Inappropriate to use DAVID for initial de novo characterization
now going to work with
this file created 5/2/111
made a file for process only
will go with 1.00E-05 (or less than 1.00E-04)
23702 contigs had SPID - GO Process.resources/Microsoft%20Excel-6.png)
| . |
57 |
| cell adhesion |
519 |
| cell cycle and proliferation |
1217 |
| cell organization and biogenesis |
1825 |
| cell-cell signaling |
58 |
| death |
545 |
| developmental processes |
1445 |
| DNA metabolism |
1242 |
| other biological processes |
3272 |
| other metabolic processes |
7461 |
| protein metabolism |
2647 |
| RNA metabolism |
3866 |
| signal transduction |
1136 |
| stress response |
1539 |
| transport |
6473 |
** note did not graph Others
--AAAAAAHHHHHHHHH! this really is double check!
follow up on SPSS
RNA-seq
46 genes were only expressed in Laby library
(note have minimally 15 hits)
78 only in control
(note have at min 14 hits)
270 greater than 4 fold in Laby
255 greater than 4 fold in Control
--
503 total p value less than .05
of those there were 215 SPIDs
235 up in Laby
268 up in control
There are a total of 90 with associated GO slim terms for BP
--
31357 unique SPID in total 90230 contigs
DAVID
0.5 genes and SP of denovo
only took <0.05 to revigo
revigo output
only ones signficantly enriched.
pathogenesis
defense response
.resources/DAVID_%20Database%20for%20Annotation,%20Visualization,%20and%20Integrated%20Discovery%20(Laboratory%20of%20Immunopathoge%20of%20Allergies%20and%20Infectious%20Diseases%20(NIAID);%20Science%20Applications%20International%20Corporation%20(SAIC)-6.png)
reponse to biotic stimulus
response to bacterium
anotmical structure morphogenesis
PICKING out the cool ones
the hook as they say
| Q9UGM3 |
| Q4A0V8 |
| Q5SC59 |
| Q9JHA8 |
| O95786 |
| P34053 |
| P00720 |
| Q90593 |
| P81783 |
| P11407 |
| O60449 |
issue is that evalues are bad
DAVID
Functional Annotation Clustering
Sea
Pathway
.resources/DAVID_%20Database%20for%20Annotation,%20Visualization,%20and%20Integrated%20Discovery%20(Laboratory%20of%20Immunopathoge%20of%20Allergies%20and%20Infectious%20Diseases%20(NIAID);%20Science%20Applications%20International%20Corporation%20(SAIC)-7.png)
FUNCTIONAL ANNOTATION TABLE
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.resources/DAVID_%20Database%20for%20Annotation,%20Visualization,%20and%20Integrated%20Discovery%20(Laboratory%20of%20Immunopathoge%20of%20Allergies%20and%20Infectious%20Diseases%20(NIAID);%20Science%20Applications%20International%20Corporation%20(SAIC)-9.png)
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.resources/DAVID_%20Database%20for%20Annotation,%20Visualization,%20and%20Integrated%20Discovery%20(Laboratory%20of%20Immunopathoge%20of%20Allergies%20and%20Infectious%20Diseases%20(NIAID);%20Science%20Applications%20International%20Corporation%20(SAIC)-4.png)
.resources/DAVID_%20Database%20for%20Annotation,%20Visualization,%20and%20Integrated%20Discovery%20(Laboratory%20of%20Immunopathoge%20of%20Allergies%20and%20Infectious%20Diseases%20(NIAID);%20Science%20Applications%20International%20Corporation%20(SAIC)-5.png)
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