NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input...
-
Upload
alfonso-wynter -
Category
Documents
-
view
220 -
download
3
Transcript of NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input...
![Page 1: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/1.jpg)
NP - Positiveset
Negative Set
Full lengthORFs
Genome
Annotated
Candidate NPs
Top ranked NPs
Input Training NP catalogue
Negative Set
Negative Set
Negative set
NP processing tools
Translated proteome ML quality:
Cross validation
NeuroPID
prediction
![Page 2: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/2.jpg)
![Page 3: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/3.jpg)
![Page 4: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/4.jpg)
Q
Y C
N
H
L D
R
W
M
T
S
G
A
V
P
F
I E
K
0
20
40
60
80
100
1-lo
g(p-
valu
e, t-
test
)
1-lo
g(p-
valu
e, t-
test
)
A B
GRAVY
Instabilit
y
Molecular
Weig
ht PI
Aromati
city
0
10
20
30
![Page 5: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/5.jpg)
![Page 6: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/6.jpg)
MRSRTSVLTSSLAFLYFFGIVGRSALAMEETPASSMNLQHYNN
MLNPMVFDDTMPEKRAYTYVSEYKRLPVYNFGIGKRWIDTNDN
KRGRDYSFGLGKRRQYSFGLGKRNDNADYPLRLNLDYLPVDNP
AFHSQENTDDFLEEKRGRQPYSFGLGKRAVHYSGGQPLGSKRP
NDMLSQRYHFGLGKRMSEDEEESSQR
![Page 7: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/7.jpg)
MRSRTSVLTSSLAFLYFFGIVGRSALAMEETPASSMNLQHYNN
MLNPMVFDDTMPEKRAYTYVSEYKRLPVYNFGIGKRWIDTNDN
KRGRDYSFGLGKRRQYSFGLGKRNDNADYPLRLNLDYLPVDNP
AFHSQENTDDFLEEKRGRQPYSFGLGKRAVHYSGGQPLGSKRP
NDMLSQRYHFGLGKRMSEDEEESSQR
![Page 8: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/8.jpg)
Random Forest Classifier RBF Linear SVC Gradient Boosting SVC Sigmoid Polynomal SVM0
0.2
0.4
0.6
0.8
1
‘accuracy’ ‘precision’ ‘recall’
Area under ROC curve
Cros
s va
lidati
on p
erfo
rman
ce
![Page 9: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/9.jpg)
![Page 10: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/10.jpg)
![Page 11: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/11.jpg)
![Page 12: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/12.jpg)
Cros
s va
lidati
on p
erfo
rman
ce
![Page 13: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/13.jpg)
![Page 14: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/14.jpg)
![Page 15: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/15.jpg)
![Page 16: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/16.jpg)
S. frugiperda (Fall armyworm) 5
H. armigera (Cotton bollworm) 6
S. gregorian (Desert locust ) 4
A. florea (Little honeybee) 0
M. rotundata (Alfalfa leafcutter bee)1
C. floridanus (Florida carpenter ant) 2
A. echinatior (Leafcutter ant) 3
A
C
B
![Page 17: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/17.jpg)
![Page 18: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/18.jpg)
![Page 19: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/19.jpg)
D
![Page 20: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/20.jpg)
D
![Page 21: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/21.jpg)
SW Arthropods
UniProt Arthropods
Random Forest
Gradient Boosting
Linear SVC
Random Forest
Gradient Boosting
Linear SVC
Mean Accuracy 0.94 0.95 0.94 0.92 0.92 0.86
Mean Precision 0.94 0.95 0.93 0.93 0.94 0.95
Mean Recall 0.92 0.92 0.92 0.95 0.95 0.85
Mean AUC 0.94 0.95 0.94 0.89 0.90 0.87SW
Chordata UniProt
Chrodata
Random Forest
Gradient Boosting
Linear SVC
Random Forest
Gradient Boosting
Linear SVC
Mean Accuracy 0.96 0.97 0.95 0.90 0.91 0.85
Mean Precision 0.94 0.94 0.88 0.91 0.92 0.89
Mean Recall 0.91 0.92 0.93 0.91 0.91 0.83
Mean AUC 0.95 0.95 0.94 0.90 0.91 0.85
![Page 22: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/22.jpg)
Organism# sequences UniProtKB
# of full length
UniProtKB# of SP
# of NP & SP
# NeuroPID All methods
Functional annotation enrichment
B. mori 17908 17069 138 6 69Innate immunity;Insulin-like; Chorion, Hormne (NP)
S. invicta 14356 84 12 2 4 Innate immunity
D. melanogaster
39961 31091 475 21 120Innate immunity; Developmental; Channel ligand; Receptor, Hormone (NP)
C.elegans 26005 25534 464 21 89Hormone (NP), Channel ligand; Receptor, Protease
![Page 23: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/23.jpg)
![Page 24: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/24.jpg)
SW Arthropods
UniProt Arthropods
Random Forest
Gradient Boosting
Linear SVC
Random Forest
Gradient Boosting
Linear SVC
Mean Accuracy 0.94 0.95 0.94 0.92 0.92 0.86Mean Precision 0.94 0.95 0.93 0.93 0.94 0.95Mean Recall 0.92 0.92 0.92 0.95 0.95 0.85Mean AUC 0.94 0.95 0.94 0.89 0.90 0.87
SW Chordates
UniProt Chordates
Random Forest
Gradient Boosting
Linear SVC
Random Forest
Gradient Boosting
Linear SVC
Mean Accuracy 0.96 0.97 0.95 0.90 0.91 0.85Mean Precision 0.94 0.94 0.88 0.91 0.92 0.89Mean Recall 0.91 0.92 0.93 0.91 0.91 0.83Mean AUC 0.95 0.95 0.94 0.90 0.91 0.85
![Page 25: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/25.jpg)
![Page 26: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/26.jpg)
organism / taxa# of UniProt (UniRef90)
# of NPP in SW
(UniRef90)
# of NPP in UniProt
(UniRef90)
PredictionNeuroPID
RBFa
Apis Melliferra 10394 6 19 7
SP in Apis Melliferab 2139 5 7
Gallus gallus 20760 5 5 5
SP in Gallus gallus 701 1 1
Bombyx mori 15250 5 17 9
SP in Bombyx mori 112 5 5 9
Octopoda 224 4 4 4
SP in Octopoda 76 3 3
![Page 27: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/27.jpg)
Updates 5 7 2013
![Page 28: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/28.jpg)
![Page 29: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/29.jpg)
RF 7
ExtraTree 8
SVM-SVC 16GBR 79
4
11
2 2
1
![Page 30: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/30.jpg)
RFExt-Tree
79
SVM-SVC
GBR
16
8786%
42%
100%100%
60%
75% RFExt-Tree
18
SVM-SVC
GBR
10
95100%
60%
100%100%
33%
80%
Apis mellifera Thaumeledone gunteri
![Page 31: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/31.jpg)
Updates 5 7 2013
![Page 32: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/32.jpg)
![Page 33: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/33.jpg)
![Page 34: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/34.jpg)
![Page 35: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/35.jpg)
![Page 36: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/36.jpg)
S. frugiperda (Fall armyworm) 5
H. armigera (Cotton bollworm) 6
S. gregorian (Desert locust ) 4
A. florea (Little honeybee) 0
M. rotundata (Alfalfa leafcutter bee)1
C. floridanus (Florida carpenter ant) 2
A. echinatior (Leafcutter ant) 3
A
C
B
![Page 37: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/37.jpg)
![Page 38: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/38.jpg)
![Page 39: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/39.jpg)
![Page 40: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/40.jpg)
0
0.3
0.6
0.9
1.2
1.5
% o
f ann
otat
ed N
Ps in
taxo
nom
y
113
77
2510
Mammalia
Insecta
Caenorhabditis
others
![Page 41: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/41.jpg)
A B
![Page 42: NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.](https://reader036.fdocuments.in/reader036/viewer/2022062404/551b708a550346a6148b4f18/html5/thumbnails/42.jpg)
66- 97 KRL....YDFG.........LG..............KRA..YsyvSEYKRL.............................pvYN..FGLGKR 98- 120 SKM....YGFG.........LG..............KR.......DG..RM...............................YS..FGLGKR 121- 164 DYD....Y.YGeededdqqaIGdedieesdvgdlmdKR..........DRL...............................YS..FGLGKR 165- 191 ARP....YSFG.........LG..............KRA..P...SGAQRL...............................YG..FGLGKR 192- 216 GGS...lYSFG.........LG..............KR........GDGRL...............................YA..FGLGKRPVN 222- 253 GRSsgsrFNFG.........LG..............KRS..D...DIDFRE...............................LEekFAEDKR 254- 316 .YPqehrFSFG.........LG..............KREveP...SELEAVrneekdnssvhdkknntndmhsgerikrslhYP..FGIRKL 347- 367 RRP....FNFG.........LG..............KRI..P........M...............................YD..FGIGKR
66- 97 KRL....YDFG.........LG..............KRA..YsyvSEYKRL........pvYN..FGLGKR98-120 SKM....YGFG.........LG..............KR.......DG..RM..........YS..FGLGKR121-164 DYD....Y.YGeededdqqaIGdedieesdvgdlmdKR..........DRL..........YS..FGLGKR165-191 ARP....YSFG.........LG..............KRA..P...SGAQRL..........YG..FGLGKR192-220 GGS...lYSFG.........LG..............KR........GDGRL..........YA..FGLGKRPVNS221-253 GRSsgsrFNFG.........LG..............KRS..D...DIDFRE..........LEekFAEDKR254-316 YPqehrFSFG.........LG..............KREveP...SELEAVrne(25)slhYP..FGIRKL346-367 RRP....FNFG.........LG..............KRI..P........M..........YD..FGIGKR