3. 10 20 30 40
0.74 0.76 1.34 1.75
2.01 2.62 0.87 0.69
0.87 0.60 1.83 1.90
1.73 1.83 0.96 0.93
x2
x2
x
x
|dx1 | + |dx2 |
dx2 + dx2
1 2
dx2
dx2
y
y
dx1
dx1
x1 x1
(A)

4. n
i=1 (xi − x)(yi − y )
¯ ¯
r= n n
i=1 (xi x)2
¯ i=1 (yi − y )2
¯
−
y
y y
x
x x
r≈0
r≈1 r ≈ −1

6. 40454_at
753_at
33355_at
40113_at
717_at
34800_at
41275_at
1044_s_at
36452_at
37981_at
37343_at
182_at
39424_at
1988_at
1389_at
35164_at
39781_at
2059_s_at
33238_at
1134_at
266_s_at
39318_at
37579_at
41139_at
1498_at
36937_s_at
41827_f_at
39929_at
38514_at
1081_at
36203_at
32378_at
1854_at
39829_at
37475_at
38063_at
40235_at
38521_at
1007_s_at
36643_at
32063_at
32529_at
1520_s_at
39402_at
39614_at
38285_at
34897_at
35260_at
37493_at
38340_at
32872_at
37625_at
36638_at
38994_at
1914_at
39003_at
32184_at
38717_at
37471_at
40396_at
1140_at
31901_at
37033_s_at
897_at
38413_at
33412_at
37544_at
34308_at
33777_at
41470_at
37809_at
37558_at
36873_at
41401_at
1065_at
34583_at
33283_at
40365_at
40782_at
33352_at
37099_at
> ALLsubset <- read.table(quot;ALLsubset.txtquot;, header=T)
> ALLhm <- apply(ALLsubset, c(1,2), as.numeric)
> library(quot;RColorBrewerquot;)
> hmcol <- colorRampPalette(brewer.pal(10,quot;RdBuquot;))(256)
> heatmap(ALLhm, col=hmcol, hclust = function(x) hclust(x, quot;wardquot;),
distfun = function(x) as.dist(1-cor(t(x))) )

7. 40454_at
753_at
33355_at
40113_at
717_at
34800_at
41275_at
1044_s_at
36452_at
37981_at
37343_at
182_at
39424_at
1988_at
1389_at
35164_at
39781_at
2059_s_at
33238_at
1134_at
266_s_at
39318_at
37579_at
41139_at
1498_at
36937_s_at
41827_f_at
39929_at
38514_at
1081_at
36203_at
32378_at
1854_at
39829_at
37475_at
38063_at
40235_at
38521_at
1007_s_at
36643_at
32063_at
32529_at
1520_s_at
39402_at
39614_at
38285_at
34897_at
35260_at
37493_at
38340_at
32872_at
37625_at
36638_at
38994_at
1914_at
39003_at
32184_at
38717_at
37471_at
40396_at
1140_at
31901_at
37033_s_at
897_at
38413_at
33412_at
37544_at
34308_at
33777_at
41470_at
37809_at
37558_at
36873_at
41401_at
1065_at
34583_at
33283_at
40365_at
40782_at
33352_at
37099_at

8. 33412_at
36638_at
1065_at
34583_at
32184_at
38994_at
41470_at
39003_at
37544_at
38413_at
897_at
40782_at
33283_at
31901_at
40365_at
40396_at
37033_s_at
1988_at
41401_at
37099_at
38717_at
33352_at
34308_at
1140_at
33777_at
37471_at
37558_at
36873_at
1914_at
37809_at
1134_at
34897_at
38340_at
35260_at
1498_at
40235_at
38063_at
38521_at
37475_at
1389_at
36937_s_at
37579_at
41827_f_at
32378_at
36452_at
1081_at
36203_at
39929_at
41139_at
1520_s_at
39318_at
38514_at
2059_s_at
33238_at
36643_at
32529_at
39424_at
1007_s_at
41275_at
39402_at
37981_at
40113_at
37343_at
266_s_at
35164_at
39781_at
1854_at
1044_s_at
182_at
37493_at
38285_at
39829_at
32063_at
37625_at
32872_at
33355_at
40454_at
717_at
39614_at
34800_at
753_at
E2A.PBX1.36001
E2A.PBX1.24019
E2A.PBX1.08018
E2A.PBX1.28003
E2A.PBX1.LAL5
ALL1.AF4.26008
ALL1.AF4.04006
ALL1.AF4.31007
ALL1.AF4.16004
ALL1.AF4.15004
ALL1.AF4.28032
ALL1.AF4.63001
ALL1.AF4.28028
ALL1.AF4.19005
ALL1.AF4.24005

10. > ALLhm.d<-dist(1-cor(t(ALLhm)))
> ALLhm.hc<-hclust(ALLhm.d, quot;wardquot;)
> ALLhm.dend <- as.dendrogram(ALLhm.hc)
> plot(ALLhm.dend)
> ALLhm.cl<-cutree(ALLhm.hc,h=100)
> ALLhm.cl
1007_s_at 1044_s_at 1065_at 1081_at 1134_at 1140_at 1389_at
1 1 2 1 1 2 1
1498_at 1520_s_at 182_at 1854_at 1914_at 1988_at 2059_s_at
1 1 1 1 2 1 1
266_s_at 31901_at 32063_at 32184_at 32378_at 32529_at 32872_at
1 2 1 2 1 1 1
33238_at 33283_at 33352_at 33355_at 33412_at 33777_at 34308_at
1 2 2 1 2 2 2
34583_at 34800_at 34897_at 35164_at 35260_at 36203_at 36452_at
2 1 1 1 1 1 1
36638_at 36643_at 36873_at 36937_s_at 37033_s_at 37099_at 37343_at
2 1 2 1 2 2 1
37471_at 37475_at 37493_at 37544_at 37558_at 37579_at 37625_at
2 1 1 2 2 1 1
37809_at 37981_at 38063_at 38285_at 38340_at 38413_at 38514_at
2 1 1 1 1 2 1
38521_at 38717_at 38994_at 39003_at 39318_at 39402_at 39424_at
1 2 2 2 1 1 1
39614_at 39781_at 39829_at 39929_at 40113_at 40235_at 40365_at
1 1 1 1 1 1 2
40396_at 40454_at 40782_at 41139_at 41275_at 41401_at 41470_at
2 1 2 1 1 2 2
41827_f_at 717_at 753_at 897_at
1 1 1 2

11. 0 100 200 300 400 500
31901_at
39003_at
1140_at
40396_at
33412_at
37544_at
38413_at
37033_s_at
897_at
33777_at
34308_at
38994_at
1914_at
36638_at
1065_at
34583_at
37558_at
36873_at
41470_at
38717_at
32184_at
37471_at
37809_at
41401_at
33352_at
37099_at
40365_at
33283_at
40782_at
40113_at
717_at
40454_at
753_at
33355_at
1044_s_at
41275_at
39402_at
1520_s_at
39614_at
32063_at
32872_at
39781_at
39424_at
37625_at
38340_at
1389_at
33238_at
1134_at
2059_s_at
34800_at
182_at
37343_at
1988_at
35164_at
266_s_at
38514_at
1081_at
36203_at
1498_at
36937_s_at
39929_at
41827_f_at
36452_at
37981_at
39318_at
37579_at
41139_at
35260_at
37493_at
34897_at
38285_at
1007_s_at
36643_at
38521_at
38063_at
40235_at
39829_at
1854_at
37475_at
32378_at
32529_at
897_at
182_at
717_at
753_at
1065_at
1140_at
1914_at
1854_at
1081_at
1498_at
1134_at
1389_at
1988_at
37099_at
33352_at
40782_at
40365_at
33283_at
34583_at
41401_at
36873_at
37558_at
37809_at
41470_at
33777_at
34308_at
37544_at
33412_at
38413_at
31901_at
40396_at
37471_at
38717_at
32184_at
39003_at
38994_at
36638_at
37625_at
32872_at
38340_at
37493_at
35260_at
34897_at
38285_at
39614_at
39402_at
32529_at
32063_at
36643_at
38521_at
40235_at
38063_at
37475_at
39829_at
32378_at
36203_at
38514_at
39929_at
41139_at
37579_at
39318_at
266_s_at
33238_at
39781_at
35164_at
39424_at
37343_at
37981_at
36452_at
41275_at
34800_at
40113_at
33355_at
40454_at
1520_s_at
1007_s_at
2059_s_at
1044_s_at
41827_f_at
37033_s_at
36937_s_at

12. 36638_at
3
34583_at
1
33238_at
1
266_s_at
1
1498_at
1
1007_s_at
3
> ALLhm.cl.h5
36643_at
1
34800_at
3
33283_at
3
31901_at
2
1520_s_at
2
1044_s_at
1
0 100 200 300 400 500
31901_at
39003_at
1140_at
40396_at
33412_at
37544_at
38413_at
37033_s_at
1
34897_at
3
33352_at
2
32063_at
1
182_at
3
1065_at
3
897_at
33777_at
34308_at
38994_at
>cutree(ALLhm.hc,h=5)
1914_at
36638_at
1065_at
34583_at
37558_at
36873_at
41470_at
38717_at
32184_at
37471_at
37809_at
41401_at
1
35164_at
2
33355_at
3
32184_at
1
1854_at
1
1081_at
1
33352_at
37099_at
40365_at
> ALLhm.cl.h5<-cutree(ALLhm.hc,h=5)
33283_at
40782_at
40113_at
717_at
40454_at
753_at
33355_at
1044_s_at
41275_at
39402_at
1520_s_at
39614_at
32063_at
36873_at 36937_s_at 37033_s_at
1
35260_at
3
33412_at
1
32378_at
3
1914_at
1
1134_at
3
32872_at
39781_at
39424_at
37625_at
38340_at
1389_at
33238_at
1134_at
2059_s_at
34800_at
182_at
37343_at
1988_at
35164_at
266_s_at
38514_at
37099_at
1
36203_at
3
33777_at
1
32529_at
1
1988_at
3
1140_at
3
1081_at
36203_at
1498_at
36937_s_at
39929_at
41827_f_at
36452_at
37981_at
39318_at
37579_at
41139_at
35260_at
37493_at
34897_at
38285_at
1007_s_at
37343_at
1
36452_at
3
34308_at
2
32872_at
1
2059_s_at
1
1389_at
1
36643_at
38521_at
38063_at
40235_at
39829_at
1854_at
37475_at
32378_at
32529_at

13. > ALLhm.cl[ALLhm.cl==2]
1065_at 1140_at 1914_at 31901_at 32184_at 33283_at 33352_at
2 2 2 2 2 2 2
33412_at 33777_at 34308_at 34583_at 36638_at 36873_at 37033_s_at
2 2 2 2 2 2 2
37099_at 37471_at 37544_at 37558_at 37809_at 38413_at 38717_at
2 2 2 2 2 2 2
38994_at 39003_at 40365_at 40396_at 40782_at 41401_at 41470_at
2 2 2 2 2 2 2
897_at
2
> names(ALLhm.cl[ALLhm.cl==2])
[1] quot;1065_atquot; quot;1140_atquot; quot;1914_atquot; quot;31901_atquot; quot;32184_atquot; quot;33283_atquot;
[7] quot;33352_atquot; quot;33412_atquot; quot;33777_atquot; quot;34308_atquot; quot;34583_atquot; quot;36638_atquot;
[13] quot;36873_atquot; quot;37033_s_atquot; quot;37099_atquot; quot;37471_atquot; quot;37544_atquot; quot;37558_atquot;
[19] quot;37809_atquot; quot;38413_atquot; quot;38717_atquot; quot;38994_atquot; quot;39003_atquot; quot;40365_atquot;
[25] quot;40396_atquot; quot;40782_atquot; quot;41401_atquot; quot;41470_atquot; quot;897_atquot;
> affyids <- names(ALLhm.cl[ALLhm.cl==2])
> affyids
[1] quot;1065_atquot; quot;1140_atquot; quot;1914_atquot; quot;31901_atquot; quot;32184_atquot; quot;33283_atquot;
[7] quot;33352_atquot; quot;33412_atquot; quot;33777_atquot; quot;34308_atquot; quot;34583_atquot; quot;36638_atquot;
[13] quot;36873_atquot; quot;37033_s_atquot; quot;37099_atquot; quot;37471_atquot; quot;37544_atquot; quot;37558_atquot;
[19] quot;37809_atquot; quot;38413_atquot; quot;38717_atquot; quot;38994_atquot; quot;39003_atquot; quot;40365_atquot;
[25] quot;40396_atquot; quot;40782_atquot; quot;41401_atquot; quot;41470_atquot; quot;897_atquot;

15. > library(quot;hgu95av2quot;)
> library(quot;genefilterquot;)
> ls(quot;package:hgu95av2quot;)
[1] quot;hgu95av2quot; quot;hgu95av2ACCNUMquot;
[3] quot;hgu95av2CHRquot; quot;hgu95av2CHRLENGTHSquot;
[5] quot;hgu95av2CHRLOCquot; quot;hgu95av2ENTREZIDquot;
[7] quot;hgu95av2ENZYMEquot; quot;hgu95av2ENZYME2PROBEquot;
[9] quot;hgu95av2GENENAMEquot; quot;hgu95av2GOquot;
[11] quot;hgu95av2GO2ALLPROBESquot; quot;hgu95av2GO2PROBEquot;
[13] quot;hgu95av2LOCUSIDquot; quot;hgu95av2MAPquot;
[15] quot;hgu95av2MAPCOUNTSquot; quot;hgu95av2OMIMquot;
[17] quot;hgu95av2ORGANISMquot; quot;hgu95av2PATHquot;
[19] quot;hgu95av2PATH2PROBEquot; quot;hgu95av2PFAMquot;
[21] quot;hgu95av2PMIDquot; quot;hgu95av2PMID2PROBEquot;
[23] quot;hgu95av2PROSITEquot; quot;hgu95av2QCquot;
[25] quot;hgu95av2REFSEQquot; quot;hgu95av2SUMFUNC_DEPRECATEDquot;
[27] quot;hgu95av2SYMBOLquot; quot;hgu95av2UNIGENEquot;

16. > mget(affyids,env=hgu95av2GENENAME)
$`1065_at`
[1] quot;fms-related tyrosine kinase 3quot;
$`1140_at`
[1] quot;integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1; alpha
polypeptide)quot;
$`1914_at`
[1] quot;cyclin A1quot;
...
> mget(affyids,env=hgu95av2SYMBOL)
$`1065_at`
[1] quot;FLT3quot;
$`1140_at`
[1] quot;ITGAEquot;
$`1914_at`
[1] quot;CCNA1quot;
$`31901_at`
[1] quot;KCNAB2quot;

17. http://www.yeastgenome.org/help/gotutorial.html

19. http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0000045

20. > library(quot;GOquot;)
> library(quot;annaffyquot;)
> aafGO(affyids, quot;hgu95av2quot;)
An object of class quot;aafListquot;
[[1]]
An object of class quot;aafGOquot;
[[1]][[1]]
An object of class quot;aafGOItemquot;
@id quot;GO:0006468quot;
@name quot;protein amino acid phosphorylationquot;
@type quot;Biological Processquot;
@evid quot;IEAquot;
[[1]][[2]]
An object of class quot;aafGOItemquot;
@id quot;GO:0007169quot;
@name quot;transmembrane receptor protein tyrosine kinase signaling
pathwayquot;
@type quot;Biological Processquot;
@evid quot;TASquot;
[[1]][[3]]
An object of class quot;aafGOItemquot;
@id quot;GO:0008284quot;
@name quot;positive regulation of cell proliferationquot;
@type quot;Biological Processquot;
@evid quot;TASquot;

21. > aafGO(affyids, quot;hgu95av2quot;)[[1]]
An object of class quot;aafGOquot;
[[1]]
An object of class quot;aafGOItemquot;
@id quot;GO:0006468quot;
@name quot;protein amino acid phosphorylationquot;
@type quot;Biological Processquot;
@evid quot;IEAquot;
...
> aafGO(affyids, quot;hgu95av2quot;)[[2]]
An object of class quot;aafGOquot;
[[1]]
An object of class quot;aafGOItemquot;
@id quot;GO:0007155quot;
@name quot;cell adhesionquot;
@type quot;Biological Processquot;
@evid quot;IEAquot;
...

22. > aafGO(affyids, quot;hgu95av2quot;)[[1]][[1]]
An object of class quot;aafGOItemquot;
@id quot;GO:0006468quot;
@name quot;protein amino acid phosphorylationquot;
@type quot;Biological Processquot;
@evid quot;IEAquot;
> getURL(aafGO(affyids, quot;hgu95av2quot;)[[1]][[1]])
[1] quot;http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?
view=details&query=GO:0006468quot;

24. curl “http://eutils.ncbi.nlm.nih.gov/entrez/
eutils/esummary.fcgi?db=gene&retmode=xml&id=2322”
<eSummaryResult>
<DocSum>
<Id>2322</Id>
<Item Name=quot;Namequot; Type=quot;Stringquot;>FLT3</Item>
<Item Name=quot;Descriptionquot; Type=quot;Stringquot;>fms-
...
</DocSum>
</eSummaryResult>

25. • element( )
• element( )
• attribute( ) 1
• element attribute
• element, attribute ) DTD
<shop>
shop
<item name=”Apple”>
<price>150</price>
<piece>1</piece>
</item> item
item
<item name=”Orange” />
</shop>
name=”Orange”
name=”Apple” price piece
150 1

26. shop
item
item
name=”Orange”
price
name=”Apple” piece
150 1

27. > mget(affyids,env=hgu95av2ENTREZID)
$`1065_at`
[1] quot;2322quot;
$`1140_at`
[1] quot;3682quot;
$`1914_at`
[1] quot;8900quot;
...
> options(repos=quot;http://cran.md.tsukuba.ac.jpquot;)
> install.packages(quot;XMLquot;)
URL 'http://cran.md.tsukuba.ac.jp/bin/macosx/universal/contrib/2.6/
XML_1.93-2.tgz'
Content type 'application/x-gzip' length 1156690 bytes (1.1 Mb)
URL
==================================================
downloaded 1.1 Mb
The downloaded packages are in
/tmp/RtmpSEwKl9/downloaded_packages
> library(quot;XMLquot;)

28. > ezURL<-quot;http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?
db=gene&retmode=xml&id=2322quot;
> doc<-xmlTreeParse(ezURL, isURL=TRUE, handlers=NULL, asTree=TRUE,
useInternalNodes=TRUE)
> chrinfo<-getNodeSet(doc, '/eSummaryResult/DocSum/
Item[@Name=quot;GenomicInfoquot;]/Item/Item')
> sapply(chrinfo, xmlAttrs)[1,]
[1] quot;ChrLocquot; quot;ChrAccVerquot; quot;ChrStartquot; quot;ChrStopquot;
> sapply(chrinfo, xmlValue)
[1] quot;13quot; quot;NC_000013.9quot; quot;27572704quot; quot;27475752quot;

30. > mget(affyids,env=hgu95av2PATH)
$`1065_at`
[1] quot;04060quot; quot;04640quot; quot;05221quot;
$`1140_at`
[1] quot;04810quot;
$`1914_at`
[1] quot;04110quot; quot;05221quot;
> sort(unlist(mget(affyids,env=hgu95av2PATH)))
40782_at1 40782_at2 37033_s_at1 33777_at 37033_s_at2 40782_at3 40782_at4
quot;00361quot; quot;00363quot; quot;00480quot; quot;00590quot; quot;00590quot; quot;00624quot; quot;00626quot;
40782_at5 40782_at6 40782_at7 33283_at1 40365_at 40396_at1 1065_at1
quot;00632quot; quot;00642quot; quot;00903quot; quot;04010quot; quot;04020quot; quot;04020quot; quot;04060quot;
34583_at1 40396_at2 1914_at1 38994_at1 1065_at2 34583_at2 33283_at2
quot;04060quot; quot;04080quot; quot;04110quot; quot;04630quot; quot;04640quot; quot;04640quot; quot;04740quot;
1140_at 38994_at2 38994_at3 37033_s_at3 1065_at3 1914_at2 34583_at3
quot;04810quot; quot;04910quot; quot;04930quot; quot;05030quot; quot;05221quot; quot;05221quot; quot;05221quot;
> source(quot;http://bioconductor.org/biocLite.Rquot;)
> biocLite(quot;KEGGSOAPquot;)
> library(quot;KEGGSOAPquot;)
SSOAP
RCurl ...

31. http://www.genome.jp/kegg/pathway/hsa/hsa04060.html

32. > get.genes.by.pathway(quot;path:hsa04060quot;)
[1] quot;hsa:10344quot; quot;hsa:10563quot; quot;hsa:10663quot; quot;hsa:10673quot; quot;hsa:10803quot; quot;hsa:10850quot;
[7] quot;hsa:10913quot; quot;hsa:11009quot; quot;hsa:115650quot; quot;hsa:116379quot; quot;hsa:1230quot; quot;hsa:1231quot;
> get.motifs.by.gene(quot;hsa:10663quot;, quot;pfamquot;)
[[1]]
$motif_id
[1] quot;pf:7tm_1quot;
$definition
[1] quot;7 transmembrane receptor (rhodopsin family)quot;
$genes_id
[1] quot;hsa:10663quot;
...
[[2]]
$motif_id
[1] quot;pf:Serpentine_recpquot;
$definition
[1] quot;Caenorhabditis serpentine receptor-like proteinquot;
...