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Revision as of 07:48, 12 March 2010 (view source) Igchoi (Talk | contribs) (→MDS) ← Older edit		Latest revision as of 06:49, 13 March 2010 (view source) Igchoi (Talk | contribs)
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-	=Pan-Genomic Universe=	+	=Pan-Genomic Space=
	==Data==		==Data==
-	*<b>Pan-Genome data version 0.1 Feb 2010</b>	+	*<b>[[w:pangenome|Pan-Genome]] data version 0.1 Feb 2010</b>
-	*Download the frequency profile (1,137 genomes x 11,912 [http://pfam.sanger.ac.uk Pfam] domains)	+	**The frequency profile (1,137 genomes x 11,912 [http://pfam.sanger.ac.uk Pfam] domains)
-	**download: [[media:profile.csv|The FP(Frequency Profile) matrix]]	+	***<b>download: [[media:profile.csv|The FP(Frequency Profile) matrix]]</b>
	==Results==		==Results==
		+	===Taxa-specific Pfam domains===
		+	*Hierarchical clustering of the FP profile<br>[[image:taxaSdom.png|800px]]
		+
	===MDS===		===MDS===
	*Procedures		*Procedures
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	#do MDS ([[w:multidimensional scaling|multidimensional scaling]]) of the distance matrix		#do MDS ([[w:multidimensional scaling|multidimensional scaling]]) of the distance matrix
	#get coordinates from the first three dimension and plot them in a 3D-space		#get coordinates from the first three dimension and plot them in a 3D-space
-	*Exact distance matrix: [[image:mds1.png||MDS exact distance matrix]]	+	*MDS results
		+	#from Exact distance matrix:<br>[[image:mds1.png]]
		+	#from distance matrix cutting off at 99% of the maximum distance:<br>[[image:mds99.png]]
		+	#from distance matrix cutting off at 98% of the maximum distance:<br>[[image:mds98.png]]
		+	#from distance matrix cutting off at 97% of the maximum distance:<br>[[image:mds97.png]]
	==R script sources==		==R script sources==
		+	*TBA

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Latest revision as of 06:49, 13 March 2010

Contents 1 Pan-Genomic Space 1.1 Data 1.2 Results 1.2.1 Taxa-specific Pfam domains 1.2.2 MDS 1.3 R script sources

Pan-Genomic Space

Data

• Pan-Genome data version 0.1 Feb 2010
  • The frequency profile (1,137 genomes x 11,912 Pfam domains)
    • download: The FP(Frequency Profile) matrix

Results

Taxa-specific Pfam domains

• Hierarchical clustering of the FP profile
  

MDS

• Procedures

1. build a pairwise distance matrix (11,912 x 11,912) from the FP matrix (1,137 x 11,912) - euclidean distance
2. do MDS (multidimensional scaling) of the distance matrix
3. get coordinates from the first three dimension and plot them in a 3D-space

• MDS results

1. from Exact distance matrix:
   
2. from distance matrix cutting off at 99% of the maximum distance:
   
3. from distance matrix cutting off at 98% of the maximum distance:
   
4. from distance matrix cutting off at 97% of the maximum distance:
   

R script sources

• TBA