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
. |
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
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
FUNCTIONAL ANNOTATION TABLE