文档介绍：Discrete works
Corey Yanofsky 0148145
Biology of works
genes are transcribed, producing mRNA
mRNA is translated into proteins
presence of newly produced proteins alters state of cell, inducing changes to the rates of some genes’ transcription
some proteins are transcription factors that directly control the rate of transcription of certain effect: genes influence each other’s transcription, turning each other on and off
Typical Gene Expression Data
Problem: how can these data be used to infer how these three genes influence each other?
gene 1
gene 2
gene 3
Modelling Gene Expression Data
assume that genes exist in two states: on and off
if expression of gene i is above level ti consider it on, otherwise, consider it off
gene 1
gene 2
gene 3
Modelling Gene Expression Data
assume that genes exist in two states: on and off
if expression of gene i is above level ti consider it on, otherwise, consider it off
gene 1
gene 2
gene 3
t2
t1
t3
Modelling Gene Expression Data
assume that genes exist in two states: on and off
if expression of gene i is above level ti consider it on, otherwise, consider it off
gene 1
gene 2
gene 3
t2
t1
t3
on
on
on
on
on
on
off
off
off
off
off
off
off
off
off
off
on
on
on
on
on
on
on
off
off
off
off
off
off
on
off
off
off
Modelling Gene Expression Data
we obtain the following discretized gene expression data:
time
0
5
10
15
20
25
30
35
40
45
50
55
gene 1
0
0
0
0
0
0
1
1
1
1
1
1
gene 2
0
0
0
0
0
0
0
1
1
0
0
0
gene 3
1
1
1
1
1
1
1
0
0
0
0
0
the gene expression data is now in the form of bit streams
Modelling Gene Expression Data
the problem can now be re-phrased:
how do the past states of the bit streams determine the present states?
we use tools from information theory to help solve this problem
first step: model genes as elements in a work
Modelling Gene Expression Data
definition of discrete work:
a directed graph whose vertices ar