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NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP.

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Presentation on theme: "NP - Positive set Negative Set Full length ORFs Genome Annotated Candidate NPs Top ranked NPs Input Training NP catalogue Negative Set Negative set NP."— Presentation transcript:

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 processing tools Translated proteome ML quality: Cross validation NeuroPID prediction

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4 1-log(p-value, t-test) A B

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6 MRSRTSVLTSSLAFLYFFGIVGRSALAMEETPASSMNLQHYNN MLNPMVFDDTMPEKRAYTYVSEYKRLPVYNFGIGKRWIDTND N KRGRDYSFGLGKRRQYSFGLGKRNDNADYPLRLNLDYLPVD NP AFHSQENTDDFLEEKRGRQPYSFGLGKRAVHYSGGQPLGSK RP NDMLSQRYHFGLGKRMSEDEEESSQR

7 MRSRTSVLTSSLAFLYFFGIVGRSALAMEETPASSMNLQHYNN MLNPMVFDDTMPEKRAYTYVSEYKRLPVYNFGIGKRWIDTND N KRGRDYSFGLGKRRQYSFGLGKRNDNADYPLRLNLDYLPVD NP AFHSQENTDDFLEEKRGRQPYSFGLGKRAVHYSGGQPLGSK RP NDMLSQRYHFGLGKRMSEDEEESSQR

8 Cross validation performance

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16 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

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19 D

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21 SW Arthropods UniProt Arthropods Random Forest Gradient Boosting Linear SVC Random Forest Gradient Boosting Linear SVC Mean Accuracy Mean Precision Mean Recall Mean AUC SW Chordata UniProt Chrodata Random Forest Gradient Boosting Linear SVC Random Forest Gradient Boosting Linear SVC Mean Accuracy Mean Precision Mean Recall Mean AUC

22 Organism # sequences UniProtKB # of full length UniProtKB # of SP # of NP & SP # NeuroPID All methods Functional annotation enrichment B. mori Innate immunity;Insulin-like; Chorion, Hormne (NP) S. invicta Innate immunity D. melanogaster Innate immunity; Developmental; Channel ligand; Receptor, Hormone (NP) C.elegans Hormone (NP), Channel ligand; Receptor, Protease

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24 SW Arthropods UniProt Arthropods Random Forest Gradient Boosting Linear SVC Random Forest Gradient Boosting Linear SVC Mean Accuracy Mean Precision Mean Recall Mean AUC SW Chordates UniProt Chordates Random Forest Gradient Boosting Linear SVC Random Forest Gradient Boosting Linear SVC Mean Accuracy Mean Precision Mean Recall Mean AUC

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26 organism / taxa # of UniProt (UniRef90) # of NPP in SW (UniRef90) # of NPP in UniProt (UniRef90) Prediction NeuroPID RBF a Apis Melliferra SP in Apis Mellifera b Gallus gallus SP in Gallus gallus70111 Bombyx mori SP in Bombyx mori Octopoda SP in Octopoda7633

27 Updates

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29 RF 7 ExtraTree 8 SVM-SVC 16 GBR

30 RF Ext-Tree 79 SVM-SVC GBR % 42% 100% 60% 75% RF Ext-Tree 18 SVM-SVC GBR % 60% 100% 33% 80% Apis melliferaThaumeledone gunteri

31 Updates

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36 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

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41 AB

42 KRL....YDFG LG KRA..YsyvSEYKRL pvYN..FGLGKR SKM....YGFG LG KR DG..RM YS..FGLGKR DYD....Y.YGeededdqqaIGdedieesdvgdlmdKR DRL YS..FGLGKR ARP....YSFG LG KRA..P...SGAQRL YG..FGLGKR GGS...lYSFG LG KR GDGRL YA..FGLGKRPVN GRSsgsrFNFG LG KRS..D...DIDFRE LEekFAEDKR YPqehrFSFG LG KREveP...SELEAVrneekdnssvhdkknntndmhsgerikrslhYP..FGIRKL RRP....FNFG LG KRI..P M YD..FGIGKR KRL....YDFG LG KRA..YsyvSEYKRL pvYN..FGLGKR SKM....YGFG LG KR DG..RM YS..FGLGKR DYD....Y.YGeededdqqaIGdedieesdvgdlmdKR DRL YS..FGLGKR ARP....YSFG LG KRA..P...SGAQRL YG..FGLGKR GGS...lYSFG LG KR GDGRL YA..FGLGKRPVNS GRSsgsrFNFG LG KRS..D...DIDFRE LEekFAEDKR YPqehrFSFG LG KREveP...SELEAVrne(25)slhYP..FGIRKL RRP....FNFG LG KRI..P M YD..FGIGKR


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