Applied bioinformatics for the identification of regulatory elements

1

• Applied bioinformatics for the identification of
  regulatory elements

Lior Moshe Ohad Manor Guide Tommy 1/5/2005
2
????????

• ??? ?? ???? ????? ???? ?????? ?????
  (micro-array)
• ?????? ??????? ????
• ??????? ???? ?????? ???????? (????? ??)

????? ????? ???????? ?????? ??????? ??????? ?????
?? ??????? ???? ????? ????.
3
??? ??????

• ???? ?????? ?????? ????? ?????
• ?????? ??? ???? ?????? ????? ???? ???????
• ?????? ???? ??? ???? ???? ???? ???? ??? ????
  ??????? ?????? ????? ?? ???

4
???? ??????
Taken from W. Wasserman et al.
5
???? ???? ???????

• ????? ???? ???????
• ???? trans
• ???? cis
• ???? ??-???????
• ????? ??????? ???????
• ??????????
• ????????
• ????????

??? ????? ????? ?- cis-regulatory elements?
6
????? ?????????based on Saeed Tavazoie et al.
(1999) Systematic determination of genetic
network architecture
7
????? ??????
????? ???? ???? ????? ???? ?????? ?????
????????? ??????
???? ???? ???? ????? ????? ????? ?????? ????
??????? (clustering)
??? ????? ???? ??????? ???? upstream ?????
????? ?? ??????? ????? ?????
8
??? ????? ?????
???? ???? ?????? ???? cho et al. ?????
micro-arrays (????? ?"? ??? ?????) ?? 6220 ????
?? S. Cervisiae ???? ??? ?????? ?? ?-15 ??????
??? ?????.
9
??? ?????? (clustering)

• ??????? ?? ??????? ?? ????? ?????.
• ????? ?? ?-3000 ???? ?? ????? ?????? ??? ??????.
• ?????? ???? ?-30 ??????? ????? ???????? ?-
  k-means.
• ?????? ?-MIPS ???????????? ???????? ??? ??
  ??????? ?? ???????? ?????????.

10
????? ??????? upstream

• ????? ?????? alignACE ?????? ???????.
• ????? ??????? ????? ????? 600 ?????? upstream
  ?????? ?-ORF ????? ??????.
• ?????????? ?????? ????? ????????????
• ????? ????? ?????? ???? ????? ?????? ??? ?????
  (?????? ???? ?????? ?? ORFs)
• ???? ??????? ???? MAP ?? ???? ????

11
????? ??????? ????? - ?????

• ????? ???? ?????? ???? ?? ?????
• ????? ??? ?? 50 ?-ORFs ??????? ????? ?????
  ??????.
• ??? ?????? ??????? ???? ???, ??? ??? ????? ????
  ??? ?? 80-50 ORFs ??????? ?????.

80
50
12
????? ??????? ????? - ?????

• ???? ??????? ??????? ???? ????? ????? 10.
• ???? ?? ????? ?????? ?-500 ????? ????????.
• ???? ???? ???? ????? ???
• ???? ????? ??????? ???? ??????.
• ????? ?????? ???? ?????? ????? ???????.

13
?????? ????????

• ????? 18 ??????? ??????? ??? 12 ??????? ??? 7 ???
  ??? ?????? ???????.
• ??? ?? ?? ????
• ????? ?????? ??? ????? ????? ???????
• ???? ????????? ????? ???? ?? ????? ???????
• ??? ????????? ?????? ????? ???

14
????? ???????

• ?????? ???????? ????? ?? ???????? ???? ?????
  ?????? ?? ???????? ???? ???????? ???????? ????.
• ??????

Taken from S. Tavazoie et al.
15
????? ???????

• ??????? ????????? ?????? ????? ????? ??? ???????
  ???? ?? ????? ??? ???? ????? ???? ?????? RAP1.
• ????? ?? ?? ??????? ??? ???? ????? ??? ??????
  ?????? ??????? ????.

16
?????? ??????

• ???? ????? ?? ???? (cluster 14) ???????? ????????
  ???? S-G2 ?? ????? ???.

Taken from S. Tavazoie et al.
17
?????? ??????

• ??? ???????? M-14a, M-14b ???? ???? ????????
  ?????? ??? ??? ?????? ?? ?? ??? ????? ?? ?????
  S-G2 ????? ???????????.
• ????? ??? ?? ???? ????????, ???? ???? ??????
  ????? ??????? ??????????? ??? MIPS ??? ??????
  ???? ?????? ?? ?????? ?????? ???? ?????? ???
  ?????? ???? ?? ???????? ???.

18
?????

• ????? ????? ??? ????? ?????? ?????????? ???
  ?????.
• ?????? ????? ?????? ????? ??????? ?????,
  ??????? ??????? ????????.
• ???? ?? ???? ????? ???!
• ????? ????? ??? ??????.

19
????? ?????????? ?? ???????based on Y. Pilpel et
al. (2001) Identifying regulatory networks
bycombinatorial analysis of promoter elements
20
The method in a scheme

• ????? ???? ?? ??????? ?????? ????????

???? clustering ?? ????? ??? ???????? ????????
?????? ????? ????. ?? ????? ??????? ??? ???????
????? ???? ?????
???? ?? ????? ???? ???? ?? ?- Expression
Coherence Score
???? ?? ????? ???????? ??????? ????????
21
???? ????????

• ????? ?????? 356 ??????? (????? 37 ??????)
• ???????? ?????? ?? - ?????? ?? alignACE ?? ????
  ???? ???? ????? (MIPS).
• ?? ?????? ??????? ???? ????? ?????? ?? ??????
  ????? ??????.
• The expression coherence score
• ??? ?????? ??? ????? ?????? ?? ????? ????.

22

Taken from Y. Pilpel et al.
??????? ??? ???????

• ??????? ???? ?? ???????? ??? ?? ????? ????????
  ?????.

23
?????? ??????

• ????? 115 ????? ??????? ??????? ????????.

• ???? ????? ??? ??????? ??? ??? ????? ??????.

• 1RAP

• ???? ???? ???? (??? ????? ?????? ?????) ???
• ???????? mRRPE ?- PAC.

24
??????????? ?? ????????
???? ????? ???? ????? ?????? ??? ??? ???????
???? ????? ??? ???? ???? ???? ?- TSS ???? ????.
????, ???? ????? 115 ?????? ????? ??-18 ???
????? ????? ????? 6 ??????? ?????? ????? ??????.
???? ?????? ???? ???? ????? ?? ?????? ?????
??????????? ?? ???????? ?????????.
25
??????????? ?? ????????
Taken from Y. Pilpel et al.
26
????? ????? ???????

• ??? ???????
• combinogram

27
??? ???????
Taken from Y. Pilpel et al.
28
????? - ????? ????? ???????????? ???? ???? ???
???????? ???????? ??????? ????? ?? ???.
??? ???????

• ???? ???? ??? ???????? ????? ??? ?????????, ????
  ???? ????? ??? ??? ????.
• ????? ???? ??? ???? ?????? ?? ??????? ????????
  ????? ??? ????? ?????? ?????? ?????? ??? ???????
  ?? ???. ???? RAP1.
• ??????? ??????? ?? ?????? ???????? ????? ???
  ??????

29
??? ???????
Taken from Y. Pilpel et al.
30
Combinogram
Cell cycle
Sporulation
Taken from Y. Pilpel et al.
31
Combinogram

• ???? ?? ?????? ?? ?? ????? ?? ???? ????? ?????.
• ???? ????? ??? ????? ???? ????? ??????? ??????
  (?? ?? ???????) ?? ???? ???? ??????? ??? ??????
  ????????? ??? ?? ????? ????? ?? ???? ??????.
• ????????? ?? ??? ??????? ??????, ???? ???? ??
  ??????? ???? ????.

32
Combinogram
Heat shock
Nucleotide excision repair
Taken from Y. Pilpel et al.
33
?????

• ?? ???? ??? ???? ????? ??? ????????
• ?? ????? ?????? ????? ?? ?? ????? (???? RAP1)
• ??????????? ????? ?? ???? ????? ????? ?? ??
  ?????? ????????, ??? ???? ?? ?????? ???????.
• ???? ??????? ???? ?????? ?? ??? ?????? ????
  ??? ???? ??"? ???? ?????? ???? ???? ???? ?????
  ?????.
• ???? ?????????.

34

• ?????

35
???? ???????? ??? ???????????? ????? ????
Based on M. A. Beer and s. Tavazoie (2004)
Predicting Gene Expression from sequence
36
The method in a scheme

• 1. ??????? ????? ????? ????? ????? (micro-array)
  ??????? ???? ???????? modified k-means clustering

???, ?? ?????? ?????? ?? ???? ???????? ?????
?????? ???????
2. ???? ?? ????? ???? ???? ?? ????? ????????
???????? ????? ???? ??????
3. ????? ???? ????????? ?? ??? ????? ?? ??????
???? ????????, ??????????? ???? ?????? ??????
???? ????? ?????? ?? ????? ????? ????
37
???? ??????

• ????? ?????? ????? ??????? ????
• ?????? ?? ???? ?????????? ?? ????? ?????? ??
  ?????? ????? ????????, ?? ????? ?????? ?? ????
  ????????.
• ???, ???? ??? ????? ?? ???? ?????? ?? ?????
  ????? (?????? ?? ???? ????) ?????? ????? ????
  ?????? ????.

38
????? ?????

• ???? ???? ????? ????? ?????? ?? ??? ??? 255
  ????? ?????. (???? ??? ????? ???????? ??????
  ????? ???).
• ??"? ???? ???? ????? ?????? ?? 2587 ???? ??????
  ?????.
• ?????? ??? ?? ????? ?????? ???? ?????? ?? ????
  ??? ??????? .
• ???? ???? ?????? ?????? ????? ???? ????? ????
  ??????? ?????? ???? ????? ????? ??? ?????.

39
Clustering

• ????????? ????? ??? modified k-means clustering
• ??? ????????? ??? ????? ???? ????? ????? 10
  ????.
• ????????? ???? 2587 ???? ????? ???? ?-49
  clusters ?????.
• ????? ??????? ??? ????? ???? ??? ???? ???? ?????
  ??? ???????.
• ????? ?????? ?????? ?????? ???? ??????? ?? ????
  ???? ???? ??? ??? ????????????? ?????? (MIPS).

40
Taken from M. A.Beer et al
41
????????????? ?????? ???? ????? ?????
Taken from M. A. Beer et al
42
????? ??????? ??????
Taken from M. A. Beer et al
43
????? ???????
???? ?? ??? ???????? ??????? ????? ?? AlignACE
?? ?? ?????? ??????? upstream ?????. ?????
??????? ????? ?? 12bp ????? ????? ??? 800bp
upstream.
44
???? ??????????

• ??? ????????? ???? ???????? ????? ?????? ????
  ???? ??? ??????.
• ????? ?? ????? ??????? ??? ???? ??????????
  ???? ???? ?? ?????? ????? ?????? ??????? ?????
  ??? ????? ???.

Taken from M. A. Beer et al
45
???? ??????????

• ???????? ??????? ???? ????????? ???? ?????
  ??????? ???? ????? ??? Friedman et al. 2000.
  Segal et al. 2003

• ?? ?????? ???? ?????????? ???? ????? ??????? ???
  ???? ?-mRNA ?? ?? ?????? ?? ???? (?????? TF ????)
  ???? ??? ?-mRNA ?? ?? ?????? ?? ???.

• ???? ???? TF ??????? ???? ???????. ???? ?
  nuclear import/export, ???????????, ?????? ????
  ?????? ?? ???? TF

46
???? ??????????

• ????? ??? ????? ??????? ??? ????? ?-TF ??????
  (????? ???? ????, ?? ????? ???') ???? ??? ?-mRNA
  ?? ??? ?????? ?? ???.
• ??????? ???? ?? ????? ?????? ????? ?? ???? ???
  ?? ??? ???? ?? ?????? ??? ??? ???? ???. ????? ???
  ???????? ???????? ????? ????? ?? ?? ???? ????
  ?-mRNA ???.

47
??????

• ???? ????????? ???? 82 ????? ???? ????? ??????.
  
• ??????? ????? ?? ???? ?? ????? ????? ???????
  ????? ????? 73 ????? ?????? ?? ???? ???.

• ??????
• ???? ??????? ?? ????? ???? ???? ?? ??????.
  ?????!
• ???? ?????? ?? ?????? ?? ????? ????? ?? ???
  ????? ?????? ???? ?????? ?????.

48
??? ???????? PAC RRPE
??? ???????? ????? ?????? ?? ???? ??????? ??????
?? rRNA.
RAP1
PAC RRPE position constraint
Taken from M. A. Beer et al
49
???? ??????? ????? ??????
??????? ????? ?????? ????? ????? ?????? ??? ?? ??
????? ????? ???????????? ??????? ?????? ??????
?????? ?? ??????????? ?? ????????. ??????
Taken from M. A. Beer et al
50
?????? ??????
??? ????????
???? PAC ????? ???? ???? ?-TSS ??? ????? ???? ??
?????? ???? ????? ?????.
Taken from M. A. Beer et al
51
?????? ??????
?????? ?????
?? ??? ???????? ??????? ?? ????????? ???? ??????
??? ?? ??-??????? ???? ??????.
Taken from M. A. Beer et al
52
??????? ??????
??????? ???? ??? ?? ???? OR ????? ??????. ?????
????? OR ?????? ?? NOT.
Taken from M. A. Beer et al
53
????
????? ????? ?????? ?? ?????? ????? ?? ??????.
Taken from M. A. Beer et al
54
?????

• ??? ??? ????? ?????? ???? ???? ???? ?????
  ??????. (73)
• ????? ???? ?????? ???? ??????? ?????? ????,
  ?????????? ????????????? ??? ???????.
• ???...

55
??????? ??????? ??????

• ????? ??? ????? ???? ????????, ??? ?? ??????
  ????? ????? ?? ?? ?????.
• ????? ???????????? ??????? ???? ???? ??????.
  (??????)
• ???? ??? ?????? ????? ???? ??????? ?????? ?????
• ??? ??????? ?????? downstream to TSS ?? ????????
  ???????.
• ???? ?????????? ?? ???? ?? ?? ??????.
• ??? / ?????? ????? ???? ????? ?????.
• ???? ??? ????? ?? ???? ?????????? ?????????.

56
?? ????? ?? ???

• S. Tavazoie et al. (1999) ???? ????????,
  bottom-up, 600bp, 10 ?????? ??????, ?? ????? ???
• (2001) Y. Pilpel et al. top-down ?????????????
  ?????, ??? ????? ??????? (?????, ??????????)
• M. beer S. Tavazoie (2004) ???? ????????,
  bottom-up, 800bp, 12 ?????? ??????, ????? ?????,
  ???????????? ??????, ???? ?????? ?????.

57
????? ??? ?????? ????????
58
???????????? ????????
?????? ??????? ??????? ?? ???? ?????

• ?????

????? ????? ?????? ???????? ???? ???? ???? ??? ??
?????? ????? ?? ??? ???? ???? ???????

• ???????

???? ?? ??????? ???? ????? ????
Phylogenetic footprinting
Regulatory potential track
cis-regulatory modules
59
Phylogenetic footprinting

• ????? ????
• ??????? ????????????? "?????" ???? ??????? ????
  ??????? ???? ??? ??? ?????????????.
• ???? ?????????? ????? ???? ????? ???????? ??
  ?????? ?????.

60
Phylogenetic footprinting

• ????? ???????? ??????????? ????
• ????? ???? ?????????? ??????? (????????) ???????
  ???? ???? ???? ?????? ??????? ??????? ?????
  ???? (COG, HOP, HomoloGene)
• ????? ???? ????? ??????? ???? ?? ??? ??????????
  ???????? ??????, ?? ????? ????? ????? ?????
  ??????? (?????? BLASTZ), ?? ????? ?????? ???????
  ????????? (?????? LAGAN).
• ????? ?? ????? ???????? ?????? ???? ?????? ????
  ?? ?????? ?? ??? ???? ??????? ???????? ???? ?????
  ??????? ?????? (VISTA browser, PipMaker) ?? ?????
  ???? ???????? ?????.

61
????? ??????? ?-Phylogenetic footprinting
Taken from W. Wasserman et al.
62
cis-regulatory modules

• ??? ?????? ????, ?? ?????? ??? ?????? ?????? ??
  ?????? ???????.
• ????? ???? ???? ?????? ?????? ??? ???? ??????
  ??????? ????????.
• ????? ?????? ????? ????? ???? ????

Taken from W. Wasserman et al.
63
Regulatory potential track

• ???? ?????? ?????? ???? ????? ???? ???????? ?????
  ?????? ????? ????? ?? ???? ?? ?????.
• ?????? ??????? ??? ???????? ????????? ????
• ?????? GC ????.
• ??????? ?? ??????? ??? ??????.
• ??????? ?? ???? ??????.

64
????? ?????

• ????? ?????????? ?? ???? ???? ????? ?????
  ?????? ?? ???? ???? ?????.
• ?? ???? ???? ??? ??????? ????? ????? ?? ?????
  ????? ???????? ????.
• ????? ?? ???????????? ????????? ??? ????????.
• ????, ????? ???????? ??? ?????? ?? ???? ?????
  ?? ????? ???...

65

• ???? ????? ????? ????????