Clustering Gene Expression Data in SQL Using Locally Adaptive Metrics
Recommend Documents
[22] Wei Zhong, Gulsah Altun, Robert Harrison, Phang C. Tai, and Yi Pan,. âImproved K-Means Clustering Algorithm for Exploring Local Protein. Sequence Motifs ...
Recent work has used graphs to modelize expression data from microarray .... set of edges; for XâV, G(X) denotes the subgraph restricted to X. A graph is said ...
World Scientific Publishing, Mauna Lani, Hawaii, USA, Jan- uary 1999. [13] M. de Hoon, S. Imoto, .... Rich Stern (CMU-USA). Ricardo L. de Queiroz (UNB-Brazil).
Nov 23, 2000 - compare six clustering algorithms on four gene expression data sets. ... of cluster quality. Availability: The software is under development.
Dec 18, 2007 - Robert Yu, Kevin DeHoff, Christopher I Amos and Sanjay Shete* ..... Wray GA, Hahn MW, Abouheif E, Balhoff JP, Pizer M, Rockman MV,.
Dec 18, 2007 - ... J Cordell, Mariza de Andrade, Marie-Claude Babron, Christopher W Bartlett, ..... Romano LA: The evolution of transcriptional regulation in.
Aug 5, 2012 - ward. Once decomposed, the components can be quantified based on their ...... [26] H. Chipman, T. Hastie, and R. Tibshirani, âClustering.
Nov 4, 1998 - Calculation of a similarity matrix S. In this matrix the entry Sij ...... X. Wen, S. Fuhrman, G. S. Michaels, D. B. Carr, S. Smith, J. L. Barker and R.
We propose a new method for tumor classification from gene expression data, which mainly contains .... sify three different DNA microarray datasets of colon.
Oct 18, 2016 - Institute of Genetic Medicine, Newcastle University, International Centre for ... ness between individuals as estimated through genome-.
hal-00361427, version 1 - 14 Feb 2009. Author manuscript, published in "N/P" ...... [71] Ziegler P, Dittrich KR. Three decades of data integration - all problems ...
Jan 28, 2009 - sets and the best number of clusters as indicated by our validation criteria. ... Related articles/pages ... Facebook ...... Chen X, Cheung ST, So S, Fan ST, Barry C, Higgins J, Lai KM, Ji J, Dudoit S, Ng IO, Rijn M, Botstein D, ...
002-00001-0011-000-5 and at the NTP Study Results & Research Projects for Toxicogenomics web ... Genomics Proteomics Bioinformatics 2003;1:279â287.
Classification Rules Evolved Using MOSES. Moshe Looks ... Evolutionary Search, or MOSES) is used to learn an ensemble of ...... and S. Levy. (2005) 'A ...
Microarray Gene Expression Data Mining: Clustering Analysis Review. Erfaneh Naghieh and Yonghong Peng. Department of Computing, University of Bradford.
Feb 24, 2017 - Hierarchical clustering (HC) iteratively merges closest clusters by initializing each sample as a cluster or partitioning a huge cluster formed by ...
the maximum Fisher Criterion max Ï . END. Assume all gene data initially belong to the same cluster. Place cluster on the stack. Data preprocessing. Is max.
bi-cluster is a sub-matrix P x Q, where P is a subset of M and. Q is a subset of N, ..... [3] Cheng, Yizong, and George M. Church, "Biclustering of expression data,".
Jan 6, 2010 - such that the weights within each region P are (almost) constant. .... q qqqqq q qqqqqqqqqqqqqqq q qqqqqqq q qqqqqqq q qqqq q qqqq q q q q.
Analysis and handling of such data is becoming one of the ... discuss supervised and unsupervised data analysis and its applications, such as predicting gene.
Figure 2: The simulated data from Figure 1 displayed as a scatterplot matrix: Can ... points in the scatterplot that are on the extremes of the scatter cloud far away.
examining the tumor site from colorectal excision specimens removed following .... and total mesorectal excision for the management of locally advanced rectal ...
Jun 4, 2009 - Department of Las Palmas de Gran Canaria University (ULPGC), Spain, .... could be significantly associated with RT toxicity, non-super-.
sification and clustering especially of gene expression time course data (Luan ... Time variation or warping is addressed in functional data analysis, an area of ...
Clustering Gene Expression Data in SQL Using Locally Adaptive Metrics
IBM T.J. Watson Research Center ..... points, but also involves a weighted distance metric, i.e., .... The resulting algorithm, that we call LAC (Locally Adap-.
Clustering Gene Expression Data in SQL Using Locally Adaptive Metrics !#" $&%& '" ' () *+$& %-, ./%10 2.1$10 " '2
3 # # 145768 9:6 ; 1" :"A@CB7%+=(A2J0 "1'2
ABSTRACT
f T 5Y97 - 5V 68WZU gK5Vh9769757 68 i T 5Y8 97=j57 klm T W#5Vn 6857 MWI 8 AmQ8I1C#9V971UK6W C975V 1IK6o 4KI &kb57In U 5p 3 K 57 6Wq 1Urs5V _mt #u T 5)9:U 5)md8 5:6 1 #6J#+kpQv? 468#C45:#6868W#mwO lU#xPmw#49: - 5V 6 T W T UK45768 6 89757 4# y T 5o:j5V1#W5o576 &k #mz#K6 4#6RkR{ T 57 5Y6|688 8975q K x5:k} ogJ54:{~pq iY9768 5=57689758 -1I6975ymw8689Vn 68 T #M5:R#kb 5y#6888Amw5:= 8 57 MC7kbgz5y 65VrJ5:9V j5p P5b 6 8975}I6 I W# T T =YUK 97=j5/ 97 - 5V 46 gUn 89757 A #665=ogko rs5/ 576RA9:yg86I #6 A#m8 5768 K#6 AjR R9:d{O57 W T 6W ~ImHm5:# U 57 :p4f T i# I9 T Ij#K ) T 54 x #mH ~ImH6mt# C# #657689786R 57 5:ZK6W g8Q4576 6# ?k 5=U9/ 6l 5:9 T 6R85: 7pM8)57 T l# R97KI 57 ) 5:9 T 97 -n 5/b{H5:W T qj579V #:{ T 5Cj## 57 y9:U 8 5C T 5C 57K5Vj#I6975YIm mt5:I 57 { T 6b T 5i97# 5: z#6JUK6WY97 - 5V:p_v&6b T J5VM{O5 57 5:6q6 5V97K5V6 S8) 8575V61# 6 mA#8q#W# T b T I 576JIg 57 Q T 5UK 97=j5/ k4Im9V8 - 5V 6Y#1 57 K68W~6 15 y 5:K= 6#AX S p
f T 55Vz68576 K#mw69/ 6C6F T T 5M5/rs5797H#m#xU 6W~ T 5 {O5: W T # I 5y 5V6 Kj#5) 9 T 6W57 A 6 # J#6o T 5/ 57mt# 5 9 T 6W57 d 6i 97#mw5:= 8 5Q 5757jI689V5pf T I K:{ KI W#57d5V 8 =j5V576R Q# {O5O8# T 5OjI 57 m8{_57 W T Q68q9V576R 5V 7 #6 T 5/ 57mt 5lPmw# - 5Vb9V81I 6£ £I9 T 57j5 T 57 9:#k T Iz5: 978 5V lw 5:8#1I 5: m 5:9 T # T 5V/ Y 6 T 5l #975 1#68 -mw# 45:bgkU KCI{H57W T ~w 575 ¨ W8 5: /p v+6) T 5 mt K:{A68WA{O5 8 5V 5:6#6yIKW## T T =¢J688 #KU 6 w 5VMmQ9:576 5V #6b{O57W T / O T #M C U9:# 6 q8Î#mQ T 5 5V _mt8689V 6PF /p e
Na
5. LOCALLY ADAPTIVE CLUSTERING ALGORITHM
f T _ 579V 6o85V 97 gz5V _8_mt5:I 5 57 57j##69V5)57 - C# 6o8 In 79 5:8 5b T #Y# KW#6 C U9:#A{O57 W T lmw5:= 8 57 Y9V97#168W T 5lR9:~97I 57= 6#m4I1#68W£57#9 T 5:68 6pÏ8 579 T 6858 #W 57 j5:kl 8 =j5V i T 5YJIK&kIm_ 6 Q97576n KU MI6JY{O57 W T :gRkYK6Rj5V - WI 6Wy T 5) #9:5)685:I_ T 5)97576n 5V i Z57 CI 5C T 5UK45768 68 y T IqCI 5/q T 5Y -:Fp 5p T 5O576 #6 Q #6WM{ T K9 T U9:I# I 5O# ki9V 57# 5=zp S z5V97¢J9:IKk{O5~ R9:575:b# Omw ={ 7p 5~ -1= A{M T ¹7ÁKÁ ?±/¿1À#´F´&¹/½1¹ ¸)z6 6 Ï# _ T 5 o97576R #K {O5A9 T U# 5A T 5O¢ - 975V6U #q#/#6oR#64 57 5:9VQ T 5_ T 5/ T I4 T 5VkÃI 5mF=mt #Ê685}I6# T 5V:H6|m T 5o¢ 9 T 5:6P975:6 5V:pZ5o 6 #k 5Vy T 5YjI#5: qIm{H57W T q-Ã#p Lj576} T 5y 68 97576R KU # JmwI ®0 s{_5i9788 5 T 5 9:# 57 z668W 5V # Q5/¢J657y 6b?# /#{ T 5V 5 # § #6 pq54 T 5:697#U 54 T 5C:j5V1IW5 -1#68975#6W5=#9 T 8 5V6 6bmt #Ç T 5iJ 6R M 6 #q #Rp 5V # U5:68-5i T :j5V1IW5~8 -16975iI6W 576 6 p f T 5~ CIK 5V # 7 T 5 # W5/O T 5M97# 57# 6Y#mz6 O##6Wy8 5V6 6 pd 58 5 T 5ijI 5 # 6#6Z57Uz#6576R #{H57W T 6WC 9 T 575i C97 5:U {O5: W T _ qmw5:I 57 iF#6 97 -57 1 N&
.
@
8+
7+
*$
F\
fFVM
_$
g.
ha
bM
ea
-M
8a
#
R
µ d % ji
ek
]la
#
µ % m
D
R
>
2i
k
} ]
#
n]a
D
-
BA
tU )
-
{ T 5/ 5 b|JI1#5V 5Vo T Ib9:#6gz5l9 T 576¤ C=8 È75 w 6 È75= T 5O 68·85768975_#m # 6 # pd T 576 ¤{O5 T :j5 # § I T 5V 5VgUki W#6# 6W)6ky rs5/ 576975HgJ57&{O57576i T 5 # p 6b T 5i# T 57 T 6s8{ T 576 A# W5y49 T I6W5i 6 # { gJ5 5Vz68576 K# k~ 5/·J579V 57q 6 # p 5O574 9: k45V 5V 685H T 5 jI 5)Im T W T 9V1# -n&jI = K#6b 6b#8A5Vz5V 5V6U O{ T q= 5:i8I1pP5 5/ T 5 j## 5 m A6~ T 5H5VUz5/ K5V6 { T 15:I8# 8p f T 5)57Uz68576R #s{O57W T 68W4 _4 5) 5:6 1 j5 9 T I6W5V 6 U9:Imw57I 8 5} 5V5VjI6975| I68 W j5V Y 5b gz5V 5VJ57 mt# C#68975q =j575:6:pMv+6}mt9V:z MK M# 5y -1#g85 gz579:#8 5Z o 57j5V6U oUK -1I69757 Ymt #É5/R 576J68W| 68¢86 57 k 6 #6Rkà 5:9V 6 Fp 5#pHÈ75V {O5: W T :pf T : T :{O5Vj5V: 9:6ÃU97978 { T 5V6}57 T 5VA 65:=#MRR1# 9){O5VW T K6W _ 5=zp f T 5){O57 W T # 5V6J#g8 5) 5: 6W# 5iUK -1I69757 M# 6WC 57 qn z# 1#6)45:68 68 7z?p 5pM4576 68 #6WC{ T 9 T z 6 )I 5 U 57kl97# 5:I 57I6Jz=y T 5 1#454 K45 b9768 - K9VyU -n 1#689757 CIK#6WZ T 5 -4K6U·J8576 K#_6857 7 Fp 5pPmw5:I 57 #68W k
Va
[
k
=m
Ia
Na
k
?# { T 57 5 # 68 # 578 5V 576R~ T 5 w T 97z#6576R ~Im_j579/ # 68 # 57 J5797 j57 klt 57 I 5~g8 #x5761#6J k8 /p f T 5A 57 Ims9:576 5V 68q{_57 W T ²/»´?¾ CÀÁ={A T 5: z579VQ ) T 5 « 89VK857#6}6 b8md T 57k 684È:5M T 5~5V IM45:# U 50 >
~XbÐ~~3 ¯= T 3 X S v-L~XZ§ I x T }#6bª57 5:# 9 T v& 57 A 6}#1CXb 6 6W#6JÐ~6:{A5:W5~ 97=j5V kJ##
JIW5i°
{ T K9 T z6 CI 5o - 68Wk|97# 57= 5:p|¦M# 5 T Iq T 5 5:9 T n 68U85b 975V6U #n?g# 5:gz5V9:#8 5o{O5: W T 68W C57z576J|6| T 5 9V5:6 Ksp f T 5q9V8 5:b{H5:W T # 5i8 5=b Ys# 5~ T 5i 5V # z6 T 5V 5VmwI 5y T 5y975:6 K Æ 9VR168# 57 7pf T 5y1R975:8 5y 5V n I 5:o86 9:6Rj5V W5:6975~ A 57#9 T 5:swp 5p 69 T 68W5~6o975:6 5V Æ 9VI18 6J= 57 AK A#g 5V j57sp f T 5 57 6Wb W T b T #~{H59: 3 R97 kM8Un j5 3 8 - 5V K6WU /8 8C= KÈ757o 6b T 5)mw ={A6Wp $
zp
S 5V u#mz6
&
#6 T 56Uigz5VO#m9VK - 57
3
I(
+
# p S 1= A{A T o68 K#97576R KU - ) U Rp S 5/ # §ImwIQ5:9 T 97576 K #U ¥ 4#6q5:I9 T mw5:= 8 5 §0 P Up ¨ Ii5=#9 T 97576R #K # ,Ï0 zI6Jmti5:#9 T 8# z6 $ H46
V R S 5V 3# { T 5/ 5 7 d ¥ / % µ ) - ) p p ¨ Ii5=#9 T 97576R #K +#R zJ#6om#5:9 T m5=I U15 0 S 5V # / ! # % µ ) 3# #{ T 57 5 3# d T 5 9:=18 6JI +kImO 5V #Z # 57 57 576 ) T 5C:j5V1#W5 U 1I6975~Imz6 A6 # m # 6W4mw5:= 8 5 & / # 8 µ % S 5V # µ % / # - ) Rp ¨ Ii5=#9 T 97576R #K # ,Ï0 zI6Jmti5:#9 T 8# z6 $ O46 V R ªA579748 5 3# +
M
h.
7.
[.
7.0
+
7
9.
7+
(
:$
fSVK;G9IJ~:Hn bhEdT;O>OV Y)DN4J VVVJ6:Hn bhE I@&Q@VY^+N a=`@bfT O>OXJ~SJ~: AC;c:nb;:VdK;G9I J :;D6? S O=T_y :XVdK6@&AIO;:-^5GHM_yHY+D J VV VV :B^R? SO =T_y :VdKI@IAIfO :U^BGHM_y Y ^ a=`@br:Hnb;:J S O =T`y : AC; C>)D`E9K;G9IJ;:;D4J VV J*:B^+NjO : E :f:VdK;G9I J : nbhEE SVY+D[T O >OV6Y)DNZ Z \`NsJ VVVJ6:Hn bhEESXVY ^`[T O> OVY^+NZZ\`N a =_@brS3J T O>OJ~: A C +DsVdK;GBIxJ :_D'? S O=T_y:VdK6@&AIJ V VV :^5? S O=T_yB:hVdK6@&AIJDC a =_@b>)D J0S O = T_y : A C hE#8V:'Fk+y&G YIH+N a =_@bL8w
+
&
¨ W 5y S) 3 8 5) T 5){H57W T it I145V 5V iI9V JIKk g 5:gRklo 9:I=~j## 58U n 6W T 5kU6#9Z6RjR9:# 6 m~ T 5l85V 5: gRk£o9V6 W1Ibp v&6 ¨ W8 5Ô} T 5o5/ kP T =49V8 57 y T 597576R- q q 5Vn 576 57pf T C - 57ÔIm T 5 3 #W# T bp£f T 5}85V k ¢8 - Å+ 6 _1gK5V { y #6 J6}#15V C9788 5~ T 5 Ym) T 5I gU 57 #m~z#K6 C T =gz57 68W P T 5Z 45 9VK 5V:pf T i 6U 5/ 5:8#-5 57 8 iWR57 ~ b 574z#1I k1g5 MON O8I6J T I _ ÈV5 sp f T 576R1Ig 5: MN I6J I 5Å 685:6q#15V )9748 5H T 5H¢6JI 57 8:wp 5pd T 5H97U# n 6JI 5V H#ms T 5A65V{ 97576R- 8 7pd¦# 5_ T I {_5A9:#686#H:j4 T 5 579V6JÅ- 6 t{ T 9 T iz5V mw# 45:P6 # 1g57 7Q#6RkU{_7k / gz5V9: 15 I T 5mt 575Q97 86 s T =dIz5:=d 6i S « « 3 f97 5 #6qI 5O66Rj j57y 6I64#WW 57W# 6imw69V 6 S ÒXuK6y 97 5= T =j5_ i#8J5=I 64 T 5L)ªAÒM 2 P¤9VK#8 5pv&6H97# 5 {O5Mz5V mt# ÍqLªAÒ |2 P #6Y97 6 65468kRU y{H59:6Un 68# 549V 6 $+;5b 6Z T 5 S « « 3 f§97 5i T = 9/ 5=I 57 y1g85 MN Hp ¡5769V5 T 5o68575:PmwI4 T 5 57976}Å-6 gz5/+{O5V5:6o1#g8 57 MONÓ#6J Hp k
