codons from the reference set of genes
http://phage.cisat.jmu.edu/bioinformatics/wp-content/uploads/2011/04/codon_table2.jpg
R**2 = 0.38
CAI score
Codon position
Codon position
Part 2:
C2
Protein pathway and complex
clustering of correlated mRNA and
protein expression analyses in
Saccharomyces cerevisiae
Washburn, et al..
Abstract
Cell growth
condition A
Cell growth
condition B
Heavy Label
Sample
ProteinX from A
Quantitative
Proteomics
ProteinX from B
Parent ion
intensity
Quantitative Proteomic
Methods have different
entry points into this scheme
(We will cover this in detail
in future lectures!)
ProteinX from B
PeptideX from
ProteinX from B
PeptideX from
ProteinX from A
Mass/charge
The major challenge of large coupled datasets is assembling the data into a biological
context.
Proteins function in pathways and complexes
Clustered loci by protein pathways and complexes according to YPD and MIPS
MET6
90
731.6
85
80
968.6
75
803.6
70
Relative Abundance
65
60
961.6
937.4
55
50
1279.6
45
1291.5
646.4
40
761.5
1266.6
35
30
574.6
887.6
717.7
481.5
25
969.5
603.4
1067.4
886.5
20
15
476.1
10
467.6
703.4
536.6
1292.6
1147.6
828.0
1241.6
1359.7
5
0
400
500
600
700
800
900
m/z
1000
1100
1200
1300
1400
Intracellular sulfate
RP
MET3
5-adenylylsulfate
MET14
Expression
Rich/Min
0.09-0.05
0.12-0.1
0.16-0.125
0.24-0.17
0.49-0.25
2.0-0.5
2.0-4.0
4.1-6.0
6.1-8.0
8.1-10.0
10.1-20.0
3-phospho-5-adenylylsulfate
MET16
sulfite
ECM17
CYS3
MET10
cystathionine
cysteine
sulfide
MET17
CYS4
homocysteine
CH3
MET6
methionine
SAM1
SAM2
S-adenosylmethionine
5-methyltetrahydrofolate
5,10-methylenetetrahydrofolate
MET13
100
95
888.0
90
85
1331.9
80
878.8
75
70
918.9
Relative Abundance
1317.1
ARG1
65
60
1359.8
55
50
45
1272.9
40
919.8
870.8
590.8
35
1179.6
30
583.9
15
581.2
10
568.1
0
400
1229.3
1099.2
780.7
20
947.6
786.7
666.5
25
1259.6
1062.6
492.6
500
659.4
600
773.2
700
800
900
m/z
1000
1100
1200
1300
1400
Loci Characterized
mRNA Expression
(rich/min)
Protein Expression
(rich/min)
Cytochrome bc1
COR1, QCR2, 7
0.67 0.09
0.42 0.14
COPI
1.16 0.10
0.42 0.10
ARF1
1.14 0.17
2.11 0.26
ARF2
0.66 0.20
1.19 0.82
GEA1
0.79 0.39
0.33 0.23
GEA2
0.94 0.47
0.72 0.29
SYT1
1.25 0.55
0.89 0.22
SEC13
1.19 0.50
0.58 0.19
SEC23
1.33 0.45
0.46 0.23
SEC24
1.18 0.30
0.97 0.52
SAR1
0.81 0.40
0.96 0.10
0.93 0.10
0.48 0.09
VMA2
1.01 0.10
1.72 0.44
VMA5
0.89 0.22
0.99 0.15
40S (N=28)
1.33 0.15
1.41 0.27
60S-1 (N=28)
1.31 0.15
1.37 0.37
60S-2 (N=8)
1.39 0.18
3.06 0.94
GTPases
GEFs
COPII
GTPase
Vacuolar H(+) ATPase
Ribosome
Anc1p
Sin4p
Loci Characterized
mRNA Expression
(rich/min)
Protein Expression
(rich/min)
RNA Pol II
Holoenzyme
0.94 0.26
0.30 0.10
SPT complex
SPT4
0.77 0.75
0.24 0.06
SPT5
1.17 1.19
0.58 0.32
SPT6
1.94 0.75
1.28 0.35
1.10 0.21
0.35 0.17
Histone
Modification
Repression
TUP1
1.10 0.27
8.39 0.53
SIN3 binding
STB2
0.23 1.8
24.0 3.6
-general transcriptional
repressor
RNA
Protein
Modification
?
?
Mutations,
Polymorphisms
(Epigenetics)
Lecture 7
Tuesday Feb. 4, 2014
TranscriptProteomics,
omics
PTMs
Phenotype
Correlation of Complex
Phenotypes to
Levels of Biopolymers
35
Across the Central Dogma