author | Don Pellegrino <don@drexel.edu> | 2009-07-23 18:10:48 (GMT) |
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committer | Don Pellegrino <don@drexel.edu> | 2009-07-23 18:10:48 (GMT) |
commit | 07724238172a740659f56dd616c624e2c3fb718c (patch) (unidiff) | |
tree | 2de83a57fb97bf5ae4392c4ac621feafde545646 | |
parent | 6ab124777a77615b396ee37163ae1bf20d4b43cc (diff) | |
download | exp005-07724238172a740659f56dd616c624e2c3fb718c.zip exp005-07724238172a740659f56dd616c624e2c3fb718c.tar.gz exp005-07724238172a740659f56dd616c624e2c3fb718c.tar.bz2 |
A sample analysis process to explore the use of the map.
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1 | By analyzing the map we can see the that 2004 Avian flu is very | ||
2 | similar to the 1957 pandemic within one of the clusters. Seven | ||
3 | proteins from the 1957 pandemic surround a single protein from the | ||
4 | 2004 avian flu. Although the strains of H2N2 and H9N2 are different | ||
5 | this particular and specific similarity is identifiable at a lower | ||
6 | level of detail. Such a relationship might be difficult to discover | ||
7 | by performing only organism to organism comparisons. | ||
8 | |||
9 | Selection | ||
10 | --------- | ||
11 | db2 => select * from vis_selection; | ||
12 | |||
13 | GI | ||
14 | -------------------------------------------------- | ||
15 | 187937439 | ||
16 | 188504364 | ||
17 | 189230513 | ||
18 | 194352176 | ||
19 | 194352214 | ||
20 | 194352233 | ||
21 | 194352252 | ||
22 | 208342867 | ||
23 | |||
24 | 8 record(s) selected. | ||
25 | |||
26 | Summary | ||
27 | ------- | ||
28 | > summary (d); | ||
29 | GI GBSEQ_LOCUS GBSEQ_ACCESSION_VERSION GBSEQ_UPDATE_DATE | ||
30 | 187937439:1 ACD37779:1 ACD37779.1:1 01-JUN-2008:1 | ||
31 | 188504364:1 ACD56299:1 ACD56299.1:1 02-OCT-2008:1 | ||
32 | 189230513:1 ACD85239:1 ACD85239.1:1 16-MAY-2008:1 | ||
33 | 194352176:1 ACF54485:1 ACF54485.1:1 19-JAN-2009:1 | ||
34 | 194352214:1 ACF54507:1 ACF54507.1:1 21-JUL-2008:4 | ||
35 | 194352233:1 ACF54518:1 ACF54518.1:1 | ||
36 | (Other) :2 (Other) :2 (Other) :2 | ||
37 | GBSEQ_CREATE_DATE ORGANISM | ||
38 | 01-JUN-2008:1 Influenza A virus (A/Ann Arbor/23/1957(H2N2)) :1 | ||
39 | 02-OCT-2008:1 Influenza A virus (A/chicken/Korea/S21/2004(H9N2)):1 | ||
40 | 16-MAY-2008:1 Influenza A virus (A/Guiyang/1/1957(H2N2)) :1 | ||
41 | 19-JAN-2009:1 Influenza A virus (A/Singapore/1/1957(H2N2)) :1 | ||
42 | 21-JUL-2008:4 Influenza A virus (A/Singapore/1-MA12A/1957(H2N2)):1 | ||
43 | Influenza A virus (A/Singapore/1-MA12B/1957(H2N2)):1 | ||
44 | (Other) :2 | ||
45 | STRAIN SEROTYPE N_CITES | ||
46 | A/Ann Arbor/23/1957 :1 H2N2:7 Min. :2 | ||
47 | A/chicken/Korea/S21/2004:1 H9N2:1 1st Qu.:2 | ||
48 | A/Guiyang/1/1957 :1 Median :2 | ||
49 | A/Singapore/1/1957 :1 Mean :2 | ||
50 | A/Singapore/1-MA12A/1957:1 3rd Qu.:2 | ||
51 | A/Singapore/1-MA12B/1957:1 Max. :2 | ||
52 | (Other) :2 | ||
53 | |||
54 | Based on this finding it might be worthwhile to investigate the | ||
55 | similarities bewteen the single protein from a chicken in Korea in | ||
56 | 2004 relative to the Singapore, Guiyang and Ann Arbor proteins from | ||
57 | 1957. One interesting observation is the geographic outlier of Ann | ||
58 | Arbor versus the others in Asia. | ||
59 | |||