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authorDon Pellegrino <don@drexel.edu>2009-07-23 18:10:48 (GMT)
committer Don Pellegrino <don@drexel.edu>2009-07-23 18:10:48 (GMT)
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A sample analysis process to explore the use of the map.
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+By analyzing the map we can see the that 2004 Avian flu is very
+similar to the 1957 pandemic within one of the clusters. Seven
+proteins from the 1957 pandemic surround a single protein from the
+2004 avian flu. Although the strains of H2N2 and H9N2 are different
+this particular and specific similarity is identifiable at a lower
+level of detail. Such a relationship might be difficult to discover
+by performing only organism to organism comparisons.
+
+Selection
+---------
+db2 => select * from vis_selection;
+
+GI
+--------------------------------------------------
+187937439
+188504364
+189230513
+194352176
+194352214
+194352233
+194352252
+208342867
+
+ 8 record(s) selected.
+
+Summary
+-------
+> summary (d);
+ GI GBSEQ_LOCUS GBSEQ_ACCESSION_VERSION GBSEQ_UPDATE_DATE
+ 187937439:1 ACD37779:1 ACD37779.1:1 01-JUN-2008:1
+ 188504364:1 ACD56299:1 ACD56299.1:1 02-OCT-2008:1
+ 189230513:1 ACD85239:1 ACD85239.1:1 16-MAY-2008:1
+ 194352176:1 ACF54485:1 ACF54485.1:1 19-JAN-2009:1
+ 194352214:1 ACF54507:1 ACF54507.1:1 21-JUL-2008:4
+ 194352233:1 ACF54518:1 ACF54518.1:1
+ (Other) :2 (Other) :2 (Other) :2
+ GBSEQ_CREATE_DATE ORGANISM
+ 01-JUN-2008:1 Influenza A virus (A/Ann Arbor/23/1957(H2N2)) :1
+ 02-OCT-2008:1 Influenza A virus (A/chicken/Korea/S21/2004(H9N2)):1
+ 16-MAY-2008:1 Influenza A virus (A/Guiyang/1/1957(H2N2)) :1
+ 19-JAN-2009:1 Influenza A virus (A/Singapore/1/1957(H2N2)) :1
+ 21-JUL-2008:4 Influenza A virus (A/Singapore/1-MA12A/1957(H2N2)):1
+ Influenza A virus (A/Singapore/1-MA12B/1957(H2N2)):1
+ (Other) :2
+ STRAIN SEROTYPE N_CITES
+ A/Ann Arbor/23/1957 :1 H2N2:7 Min. :2
+ A/chicken/Korea/S21/2004:1 H9N2:1 1st Qu.:2
+ A/Guiyang/1/1957 :1 Median :2
+ A/Singapore/1/1957 :1 Mean :2
+ A/Singapore/1-MA12A/1957:1 3rd Qu.:2
+ A/Singapore/1-MA12B/1957:1 Max. :2
+ (Other) :2
+
+Based on this finding it might be worthwhile to investigate the
+similarities bewteen the single protein from a chicken in Korea in
+2004 relative to the Singapore, Guiyang and Ann Arbor proteins from
+1957. One interesting observation is the geographic outlier of Ann
+Arbor versus the others in Asia.
+

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