Variational graph autoencoder for reconstructed transcriptomic data associated with NLRP3 mediated pyroptosis in periodontitis

The NLRP3 inflammasome, regulated by TLR4, plays a pivotal role in periodontitis by mediating inflammatory cytokine release and bone loss induced by Porphyromonas gingivalis . Periodontal disease creates a hypoxic environment, favoring anaerobic bacteria survival and exacerbating inflammation. The N...

Full description

Saved in:
Bibliographic Details
Published in:Scientific reports Vol. 15; no. 1; pp. 1962 - 11
Main Authors: Yadalam, Pradeep K., Natarajan, Prabhu Manickam, Ardila, Carlos M.
Format: Journal Article
Language:English
Published: London Nature Publishing Group UK 14.01.2025
Nature Publishing Group
Nature Portfolio
Subjects:
631/114
692/308
Anaerobic bacteria
Apoptosis
Autoencoder
Bone loss
Cell death
Cell survival
Deep learning
Gene expression
Gene Expression Profiling
Gum disease
Humanities and Social Sciences
Humans
Hypoxia
Inflammasome
Inflammasomes
Inflammasomes - genetics
Inflammasomes - metabolism
K means clustering
multidisciplinary
NLR Family, Pyrin Domain-Containing 3 Protein - genetics
NLR Family, Pyrin Domain-Containing 3 Protein - metabolism
Periodontal diseases
Periodontitis
Periodontitis - genetics
Periodontitis - metabolism
Periodontitis - microbiology
Periodontitis - pathology
Porphyromonas gingivalis
Pyroptosis
Pyroptosis - genetics
Science
Science (multidisciplinary)
TLR4 protein
Toll-like receptors
Transcriptome
Transcriptomics
Variational autoencoders
Variational autoencoders
Inflammasome
Periodontitis
K means clustering
ISSN:2045-2322, 2045-2322
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Abstract The NLRP3 inflammasome, regulated by TLR4, plays a pivotal role in periodontitis by mediating inflammatory cytokine release and bone loss induced by Porphyromonas gingivalis . Periodontal disease creates a hypoxic environment, favoring anaerobic bacteria survival and exacerbating inflammation. The NLRP3 inflammasome triggers pyroptosis, a programmed cell death that amplifies inflammation and tissue damage. This study evaluates the efficacy of Variational Graph Autoencoders (VGAEs) in reconstructing gene data related to NLRP3-mediated pyroptosis in periodontitis. The NCBI GEO dataset GSE262663, containing three samples with and without hypoxia exposure, was analyzed using unsupervised K-means clustering. This method identifies natural groupings within biological data without prior labels. VGAE, a deep learning model, captures complex graph relationships for tasks like link prediction and edge detection. The VGAE model demonstrated exceptional performance with an accuracy of 99.42% and perfect precision. While it identified 5,820 false negatives, indicating a conservative approach, it accurately predicted 4,080 out of 9,900 positive samples. The model’s latent space distribution differed significantly from the original data, suggesting a tightly clustered representation of the gene expression patterns. K-means clustering and VGAE show promise in gene expression analysis and graph structure reconstruction for periodontitis research.
AbstractList The NLRP3 inflammasome, regulated by TLR4, plays a pivotal role in periodontitis by mediating inflammatory cytokine release and bone loss induced by Porphyromonas gingivalis . Periodontal disease creates a hypoxic environment, favoring anaerobic bacteria survival and exacerbating inflammation. The NLRP3 inflammasome triggers pyroptosis, a programmed cell death that amplifies inflammation and tissue damage. This study evaluates the efficacy of Variational Graph Autoencoders (VGAEs) in reconstructing gene data related to NLRP3-mediated pyroptosis in periodontitis. The NCBI GEO dataset GSE262663, containing three samples with and without hypoxia exposure, was analyzed using unsupervised K-means clustering. This method identifies natural groupings within biological data without prior labels. VGAE, a deep learning model, captures complex graph relationships for tasks like link prediction and edge detection. The VGAE model demonstrated exceptional performance with an accuracy of 99.42% and perfect precision. While it identified 5,820 false negatives, indicating a conservative approach, it accurately predicted 4,080 out of 9,900 positive samples. The model’s latent space distribution differed significantly from the original data, suggesting a tightly clustered representation of the gene expression patterns. K-means clustering and VGAE show promise in gene expression analysis and graph structure reconstruction for periodontitis research.
The NLRP3 inflammasome, regulated by TLR4, plays a pivotal role in periodontitis by mediating inflammatory cytokine release and bone loss induced by Porphyromonas gingivalis. Periodontal disease creates a hypoxic environment, favoring anaerobic bacteria survival and exacerbating inflammation. The NLRP3 inflammasome triggers pyroptosis, a programmed cell death that amplifies inflammation and tissue damage. This study evaluates the efficacy of Variational Graph Autoencoders (VGAEs) in reconstructing gene data related to NLRP3-mediated pyroptosis in periodontitis. The NCBI GEO dataset GSE262663, containing three samples with and without hypoxia exposure, was analyzed using unsupervised K-means clustering. This method identifies natural groupings within biological data without prior labels. VGAE, a deep learning model, captures complex graph relationships for tasks like link prediction and edge detection. The VGAE model demonstrated exceptional performance with an accuracy of 99.42% and perfect precision. While it identified 5,820 false negatives, indicating a conservative approach, it accurately predicted 4,080 out of 9,900 positive samples. The model’s latent space distribution differed significantly from the original data, suggesting a tightly clustered representation of the gene expression patterns. K-means clustering and VGAE show promise in gene expression analysis and graph structure reconstruction for periodontitis research.
Abstract The NLRP3 inflammasome, regulated by TLR4, plays a pivotal role in periodontitis by mediating inflammatory cytokine release and bone loss induced by Porphyromonas gingivalis. Periodontal disease creates a hypoxic environment, favoring anaerobic bacteria survival and exacerbating inflammation. The NLRP3 inflammasome triggers pyroptosis, a programmed cell death that amplifies inflammation and tissue damage. This study evaluates the efficacy of Variational Graph Autoencoders (VGAEs) in reconstructing gene data related to NLRP3-mediated pyroptosis in periodontitis. The NCBI GEO dataset GSE262663, containing three samples with and without hypoxia exposure, was analyzed using unsupervised K-means clustering. This method identifies natural groupings within biological data without prior labels. VGAE, a deep learning model, captures complex graph relationships for tasks like link prediction and edge detection. The VGAE model demonstrated exceptional performance with an accuracy of 99.42% and perfect precision. While it identified 5,820 false negatives, indicating a conservative approach, it accurately predicted 4,080 out of 9,900 positive samples. The model’s latent space distribution differed significantly from the original data, suggesting a tightly clustered representation of the gene expression patterns. K-means clustering and VGAE show promise in gene expression analysis and graph structure reconstruction for periodontitis research.
The NLRP3 inflammasome, regulated by TLR4, plays a pivotal role in periodontitis by mediating inflammatory cytokine release and bone loss induced by Porphyromonas gingivalis. Periodontal disease creates a hypoxic environment, favoring anaerobic bacteria survival and exacerbating inflammation. The NLRP3 inflammasome triggers pyroptosis, a programmed cell death that amplifies inflammation and tissue damage. This study evaluates the efficacy of Variational Graph Autoencoders (VGAEs) in reconstructing gene data related to NLRP3-mediated pyroptosis in periodontitis. The NCBI GEO dataset GSE262663, containing three samples with and without hypoxia exposure, was analyzed using unsupervised K-means clustering. This method identifies natural groupings within biological data without prior labels. VGAE, a deep learning model, captures complex graph relationships for tasks like link prediction and edge detection. The VGAE model demonstrated exceptional performance with an accuracy of 99.42% and perfect precision. While it identified 5,820 false negatives, indicating a conservative approach, it accurately predicted 4,080 out of 9,900 positive samples. The model's latent space distribution differed significantly from the original data, suggesting a tightly clustered representation of the gene expression patterns. K-means clustering and VGAE show promise in gene expression analysis and graph structure reconstruction for periodontitis research.The NLRP3 inflammasome, regulated by TLR4, plays a pivotal role in periodontitis by mediating inflammatory cytokine release and bone loss induced by Porphyromonas gingivalis. Periodontal disease creates a hypoxic environment, favoring anaerobic bacteria survival and exacerbating inflammation. The NLRP3 inflammasome triggers pyroptosis, a programmed cell death that amplifies inflammation and tissue damage. This study evaluates the efficacy of Variational Graph Autoencoders (VGAEs) in reconstructing gene data related to NLRP3-mediated pyroptosis in periodontitis. The NCBI GEO dataset GSE262663, containing three samples with and without hypoxia exposure, was analyzed using unsupervised K-means clustering. This method identifies natural groupings within biological data without prior labels. VGAE, a deep learning model, captures complex graph relationships for tasks like link prediction and edge detection. The VGAE model demonstrated exceptional performance with an accuracy of 99.42% and perfect precision. While it identified 5,820 false negatives, indicating a conservative approach, it accurately predicted 4,080 out of 9,900 positive samples. The model's latent space distribution differed significantly from the original data, suggesting a tightly clustered representation of the gene expression patterns. K-means clustering and VGAE show promise in gene expression analysis and graph structure reconstruction for periodontitis research.
ArticleNumber 1962
Author Yadalam, Pradeep K.
Natarajan, Prabhu Manickam
Ardila, Carlos M.
Author_xml – sequence: 1
  givenname: Pradeep K.
  surname: Yadalam
  fullname: Yadalam, Pradeep K.
  organization: Department of Periodontics, Saveetha Dental College, Saveetha Institute of Medical and Technology Sciences, SIMATS, Saveetha University
– sequence: 2
  givenname: Prabhu Manickam
  surname: Natarajan
  fullname: Natarajan, Prabhu Manickam
  email: prabhuperio@gmail.com
  organization: Department of Clinical Sciences, Center of Medical and Bio-allied Health Sciences and Research, College of Dentistry, Ajman University
– sequence: 3
  givenname: Carlos M.
  surname: Ardila
  fullname: Ardila, Carlos M.
  email: martin.ardila@udea.edu.co
  organization: Department of Basic Sciences, Faculty of Dentistry, Universidad de Antioquia U de A
BackLink https://www.ncbi.nlm.nih.gov/pubmed/39809940$$D View this record in MEDLINE/PubMed
BookMark eNp9kk1v1DAQhiNUREvpH-CALHHhEvBXEueEUMVHpRUgBFyt2bGz61XWDrYD6oXfjtm00PZQH2xr5n0fjT3zuDrywduqesroS0aFepUka3pVU97UqpVNU8sH1Qmnsqm54Pzoxv24OktpR8tqeC9Z_6g6Fr2ifS_pSfX7O0QH2QUPI9lEmLYE5hysx2BsJEOIJFoMPuU4Y7aG5Ag-YXRTDnuHxEAGAikFLJSS_uXylnxcffksyN6aJTZdxlDkySXiPJlsdMEEn1126Un1cIAx2bOr87T69u7t1_MP9erT-4vzN6saG8ly2fsOlOSm6ZTCtUGAoWMIFhhIZgQDLgDRmKExcmiVpdAOEkEJlAI5iNPqYuGaADs9RbeHeKkDOH0IhLjRELPD0epOiMG2klKwKM0a-7JaJltuJOVs6Arr9cKa5nV5I1pf_mS8Bb2d8W6rN-GnZqyweUsL4cUVIYYfs01Z711CO47gbZiTFqxpOqY4VUX6_I50F-ZYmrWoZNsL0RbVs5sl_avlus9FoBYBxpBStINGlw9tLxW6UTOq_06VXqZKl6nSh6nSslj5Hes1_V6TWEypiP3Gxv9l3-P6A7Ze4uw
CitedBy_id crossref_primary_10_1016_j_jtice_2025_106127
crossref_primary_10_3390_medsci13030187
crossref_primary_10_51583_IJLTEMAS_2025_1406000109
Cites_doi 10.1186/s12964-022-01005-z
10.1016/j.jbi.2023.104512
10.1038/s42256-023-00663-z
10.1007/s00784-021-03891-y
10.1007/s13577-024-01101-x
10.1111/odi.14800
10.4103/jpbs.jpbs_1118_23
10.1080/20002297.2021.2015130
10.1093/bib/bbae173
10.1155/2019/1029857
10.18097/pbmc20236906333
10.1016/j.compbiomed.2022.106085
10.1002/eji.202350455
10.1016/j.intimp.2023.110749
10.1371/journal.pcbi.1010921
10.1038/s41587-022-01520-x
10.3389/fphar.2022.1098851
10.3390/ijms24087375
10.1186/s12903-023-03827-w
10.1093/bib/bbae619
10.1111/cpr.13539
10.1155/2023/5617800
10.3389/fcimb.2022.953277
10.7150/ijbs.85851
10.1016/j.compbiomed.2024.108561
10.3389/fgene.2019.01205
10.1111/jcpe.13517
10.1007/s10495-023-01839-z
10.1002/advs.202308786
10.1371/journal.pone.0292126
10.1162/neco_a_01458
10.1111/jre.13106
10.1093/bib/bbab315
10.1093/nar/gks1193
10.1016/j.archoralbio.2020.104763
10.1038/s41598-021-85285-4
ContentType Journal Article
Copyright The Author(s) 2025
2025. The Author(s).
Copyright Nature Publishing Group 2025
The Author(s) 2025 2025
Copyright_xml – notice: The Author(s) 2025
– notice: 2025. The Author(s).
– notice: Copyright Nature Publishing Group 2025
– notice: The Author(s) 2025 2025
DBID C6C
AAYXX
CITATION
CGR
CUY
CVF
ECM
EIF
NPM
3V.
7X7
7XB
88A
88E
88I
8FE
8FH
8FI
8FJ
8FK
ABUWG
AEUYN
AFKRA
AZQEC
BBNVY
BENPR
BHPHI
CCPQU
DWQXO
FYUFA
GHDGH
GNUQQ
HCIFZ
K9.
LK8
M0S
M1P
M2P
M7P
PHGZM
PHGZT
PIMPY
PJZUB
PKEHL
PPXIY
PQEST
PQGLB
PQQKQ
PQUKI
PRINS
Q9U
7X8
5PM
DOA
DOI 10.1038/s41598-025-86455-4
DatabaseName Springer Nature OA Free Journals
CrossRef
Medline
MEDLINE
MEDLINE (Ovid)
MEDLINE
MEDLINE
PubMed
ProQuest Central (Corporate)
Health & Medical Collection
ProQuest Central (purchase pre-March 2016)
Biology Database (Alumni Edition)
Medical Database (Alumni Edition)
Science Database (Alumni Edition)
ProQuest SciTech Collection
ProQuest Natural Science Collection
ProQuest Hospital Collection
Hospital Premium Collection (Alumni Edition)
ProQuest Central (Alumni) (purchase pre-March 2016)
ProQuest Central (Alumni)
ProQuest One Sustainability
ProQuest Central UK/Ireland
ProQuest Central Essentials
Biological Science Collection
ProQuest Central
Natural Science Collection
ProQuest One
ProQuest Central Korea
Health Research Premium Collection
Health Research Premium Collection (Alumni)
ProQuest Central Student
SciTech Premium Collection
ProQuest Health & Medical Complete (Alumni)
ProQuest Biological Science Collection
ProQuest Health & Medical Collection
Medical Database
Science Database
Biological Science Database
ProQuest Central Premium
ProQuest One Academic (New)
ProQuest Publicly Available Content Database
ProQuest Health & Medical Research Collection
ProQuest One Academic Middle East (New)
ProQuest One Health & Nursing
ProQuest One Academic Eastern Edition (DO NOT USE)
ProQuest One Applied & Life Sciences
ProQuest One Academic (retired)
ProQuest One Academic UKI Edition
ProQuest Central China
ProQuest Central Basic
MEDLINE - Academic
PubMed Central (Full Participant titles)
DOAJ Directory of Open Access Journals
DatabaseTitle CrossRef
MEDLINE
Medline Complete
MEDLINE with Full Text
PubMed
MEDLINE (Ovid)
Publicly Available Content Database
ProQuest Central Student
ProQuest One Academic Middle East (New)
ProQuest Central Essentials
ProQuest Health & Medical Complete (Alumni)
ProQuest Central (Alumni Edition)
SciTech Premium Collection
ProQuest One Community College
ProQuest One Health & Nursing
ProQuest Natural Science Collection
ProQuest Central China
ProQuest Biology Journals (Alumni Edition)
ProQuest Central
ProQuest One Applied & Life Sciences
ProQuest One Sustainability
ProQuest Health & Medical Research Collection
Health Research Premium Collection
Health and Medicine Complete (Alumni Edition)
Natural Science Collection
ProQuest Central Korea
Health & Medical Research Collection
Biological Science Collection
ProQuest Central (New)
ProQuest Medical Library (Alumni)
ProQuest Science Journals (Alumni Edition)
ProQuest Biological Science Collection
ProQuest Central Basic
ProQuest Science Journals
ProQuest One Academic Eastern Edition
ProQuest Hospital Collection
Health Research Premium Collection (Alumni)
Biological Science Database
ProQuest SciTech Collection
ProQuest Hospital Collection (Alumni)
ProQuest Health & Medical Complete
ProQuest Medical Library
ProQuest One Academic UKI Edition
ProQuest One Academic
ProQuest One Academic (New)
ProQuest Central (Alumni)
MEDLINE - Academic
DatabaseTitleList
Publicly Available Content Database

MEDLINE

MEDLINE - Academic
Database_xml – sequence: 1
  dbid: DOA
  name: DOAJ: Directory of Open Access Journal (DOAJ)
  url: https://www.doaj.org/
  sourceTypes: Open Website
– sequence: 2
  dbid: NPM
  name: PubMed
  url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
  sourceTypes: Index Database
– sequence: 3
  dbid: PIMPY
  name: ProQuest Publicly Available Content Database
  url: http://search.proquest.com/publiccontent
  sourceTypes: Aggregation Database
DeliveryMethod fulltext_linktorsrc
Discipline Biology
EISSN 2045-2322
EndPage 11
ExternalDocumentID oai_doaj_org_article_733fe6400aec4dbc999961462d4021f7
PMC11733260
39809940
10_1038_s41598_025_86455_4
Genre Journal Article
GroupedDBID 0R~
4.4
53G
5VS
7X7
88E
88I
8FE
8FH
8FI
8FJ
AAFWJ
AAJSJ
AAKDD
AASML
ABDBF
ABUWG
ACGFS
ACUHS
ADBBV
ADRAZ
AENEX
AEUYN
AFKRA
AFPKN
ALIPV
ALMA_UNASSIGNED_HOLDINGS
AOIJS
AZQEC
BAWUL
BBNVY
BCNDV
BENPR
BHPHI
BPHCQ
BVXVI
C6C
CCPQU
DIK
DWQXO
EBD
EBLON
EBS
ESX
FYUFA
GNUQQ
GROUPED_DOAJ
GX1
HCIFZ
HH5
HMCUK
HYE
KQ8
LK8
M1P
M2P
M48
M7P
M~E
NAO
OK1
PHGZM
PHGZT
PIMPY
PJZUB
PPXIY
PQGLB
PQQKQ
PROAC
PSQYO
RNT
RNTTT
RPM
SNYQT
UKHRP
AAYXX
AFFHD
CITATION
CGR
CUY
CVF
ECM
EIF
NPM
3V.
7XB
88A
8FK
K9.
PKEHL
PQEST
PQUKI
PRINS
Q9U
7X8
5PM
ID FETCH-LOGICAL-c541t-c597a842d5788cbdcaaf71caea1a41d31a23accddf5d4f68e0a6f4ca83c43c2a3
IEDL.DBID M2P
ISICitedReferencesCount 2
ISICitedReferencesURI http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=001397940300015&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D
ISSN 2045-2322
IngestDate Tue Oct 14 19:09:19 EDT 2025
Tue Nov 04 02:04:59 EST 2025
Sun Nov 09 12:36:15 EST 2025
Tue Oct 07 09:11:23 EDT 2025
Mon Jul 21 06:03:01 EDT 2025
Sat Nov 29 03:22:19 EST 2025
Tue Nov 18 22:24:27 EST 2025
Mon Jul 21 06:08:37 EDT 2025
IsDoiOpenAccess true
IsOpenAccess true
IsPeerReviewed true
IsScholarly true
Issue 1
Keywords Variational autoencoders
Inflammasome
Periodontitis
K means clustering
Language English
License 2025. The Author(s).
Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
LinkModel DirectLink
MergedId FETCHMERGED-LOGICAL-c541t-c597a842d5788cbdcaaf71caea1a41d31a23accddf5d4f68e0a6f4ca83c43c2a3
Notes ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 14
content type line 23
OpenAccessLink https://www.proquest.com/docview/3155469336?pq-origsite=%requestingapplication%
PMID 39809940
PQID 3155469336
PQPubID 2041939
PageCount 11
ParticipantIDs doaj_primary_oai_doaj_org_article_733fe6400aec4dbc999961462d4021f7
pubmedcentral_primary_oai_pubmedcentral_nih_gov_11733260
proquest_miscellaneous_3155718208
proquest_journals_3155469336
pubmed_primary_39809940
crossref_citationtrail_10_1038_s41598_025_86455_4
crossref_primary_10_1038_s41598_025_86455_4
springer_journals_10_1038_s41598_025_86455_4
PublicationCentury 2000
PublicationDate 2025-01-14
PublicationDateYYYYMMDD 2025-01-14
PublicationDate_xml – month: 01
  year: 2025
  text: 2025-01-14
  day: 14
PublicationDecade 2020
PublicationPlace London
PublicationPlace_xml – name: London
– name: England
PublicationTitle Scientific reports
PublicationTitleAbbrev Sci Rep
PublicationTitleAlternate Sci Rep
PublicationYear 2025
Publisher Nature Publishing Group UK
Nature Publishing Group
Nature Portfolio
Publisher_xml – name: Nature Publishing Group UK
– name: Nature Publishing Group
– name: Nature Portfolio
References Z Wang (86455_CR20) 2024; 30
Z Zhao (86455_CR6) 2023; 24
86455_CR9
Z Wang (86455_CR21) 2023; 123
Y Wang (86455_CR3) 2023; 28
J Marino (86455_CR34) 2021; 34
NC Kalafut (86455_CR37) 2023; 5
S Xu (86455_CR24) 2024; 37
X Xu (86455_CR4) 2022; 12
RL Allesøe (86455_CR33) 2023; 41
S Pan (86455_CR11) 2022; 13
X Jiang (86455_CR23) 2024; 20
T Zhang (86455_CR36) 2024; 26
N Simidjievski (86455_CR29) 2019; 10
S Ranjbari (86455_CR35) 2023; 147
H Liu (86455_CR7) 2022; 20
P Zhao (86455_CR5) 2021; 48
H Benkirane (86455_CR12) 2023; 19
CCC Ribeiro (86455_CR2) 2021; 25
86455_CR10
L Lei (86455_CR28) 2024; 25
M Eltager (86455_CR31) 2023; 18
L Huang (86455_CR27) 2023; 12
T Barrett (86455_CR15) 2013; 41
I Rivero-Garcia (86455_CR32) 2024; 176
X Zhou (86455_CR18) 2020; 116
N Hashim (86455_CR17) 2024; 16
Z Rong (86455_CR30) 2022; 150
O Ozkocer (86455_CR8) 2023; 58
L Wang (86455_CR19) 2022; 14
X Zhou (86455_CR25) 2024; 11
Y Xu (86455_CR16) 2024; 24
E Lin (86455_CR38) 2023; 4
NY Rusetskaya (86455_CR26) 2023; 69
K Boonyaleka (86455_CR1) 2023; 53
MT Hira (86455_CR13) 2021; 11
A Hu (86455_CR22) 2024; 57
E Withnell (86455_CR14) 2021; 22
References_xml – volume: 20
  start-page: 196
  year: 2022
  ident: 86455_CR7
  publication-title: Cell. Commun. Signal.
  doi: 10.1186/s12964-022-01005-z
– volume: 147
  start-page: 104512
  year: 2023
  ident: 86455_CR35
  publication-title: J. Biomed. Inf.
  doi: 10.1016/j.jbi.2023.104512
– volume: 5
  start-page: 631
  year: 2023
  ident: 86455_CR37
  publication-title: Nat. Mach. Intell.
  doi: 10.1038/s42256-023-00663-z
– volume: 25
  start-page: 5855
  year: 2021
  ident: 86455_CR2
  publication-title: Clin. Oral Investig
  doi: 10.1007/s00784-021-03891-y
– volume: 37
  start-page: 1276
  year: 2024
  ident: 86455_CR24
  publication-title: Hum. Cell
  doi: 10.1007/s13577-024-01101-x
– volume: 30
  start-page: 3272
  year: 2024
  ident: 86455_CR20
  publication-title: Oral Dis.
  doi: 10.1111/odi.14800
– volume: 16
  start-page: S1110
  year: 2024
  ident: 86455_CR17
  publication-title: J. Pharm. Bioallied Sci.
  doi: 10.4103/jpbs.jpbs_1118_23
– volume: 14
  start-page: 2015130
  year: 2022
  ident: 86455_CR19
  publication-title: J. Oral Microbiol.
  doi: 10.1080/20002297.2021.2015130
– volume: 25
  start-page: bbae173
  year: 2024
  ident: 86455_CR28
  publication-title: Brief. Bioinform
  doi: 10.1093/bib/bbae173
– ident: 86455_CR10
  doi: 10.1155/2019/1029857
– volume: 69
  start-page: 333
  year: 2023
  ident: 86455_CR26
  publication-title: Biomed. Khim.
  doi: 10.18097/pbmc20236906333
– volume: 150
  start-page: 106085
  year: 2022
  ident: 86455_CR30
  publication-title: Comput. Biol. Med.
  doi: 10.1016/j.compbiomed.2022.106085
– volume: 53
  start-page: e2350455
  year: 2023
  ident: 86455_CR1
  publication-title: Eur. J. Immunol.
  doi: 10.1002/eji.202350455
– volume: 123
  start-page: 110749
  year: 2023
  ident: 86455_CR21
  publication-title: Int. Immunopharmacol.
  doi: 10.1016/j.intimp.2023.110749
– volume: 19
  start-page: e1010921
  year: 2023
  ident: 86455_CR12
  publication-title: PLoS Comput. Biol.
  doi: 10.1371/journal.pcbi.1010921
– volume: 41
  start-page: 399
  year: 2023
  ident: 86455_CR33
  publication-title: Nat. Biotechnol.
  doi: 10.1038/s41587-022-01520-x
– volume: 13
  start-page: 1098851
  year: 2022
  ident: 86455_CR11
  publication-title: Front. Pharmacol.
  doi: 10.3389/fphar.2022.1098851
– volume: 24
  start-page: e7375
  year: 2023
  ident: 86455_CR6
  publication-title: Int. J. Mol. Sci.
  doi: 10.3390/ijms24087375
– volume: 24
  start-page: 40
  year: 2024
  ident: 86455_CR16
  publication-title: BMC Oral Health
  doi: 10.1186/s12903-023-03827-w
– volume: 26
  start-page: bbae619
  year: 2024
  ident: 86455_CR36
  publication-title: Brief. Bioinform
  doi: 10.1093/bib/bbae619
– volume: 57
  start-page: e13539
  year: 2024
  ident: 86455_CR22
  publication-title: Cell. Prolif.
  doi: 10.1111/cpr.13539
– ident: 86455_CR9
  doi: 10.1155/2023/5617800
– volume: 12
  start-page: 953277
  year: 2022
  ident: 86455_CR4
  publication-title: Front. Cell. Infect. Microbiol.
  doi: 10.3389/fcimb.2022.953277
– volume: 4
  start-page: 035013
  year: 2023
  ident: 86455_CR38
  publication-title: Mach. Learn. : Sci. Technol.
– volume: 20
  start-page: 1375
  year: 2024
  ident: 86455_CR23
  publication-title: Int. J. Biol. Sci.
  doi: 10.7150/ijbs.85851
– volume: 12
  start-page: 1297
  year: 2023
  ident: 86455_CR27
  publication-title: Biology (Basel)
– volume: 176
  start-page: 108561
  year: 2024
  ident: 86455_CR32
  publication-title: Comput. Biol. Med.
  doi: 10.1016/j.compbiomed.2024.108561
– volume: 10
  start-page: 1205
  year: 2019
  ident: 86455_CR29
  publication-title: Front. Genet.
  doi: 10.3389/fgene.2019.01205
– volume: 48
  start-page: 1379
  year: 2021
  ident: 86455_CR5
  publication-title: J. Clin. Periodontol
  doi: 10.1111/jcpe.13517
– volume: 28
  start-page: 1012
  year: 2023
  ident: 86455_CR3
  publication-title: Apoptosis
  doi: 10.1007/s10495-023-01839-z
– volume: 11
  start-page: e2308786
  year: 2024
  ident: 86455_CR25
  publication-title: Adv. Sci. (Weinh)
  doi: 10.1002/advs.202308786
– volume: 18
  start-page: e0292126
  year: 2023
  ident: 86455_CR31
  publication-title: PLoS One
  doi: 10.1371/journal.pone.0292126
– volume: 34
  start-page: 1
  year: 2021
  ident: 86455_CR34
  publication-title: Neural Comput.
  doi: 10.1162/neco_a_01458
– volume: 58
  start-page: 456
  year: 2023
  ident: 86455_CR8
  publication-title: J. Periodontal Res.
  doi: 10.1111/jre.13106
– volume: 22
  start-page: bbab454
  year: 2021
  ident: 86455_CR14
  publication-title: Brief. Bioinform
  doi: 10.1093/bib/bbab315
– volume: 41
  start-page: D991
  year: 2013
  ident: 86455_CR15
  publication-title: Nucleic Acids Res.
  doi: 10.1093/nar/gks1193
– volume: 116
  start-page: 104763
  year: 2020
  ident: 86455_CR18
  publication-title: Arch. Oral Biol.
  doi: 10.1016/j.archoralbio.2020.104763
– volume: 11
  start-page: 6265
  year: 2021
  ident: 86455_CR13
  publication-title: Sci. Rep.
  doi: 10.1038/s41598-021-85285-4
SSID ssj0000529419
Score 2.4514942
Snippet The NLRP3 inflammasome, regulated by TLR4, plays a pivotal role in periodontitis by mediating inflammatory cytokine release and bone loss induced by...
Abstract The NLRP3 inflammasome, regulated by TLR4, plays a pivotal role in periodontitis by mediating inflammatory cytokine release and bone loss induced by...
SourceID doaj
pubmedcentral
proquest
pubmed
crossref
springer
SourceType Open Website
Open Access Repository
Aggregation Database
Index Database
Enrichment Source
Publisher
StartPage 1962
SubjectTerms 631/114
692/308
Anaerobic bacteria
Apoptosis
Autoencoder
Bone loss
Cell death
Cell survival
Deep learning
Gene expression
Gene Expression Profiling
Gum disease
Humanities and Social Sciences
Humans
Hypoxia
Inflammasome
Inflammasomes
Inflammasomes - genetics
Inflammasomes - metabolism
K means clustering
multidisciplinary
NLR Family, Pyrin Domain-Containing 3 Protein - genetics
NLR Family, Pyrin Domain-Containing 3 Protein - metabolism
Periodontal diseases
Periodontitis
Periodontitis - genetics
Periodontitis - metabolism
Periodontitis - microbiology
Periodontitis - pathology
Porphyromonas gingivalis
Pyroptosis
Pyroptosis - genetics
Science
Science (multidisciplinary)
TLR4 protein
Toll-like receptors
Transcriptome
Transcriptomics
Variational autoencoders
SummonAdditionalLinks – databaseName: DOAJ Directory of Open Access Journals
  dbid: DOA
  link: http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwrV1Lb9QwEB6hCiQuiDeBgozEDazGj8T2ERAVh2pVIUC9WV4_xEooW222lXrpb-_Yzi5dnhcuOcSTaOT5JjMTez4DvIqtUjmvpRideorx2NG5VoIK3hqVYvJCl0bhIzWb6ZMTc3ztqK-8J6zSA9eJO1BCpNgj0lz0Msy9yRk6ujcPWPmwVPrIW2WuFVOV1ZsbyczUJdMKfTBipMrdZLyjupddR-VOJCqE_b_LMn_dLPnTimkJRId34c6UQZK3VfN7cCMO9-FWPVPy4gFcfsXqd_rDRwodNXFn62XmqwxxRTBHJaUIrsSxMZB1jlbl25EblEneMkrcZDQczj9qyezo07Egpcsk3zu9WC1RfFyMZDGQzJWMxW0hZx0fwpfDD5_ff6TTIQvUd5Kt8WqU05IHdF3t58E7lxTzLjrmJAuCOS6c9yGkLsjU69i6PknvtPBSeO7EI9gblkN8AsRIfLx3TOuEovimTseACZBMrPOi5Q2wzYRbPzGQ54MwvtuyEi60rUayaCRbjGRlA6-3z5xW_o2_Sr_LdtxKZu7scgMRZSdE2X8hqoH9DQrs5NCjFTnv6o0QfQMvt8Poinl9xQ1xeVZlVCbE1w08rqDZaiKMxlxctg3oHTjtqLo7Miy-FbpvxlBjLDsbeLNB3g-9_jwXT__HXDyD2zy7TMsok_uwh9CMz-GmP0dArV4Un7sCFUgxQA
  priority: 102
  providerName: Directory of Open Access Journals
Title Variational graph autoencoder for reconstructed transcriptomic data associated with NLRP3 mediated pyroptosis in periodontitis
URI https://link.springer.com/article/10.1038/s41598-025-86455-4
https://www.ncbi.nlm.nih.gov/pubmed/39809940
https://www.proquest.com/docview/3155469336
https://www.proquest.com/docview/3155718208
https://pubmed.ncbi.nlm.nih.gov/PMC11733260
https://doaj.org/article/733fe6400aec4dbc999961462d4021f7
Volume 15
WOSCitedRecordID wos001397940300015&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D
hasFullText 1
inHoldings 1
isFullTextHit
isPrint
journalDatabaseRights – providerCode: PRVAON
  databaseName: DOAJ: Directory of Open Access Journal (DOAJ)
  customDbUrl:
  eissn: 2045-2322
  dateEnd: 99991231
  omitProxy: false
  ssIdentifier: ssj0000529419
  issn: 2045-2322
  databaseCode: DOA
  dateStart: 20110101
  isFulltext: true
  titleUrlDefault: https://www.doaj.org/
  providerName: Directory of Open Access Journals
– providerCode: PRVHPJ
  databaseName: ROAD: Directory of Open Access Scholarly Resources (ISSN International Center)
  customDbUrl:
  eissn: 2045-2322
  dateEnd: 99991231
  omitProxy: false
  ssIdentifier: ssj0000529419
  issn: 2045-2322
  databaseCode: M~E
  dateStart: 20110101
  isFulltext: true
  titleUrlDefault: https://road.issn.org
  providerName: ISSN International Centre
– providerCode: PRVPQU
  databaseName: Biological Science Database (ProQuest)
  customDbUrl:
  eissn: 2045-2322
  dateEnd: 99991231
  omitProxy: false
  ssIdentifier: ssj0000529419
  issn: 2045-2322
  databaseCode: M7P
  dateStart: 20110101
  isFulltext: true
  titleUrlDefault: http://search.proquest.com/biologicalscijournals
  providerName: ProQuest
– providerCode: PRVPQU
  databaseName: Health & Medical Collection
  customDbUrl:
  eissn: 2045-2322
  dateEnd: 99991231
  omitProxy: false
  ssIdentifier: ssj0000529419
  issn: 2045-2322
  databaseCode: 7X7
  dateStart: 20110101
  isFulltext: true
  titleUrlDefault: https://search.proquest.com/healthcomplete
  providerName: ProQuest
– providerCode: PRVPQU
  databaseName: ProQuest Central Database Suite (ProQuest)
  customDbUrl:
  eissn: 2045-2322
  dateEnd: 99991231
  omitProxy: false
  ssIdentifier: ssj0000529419
  issn: 2045-2322
  databaseCode: BENPR
  dateStart: 20110101
  isFulltext: true
  titleUrlDefault: https://www.proquest.com/central
  providerName: ProQuest
– providerCode: PRVPQU
  databaseName: ProQuest Publicly Available Content Database
  customDbUrl:
  eissn: 2045-2322
  dateEnd: 99991231
  omitProxy: false
  ssIdentifier: ssj0000529419
  issn: 2045-2322
  databaseCode: PIMPY
  dateStart: 20110101
  isFulltext: true
  titleUrlDefault: http://search.proquest.com/publiccontent
  providerName: ProQuest
– providerCode: PRVPQU
  databaseName: Science Database
  customDbUrl:
  eissn: 2045-2322
  dateEnd: 99991231
  omitProxy: false
  ssIdentifier: ssj0000529419
  issn: 2045-2322
  databaseCode: M2P
  dateStart: 20110101
  isFulltext: true
  titleUrlDefault: https://search.proquest.com/sciencejournals
  providerName: ProQuest
link http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpV3db9MwED-xFaS98M0IjMpIvEG0OHZi5wkxtAmkrYomQOUpcm0HKqGkNB3SXvjbuXPSTuVjL7z4Ib5UTu98X_b9DuCFT5QivzZG65THaI9NPNNKxCJNClX72godCoVP1WSip9OiHBJu3XCtcq0Tg6J2raUc-aEgw5dj-J2_XnyPqWsUna4OLTR2YISeDacrXWdpucmx0CmW5MVQK5MIfdihvaKasjSLdS6zLJZb9ijA9v_N1_zzyuRv56bBHJ3c-d8PuQu3B0eUvekl5x7c8M19uNW3prx8AD8_YRA9JApZQLVm5mLVEuyl80uGri4LsXSPP-sdW5HRCyqI6pwZ3TxlZuA9TlO-l01Oz0vBQrEKPVtcLlsk7-YdmzeMIJcxRg4Yr91D-Hhy_OHtu3jo1RDbTPIVjoUyWqYONYC2M2eNqRW3xhtuJHeCm1QYa52rMyfrXPvE5LW0RgsrhU2NeAS7Tdv4x8AKia_nhmtdIyn-Uqa9Qz9K1jyzIkkj4GuOVXYAMqd-Gt-qcKAudNVzuUIuV4HLlYzg5eadRQ_jcS31EQnChpIguMODdvmlGnZ0pYSofY4q0Hgr3cwWFDqi3UkdhuS8VhEcrPlfDXqhq66YH8HzzTTuaDqmMY1vL3oaRbj6OoL9Xuo2KxGFRpdeJhHoLXncWur2TDP_GlDDOccVY_Qawau16F6t69__xZPrP-Mp7KW0mxIec3kAuyh0_hnctD9QVJZj2FFTFUY9htHR8aQ8H4esxzhsVBoVjqPy_Vn5-RcJfUb3
linkProvider ProQuest
linkToHtml http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMw1V1Lb9QwEB6VAoIL70eggJHgBFHj2EmcA0K8qlZdVitUUG_BazuwEkqWZAvaCz-J38iMk2y1PHrrgcseYidysp_n5ZlvAB65KMvIrg1RO6Uh6mMdTlUmQhFHeVa60gjlC4VH2XisDg_zyQb8HGphKK1ykIleUNvaUIx8W5DiS9H9Tp_Pv4bUNYpOV4cWGh0s9t3yO7ps7bO91_j_Po7jnTcHr3bDvqtAaBLJF_ibZ1rJ2CJWlZlao3WZcaOd5lpyK7iOhTbG2jKxskyVi3RaSqOVMFKYWAt87hk4K4lZjFIF48kqpkOnZpLnfW1OJNR2i_qRatjiJFSpTJJQruk_3ybgb7btnymav53TevW3c_l_-3BX4FJvaLMX3c64Chuuugbnu9aby-vw44NuZn0glHnWbqaPFjXRelrXMDTlmY8VdPy6zrIFKXUvYqmOm1FmLdM9tnGY4tlsPHo3EcwX49C1-bKpcXo7a9msYkQpXdvac9i2N-D9qbz8Tdis6srdBpZLvD3VXKkSp-KTEuUs2omy5IkRURwAHxBSmJ6onfqFfCl8woBQRYeqAlFVeFQVMoAnq3vmHU3JibNfEvBWM4li3F-om09FL7GKTIjSpSjitTPSTk1OrjHq1dhKtAvLLICtAW9FL_fa4hhsATxcDaPEomMoXbn6qJuTUd8AFcCtDuWrlYhcocsiowDUGv7Xlro-Us0-e1Z0znHF6J0H8HTYKsfr-ve3uHPyazyAC7sHb0fFaG-8fxcuxrSTIx5yuQWbCEB3D86Zbwib5r4XBQw-nvYW-gXYZaFO
linkToPdf http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMw1V1Jb9NAFH4qKVRc2BdDgUGCE1jxLLbHB4SAEhE1RBEC1J7MZGZcIiE7xCkoF34Yv443YztVWHrrgUsOnmdr7HxvnbcAPLJRmjq7NkTtlISoj1U4lSkPOYuytLCF5tIXCo_S8VgeHGSTLfjZ1cK4tMpOJnpBbSrtYuR97hRfgu530i_atIjJ3uD5_GvoJki5k9ZunEYDkX27-o7uW_1suIf_9WPGBq_fv3oTthMGQh0LusTfLFVSMIO4lXpqtFJFSrWyiipBDaeKcaW1MUVsRJFIG6mkEFpJrgXXTHF87jnYRpNcsB5sT4ZvJ4frCI87QxM0ayt1Ii77NWpLV9HG4lAmIo5DsaEN_dCAv1m6fyZs_nZq65Xh4PL__BmvwKXWBCcvGp65Clu2vAYXmqGcq-vw46NazNoQKfH9vIk6Xlau4aexC4JGPvFRhKbzrjVk6dS9F76uwpu4nFuiWtTjsot0k_Ho3YQTX6bjrs1XiwrJ61lNZiVxzaYrU_nutvUN-HAmL38TemVV2ttAMoG3J4pKWSApPimW1qAFKQoaax6xAGiHlly3LdzdJJEvuU8l4DJvEJYjwnKPsFwE8GR9z7xpYHIq9UsHwjWlaz7uL1SLo7yVZXnKeWETFP7KamGmOnNOM2pcZgRajEUawG6HvbyViHV-ArwAHq6XUZa5AypV2uq4oUndRAEZwK0G8eud8EyiMyOiAOQGL2xsdXOlnH32_dIpxR2j3x7A045tTvb1729x5_TXeAA7yDn5aDjevwsXmWPqiIZU7EIP8WfvwXn9DVGzuN_KBQKfzpqHfgGzuKuX
openUrl ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Variational+graph+autoencoder+for+reconstructed+transcriptomic+data+associated+with+NLRP3+mediated+pyroptosis+in+periodontitis&rft.jtitle=Scientific+reports&rft.date=2025-01-14&rft.pub=Nature+Publishing+Group&rft.eissn=2045-2322&rft.volume=15&rft.issue=1&rft.spage=1962&rft_id=info:doi/10.1038%2Fs41598-025-86455-4&rft.externalDBID=HAS_PDF_LINK
thumbnail_l http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=2045-2322&client=summon
thumbnail_m http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=2045-2322&client=summon
thumbnail_s http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=2045-2322&client=summon