GraphCVAE: Uncovering cell heterogeneity and therapeutic target discovery through residual and contrastive learning

Advancements in Spatial Transcriptomics (ST) technologies in recent years have transformed the analysis of tissue structure and function within spatial contexts. However, accurately identifying spatial domains remains challenging due to data sparsity and noise. Traditional clustering methods often f...

Full description

Saved in:

Bibliographic Details
Published in:	Life sciences (1973) Vol. 359; p. 123208
Main Authors:	Zhang, Zhiwei, Wang, Mengqiu, Dai, Ruoyan, Wang, Zhenghui, Lei, Lixin, Zhao, Xudong, Han, Kaitai, Shi, Chaojing, Guo, Qianjin
Format:	Journal Article
Language:	English
Published:	Netherlands Elsevier Inc 15.12.2024
Subjects:	colorectal neoplasms Colorectal Neoplasms - genetics Colorectal Neoplasms - pathology Contrastive learning data collection Deep learning domain extracellular matrix Gene expression Gene Expression Profiling - methods glioblastoma Glioblastoma - genetics Glioblastoma - pathology Humans Machine Learning Neural Networks, Computer Prefrontal Cortex Spatial clustering spatial data Spatial transcriptomics therapeutics Transcriptome transcriptomics Variational graph autoencoder Deep learning Spatial clustering Gene expression Spatial transcriptomics Variational graph autoencoder Contrastive learning
ISSN:	0024-3205, 1879-0631, 1879-0631
Online Access:	Get full text
Tags:	Add Tag No Tags, Be the first to tag this record!

Abstract	Advancements in Spatial Transcriptomics (ST) technologies in recent years have transformed the analysis of tissue structure and function within spatial contexts. However, accurately identifying spatial domains remains challenging due to data sparsity and noise. Traditional clustering methods often fail to capture spatial dependencies, while spatial clustering methods struggle with batch effects and data integration. We introduce GraphCVAE, a model designed to enhance spatial domain identification by integrating spatial and morphological information, correcting batch effects, and managing heterogeneous data. GraphCVAE employs a multi-layer Graph Convolutional Network (GCN) and a variational autoencoder to improve the representation and integration of spatial information. Through contrastive learning, the model captures subtle differences between cell types and states. Extensive testing on various ST datasets demonstrates GraphCVAE's robustness and biological contributions. In the dorsolateral prefrontal cortex (DLPFC) dataset, it accurately delineates cortical layer boundaries. In glioblastoma, GraphCVAE reveals critical therapeutic targets such as TF and NFIB. In colorectal cancer, it explores the role of the extracellular matrix in colorectal cancer. The model's performance metrics consistently surpass existing methods, validating its effectiveness. GraphCVAE's advanced visualization capabilities further highlight its precision in resolving spatial structures, making it a powerful tool for spatial transcriptomics analysis and offering new insights into disease studies.
AbstractList	Advancements in Spatial Transcriptomics (ST) technologies in recent years have transformed the analysis of tissue structure and function within spatial contexts. However, accurately identifying spatial domains remains challenging due to data sparsity and noise. Traditional clustering methods often fail to capture spatial dependencies, while spatial clustering methods struggle with batch effects and data integration. We introduce GraphCVAE, a model designed to enhance spatial domain identification by integrating spatial and morphological information, correcting batch effects, and managing heterogeneous data. GraphCVAE employs a multi-layer Graph Convolutional Network (GCN) and a variational autoencoder to improve the representation and integration of spatial information. Through contrastive learning, the model captures subtle differences between cell types and states. Extensive testing on various ST datasets demonstrates GraphCVAE's robustness and biological contributions. In the dorsolateral prefrontal cortex (DLPFC) dataset, it accurately delineates cortical layer boundaries. In glioblastoma, GraphCVAE reveals critical therapeutic targets such as TF and NFIB. In colorectal cancer, it explores the role of the extracellular matrix in colorectal cancer. The model's performance metrics consistently surpass existing methods, validating its effectiveness. GraphCVAE's advanced visualization capabilities further highlight its precision in resolving spatial structures, making it a powerful tool for spatial transcriptomics analysis and offering new insights into disease studies. Advancements in Spatial Transcriptomics (ST) technologies in recent years have transformed the analysis of tissue structure and function within spatial contexts. However, accurately identifying spatial domains remains challenging due to data sparsity and noise. Traditional clustering methods often fail to capture spatial dependencies, while spatial clustering methods struggle with batch effects and data integration. We introduce GraphCVAE, a model designed to enhance spatial domain identification by integrating spatial and morphological information, correcting batch effects, and managing heterogeneous data. GraphCVAE employs a multi-layer Graph Convolutional Network (GCN) and a variational autoencoder to improve the representation and integration of spatial information. Through contrastive learning, the model captures subtle differences between cell types and states. Extensive testing on various ST datasets demonstrates GraphCVAE's robustness and biological contributions. In the dorsolateral prefrontal cortex (DLPFC) dataset, it accurately delineates cortical layer boundaries. In glioblastoma, GraphCVAE reveals critical therapeutic targets such as TF and NFIB. In colorectal cancer, it explores the role of the extracellular matrix in colorectal cancer. The model's performance metrics consistently surpass existing methods, validating its effectiveness. GraphCVAE's advanced visualization capabilities further highlight its precision in resolving spatial structures, making it a powerful tool for spatial transcriptomics analysis and offering new insights into disease studies.Advancements in Spatial Transcriptomics (ST) technologies in recent years have transformed the analysis of tissue structure and function within spatial contexts. However, accurately identifying spatial domains remains challenging due to data sparsity and noise. Traditional clustering methods often fail to capture spatial dependencies, while spatial clustering methods struggle with batch effects and data integration. We introduce GraphCVAE, a model designed to enhance spatial domain identification by integrating spatial and morphological information, correcting batch effects, and managing heterogeneous data. GraphCVAE employs a multi-layer Graph Convolutional Network (GCN) and a variational autoencoder to improve the representation and integration of spatial information. Through contrastive learning, the model captures subtle differences between cell types and states. Extensive testing on various ST datasets demonstrates GraphCVAE's robustness and biological contributions. In the dorsolateral prefrontal cortex (DLPFC) dataset, it accurately delineates cortical layer boundaries. In glioblastoma, GraphCVAE reveals critical therapeutic targets such as TF and NFIB. In colorectal cancer, it explores the role of the extracellular matrix in colorectal cancer. The model's performance metrics consistently surpass existing methods, validating its effectiveness. GraphCVAE's advanced visualization capabilities further highlight its precision in resolving spatial structures, making it a powerful tool for spatial transcriptomics analysis and offering new insights into disease studies.
ArticleNumber	123208
Author	Zhao, Xudong Zhang, Zhiwei Wang, Zhenghui Dai, Ruoyan Shi, Chaojing Lei, Lixin Wang, Mengqiu Han, Kaitai Guo, Qianjin
Author_xml	– sequence: 1 givenname: Zhiwei surname: Zhang fullname: Zhang, Zhiwei – sequence: 2 givenname: Mengqiu surname: Wang fullname: Wang, Mengqiu – sequence: 3 givenname: Ruoyan surname: Dai fullname: Dai, Ruoyan – sequence: 4 givenname: Zhenghui surname: Wang fullname: Wang, Zhenghui – sequence: 5 givenname: Lixin surname: Lei fullname: Lei, Lixin – sequence: 6 givenname: Xudong surname: Zhao fullname: Zhao, Xudong – sequence: 7 givenname: Kaitai surname: Han fullname: Han, Kaitai – sequence: 8 givenname: Chaojing surname: Shi fullname: Shi, Chaojing – sequence: 9 givenname: Qianjin surname: Guo fullname: Guo, Qianjin email: guoqj@iccas.ac.cn, guoqianjin@bipt.edu.cn
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/39488267$$D View this record in MEDLINE/PubMed
BookMark	eNqNkU1vEzEQhi1URNPCD-CCfOSywR_xx8KpikpBqsSFcrX8MZs42niD7Y2Uf1-3KRwRp5E8zzMaz3uFLtKUAKH3lCwpofLTbjkOZckIWy0p44zoV2hBteo7Ijm9QAvSOl17F5foqpQdIUQIxd-gS96vtGZSLVC5y_awXf-6uf2MH5KfjpBj2mAP44i3UCFPG0gQ6wnbFHDdQsNhrtHjavMGKg6xPFun1szTvNniDCWG2Y7Php9SzbbUeAQ8gs2pTX-LXg92LPDupV6jh6-3P9ffuvsfd9_XN_ed51zXjlHwXBMVBtY7JaFXTjmvqWVMDGEFwgbimAsOqLVSDkpwr4PzkugepHL8Gn08zz3k6fcMpZp9W7b9zCaY5mI4FSsmZS_1f6CMC0GZIA398ILObg_BHHLc23wyf27aAHoGfJ5KyTD8RSgxT7mZnWm5mafczDm35nw5O9DucYyQTfERkocQM_hqwhT_YT8CJZOhkw
Cites_doi	10.1038/s41593-020-00787-0 10.1177/0192623309335060 10.1101/gad.1632008 10.1039/C0AN00560F 10.1038/s41467-022-29439-6 10.32614/RJ-2016-021 10.1038/s41587-020-0739-1 10.1016/j.nlm.2007.04.013 10.1038/s41592-019-0619-0 10.1126/science.abp9444 10.1109/3477.764879 10.1002/iub.1956 10.1093/nar/gkac901 10.1109/TNN.2008.2005601 10.1038/s41467-023-36796-3 10.1093/bib/bbae016 10.1371/journal.pgen.1005175 10.1038/s41467-023-43458-x 10.1186/s13059-019-1663-x 10.1016/j.expneurol.2024.114804 10.18632/oncotarget.8720 10.3389/fphar.2022.1071897 10.1038/ncomms13998 10.3390/ijms23136879 10.1523/JNEUROSCI.0590-08.2008 10.1371/journal.pcbi.1002488 10.1523/JNEUROSCI.1588-14.2014 10.1186/s13059-017-1382-0 10.1038/s41587-021-00935-2 10.1038/s41467-022-33619-9 10.4161/cc.7.10.5953 10.1088/1742-5468/2008/10/P10008 10.1517/14728222.12.4.491 10.1038/bjc.2014.226 10.1016/j.canlet.2015.02.021 10.1038/ncomms14495 10.1038/s41592-022-01409-2
ContentType	Journal Article
Copyright	2024 Elsevier Inc. Copyright © 2024 Elsevier Inc. All rights reserved.
Copyright_xml	– notice: 2024 Elsevier Inc. – notice: Copyright © 2024 Elsevier Inc. All rights reserved.
DBID	AAYXX CITATION CGR CUY CVF ECM EIF NPM 7X8 7S9 L.6
DOI	10.1016/j.lfs.2024.123208
DatabaseName	CrossRef Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed MEDLINE - Academic AGRICOLA AGRICOLA - Academic
DatabaseTitle	CrossRef MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) MEDLINE - Academic AGRICOLA AGRICOLA - Academic
DatabaseTitleList	MEDLINE MEDLINE - Academic AGRICOLA
Database_xml	– sequence: 1 dbid: NPM name: PubMed url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: 7X8 name: MEDLINE - Academic url: https://search.proquest.com/medline sourceTypes: Aggregation Database
DeliveryMethod	fulltext_linktorsrc
Discipline	Sciences (General) Biology
EISSN	1879-0631
ExternalDocumentID	39488267 10_1016_j_lfs_2024_123208 S0024320524007987
Genre	Journal Article
GroupedDBID	--- --K --M -~X .~1 0R~ 1B1 1RT 1~. 4.4 457 5GY 5RE 5VS 6TJ 7-5 71M 8P~ 9JM AABNK AACTN AAEDT AAEDW AAHBH AAIKJ AAKOC AALRI AAOAW AAQFI AAXKI AAXUO ABFNM ABFRF ABJNI ABLJU ABMAC ABMZM ABZDS ACDAQ ACGFO ACGFS ACIUM ACIWK ACPRK ACRLP ADBBV ADEZE AEBSH AEFWE AEIPS AEKER AENEX AFJKZ AFKWA AFRAH AFTJW AFXIZ AGUBO AGYEJ AIEXJ AIKHN AITUG AJOXV AJRQY AKRWK ALCLG ALMA_UNASSIGNED_HOLDINGS AMFUW AMRAJ ANKPU ANZVX AXJTR BKOJK BLXMC BNPGV C45 CNWQP CS3 DU5 EBS EFJIC EO8 EO9 EP2 EP3 F5P FDB FIRID FNPLU FYGXN G-Q GBLVA IH2 IHE J1W K-O KOM L7B M34 M41 MO0 N9A O-L O9- OAUVE OGGZJ OVD OZT P-8 P-9 P2P PC. Q38 ROL RPZ SDF SDG SDP SES SEW SPCBC SSH SSP SSZ T5K TEORI YZZ ~G- .55 .GJ 29L 3O- 53G 9DU AAQXK AATTM AAYWO AAYXX ABUFD ABWVN ABXDB ACIEU ACLOT ACRPL ACVFH ADCNI ADMUD ADNMO AEUPX AFFNX AFPUW AGHFR AGQPQ AHHHB AIGII AIIUN AKBMS AKYEP APXCP ASPBG AVWKF AZFZN CITATION EFKBS EFLBG EJD FEDTE FGOYB G-2 HMG HMT HVGLF HZ~ H~9 J5H MVM R2- SIN SPT WUQ X7M Y6R YYP ZGI ZKB ZXP ZY4 ~HD CGR CUY CVF ECM EIF NPM 7X8 7S9 L.6
ID	FETCH-LOGICAL-c338t-21ec3807df29b76e97b7bc81a225fd4e5ad0b2bdbe1aa66f753c8dbc6089e67b3
ISICitedReferencesCount	0
ISICitedReferencesURI	http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=001350528900001&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D
ISSN	0024-3205 1879-0631
IngestDate	Sun Sep 28 05:34:35 EDT 2025 Wed Oct 01 12:13:03 EDT 2025 Thu Apr 03 06:58:51 EDT 2025 Sat Nov 29 06:25:02 EST 2025 Sat Feb 08 15:52:10 EST 2025
IsPeerReviewed	true
IsScholarly	true
Keywords	Deep learning Spatial clustering Gene expression Spatial transcriptomics Variational graph autoencoder Contrastive learning
Language	English
License	Copyright © 2024 Elsevier Inc. All rights reserved.
LinkModel	OpenURL
MergedId	FETCHMERGED-LOGICAL-c338t-21ec3807df29b76e97b7bc81a225fd4e5ad0b2bdbe1aa66f753c8dbc6089e67b3
Notes	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
PMID	39488267
PQID	3123551250
PQPubID	23479
ParticipantIDs	proquest_miscellaneous_3154266968 proquest_miscellaneous_3123551250 pubmed_primary_39488267 crossref_primary_10_1016_j_lfs_2024_123208 elsevier_sciencedirect_doi_10_1016_j_lfs_2024_123208
PublicationCentury	2000
PublicationDate	2024-12-15
PublicationDateYYYYMMDD	2024-12-15
PublicationDate_xml	– month: 12 year: 2024 text: 2024-12-15 day: 15
PublicationDecade	2020
PublicationPlace	Netherlands
PublicationPlace_xml	– name: Netherlands
PublicationTitle	Life sciences (1973)
PublicationTitleAlternate	Life Sci
PublicationYear	2024
Publisher	Elsevier Inc
Publisher_xml	– name: Elsevier Inc
References	Krishna, Narasimha Murty (bb0025) 1999; 29 Salomon (bb0190) 2017; 8 Chiang (bb0075) 2019 Goossens-Beumer (bb0185) 2014; 110 Hu (bb0060) 2024; 25 Xiang, Yan, Li, Li (bb0215) 2015; 11 Mack, Brown, Tew (bb0170) 2008; 12 Zhao (bb0030) 2021; 39 Zhang, Lei, Huang, Wang (bb0145) 2022; 13 Janesick (bb0010) 2023; 14 Dong, Zhang (bb0055) 2022; 13 Meilandt (bb0210) 2008; 28 1 Integrating gene expression, spatial location and histology to identify spatial 2 domains and spatially variable genes by graph convolutional network. Wolf (bb0120) 2019; 20 Savolainen, Foley, Elmore (bb0230) 2009; 37 Shi (bb0225) 2014; 34 Wei (bb0020) 2022; 377 Hu, J. McInnes, Healy, Melville (bb0125) 2020 Wolf, Angerer, Theis (bb0105) 2018; 19 Zhang (bb0220) 2019; 71 Fu, H. Lv (bb0205) 2024; 377 Papavassiliou, Papavassiliou (bb0155) 2022; 1877 1 Unsupervised Spatially Embedded Deep Representation of Spatial 2 Transcriptomics. Sun, Gong, Purow, Zhao (bb0135) 2012; 8 Scrucca, Fop, Murphy, Brendan, Raftery (bb0110) 2016; 8 Zhou, Zhang (bb0160) 2008; 7 Xu (bb0100) 2022; 50 Stringer (bb0140) 2016; 7 Stickels (bb0015) 2021; 39 Zuo, Zhang, Cao (bb0065) 2022; 13 Zhang, Liang, Lin (bb0070) July 2024; Volume 25, Issue 4 Blondel, Guillaume, Lambiotte, Lefebvre (bb0130) 2008; 2008 Fukuda (bb0235) 2017; 8 Hoge, Kesner (bb0200) 2007; 88 Moses, Pachter (bb0005) 2022; 19 De Souza (bb0150) 2022; 23 Kipf, Welling (bb0080) 2016 Maynard (bb0085) 2021; 24 Estevez, Tesmer, Perez, Zurada (bb0115) 2009; 20 Xu (bb0165) 2012; 7 Ma (bb0175) 2008; 22 Korsunsky, Millard, Fan, Slowikowski, Zhang, Wei (bb0050) 2019; 16 Xiao (bb0195) 2015; 361 Pham (bb0035) 2020 Long (bb0090) 2023; 14 Makiewicz, A. & Ratajczak, W. Principal components analysis (PCA). Princ. Compon. Anal. Hong, Kandasamy, Marimuthu, Choi, Kim (bb0180) 2011; 136 Maynard (10.1016/j.lfs.2024.123208_bb0085) 2021; 24 Xu (10.1016/j.lfs.2024.123208_bb0100) 2022; 50 Papavassiliou (10.1016/j.lfs.2024.123208_bb0155) 2022; 1877 Meilandt (10.1016/j.lfs.2024.123208_bb0210) 2008; 28 Zhang (10.1016/j.lfs.2024.123208_bb0070) 2024; Volume 25, Issue 4 Zuo (10.1016/j.lfs.2024.123208_bb0065) 2022; 13 McInnes (10.1016/j.lfs.2024.123208_bb0125) Mack (10.1016/j.lfs.2024.123208_bb0170) 2008; 12 Long (10.1016/j.lfs.2024.123208_bb0090) 2023; 14 Xu (10.1016/j.lfs.2024.123208_bb0165) 2012; 7 Zhou (10.1016/j.lfs.2024.123208_bb0160) 2008; 7 Hoge (10.1016/j.lfs.2024.123208_bb0200) 2007; 88 Dong (10.1016/j.lfs.2024.123208_bb0055) 2022; 13 Zhang (10.1016/j.lfs.2024.123208_bb0220) 2019; 71 Sun (10.1016/j.lfs.2024.123208_bb0135) 2012; 8 De Souza (10.1016/j.lfs.2024.123208_bb0150) 2022; 23 Moses (10.1016/j.lfs.2024.123208_bb0005) 2022; 19 Wolf (10.1016/j.lfs.2024.123208_bb0105) 2018; 19 Blondel (10.1016/j.lfs.2024.123208_bb0130) 2008; 2008 Shi (10.1016/j.lfs.2024.123208_bb0225) 2014; 34 10.1016/j.lfs.2024.123208_bb0045 Estevez (10.1016/j.lfs.2024.123208_bb0115) 2009; 20 Xiang (10.1016/j.lfs.2024.123208_bb0215) 2015; 11 Scrucca (10.1016/j.lfs.2024.123208_bb0110) 2016; 8 Wolf (10.1016/j.lfs.2024.123208_bb0120) 2019; 20 10.1016/j.lfs.2024.123208_bb0040 Ma (10.1016/j.lfs.2024.123208_bb0175) 2008; 22 Xiao (10.1016/j.lfs.2024.123208_bb0195) 2015; 361 Stickels (10.1016/j.lfs.2024.123208_bb0015) 2021; 39 Zhang (10.1016/j.lfs.2024.123208_bb0145) 2022; 13 Chiang (10.1016/j.lfs.2024.123208_bb0075) 2019 Krishna (10.1016/j.lfs.2024.123208_bb0025) 1999; 29 Stringer (10.1016/j.lfs.2024.123208_bb0140) 2016; 7 Wei (10.1016/j.lfs.2024.123208_bb0020) 2022; 377 Hu (10.1016/j.lfs.2024.123208_bb0060) 2024; 25 Fukuda (10.1016/j.lfs.2024.123208_bb0235) 2017; 8 Goossens-Beumer (10.1016/j.lfs.2024.123208_bb0185) 2014; 110 Savolainen (10.1016/j.lfs.2024.123208_bb0230) 2009; 37 Korsunsky (10.1016/j.lfs.2024.123208_bb0050) 2019; 16 Zhao (10.1016/j.lfs.2024.123208_bb0030) 2021; 39 Pham (10.1016/j.lfs.2024.123208_bb0035) 2020 Salomon (10.1016/j.lfs.2024.123208_bb0190) 2017; 8 Kipf (10.1016/j.lfs.2024.123208_bb0080) Janesick (10.1016/j.lfs.2024.123208_bb0010) 2023; 14 Hong (10.1016/j.lfs.2024.123208_bb0180) 2011; 136 10.1016/j.lfs.2024.123208_bb0095 Lv (10.1016/j.lfs.2024.123208_bb0205) 2024; 377
References_xml	– volume: 8 start-page: 289 year: 2016 ident: bb0110 article-title: E. mclust 5: clustering, classification and density estimation using Gaussian finite mixture models publication-title: R J. – volume: 71 start-page: 213 year: 2019 end-page: 222 ident: bb0220 article-title: SLC1A2 mediates refractory temporal lobe epilepsy with an initial precipitating injury by targeting the glutamatergic synapse pathway publication-title: IUBMB Life – volume: 24 start-page: 425 year: 2021 end-page: 436 ident: bb0085 article-title: Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex publication-title: Nat. Neurosci. – volume: 7 start-page: 1360 year: 2008 end-page: 1370 ident: bb0160 article-title: Cancer stem cells: models, mechanisms and implications for improved treatment publication-title: Cell Cycle – reference: 1 Unsupervised Spatially Embedded Deep Representation of Spatial 2 Transcriptomics. – volume: 11 year: 2015 ident: bb0215 article-title: Postnatal loss of Hap1 reduces hippocampal neurogenesis and causes adult depressive-like behavior in mice publication-title: PLoS Genet. – volume: 19 start-page: 534 year: 2022 end-page: 546 ident: bb0005 article-title: Museum of spatial transcriptomics publication-title: Nat. Methods – reference: Hu, J. – volume: 22 start-page: 308 year: 2008 end-page: 321 ident: bb0175 article-title: Extracellular matrix protein βig-h3/TGFBI promotes metastasis of colon cancer by enhancing cell extravasation publication-title: Genes Dev. – volume: 12 start-page: 491 year: 2008 end-page: 504 ident: bb0170 article-title: ABCA2 as a therapeutic target in cancer and nervous system disorders publication-title: Expert Opin. Ther. Targets – volume: 14 start-page: 1155 year: 2023 ident: bb0090 article-title: Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with GraphST publication-title: Nat. Commun. – volume: 7 year: 2012 ident: bb0165 article-title: Neuronatin in a subset of glioblastoma multiforme tumor progenitor cells is associated with increased cell proliferation and shorter patient survival publication-title: PloS One – volume: 20 start-page: 59 year: 2019 ident: bb0120 article-title: PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells publication-title: Genome Biol. – year: 2020 ident: bb0125 article-title: UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction – volume: 13 start-page: 1739 year: 2022 ident: bb0055 article-title: Deciphering spatial domains from spatially resolved transcriptomics with an adaptive graph attention auto-encoder publication-title: Nat. Commun. – year: 2020 ident: bb0035 article-title: stLearn: integrating spatial location, tissue morphology and gene expression to find cell types, cell-cell interactions and spatial trajectories within undissociated tissues – volume: 13 start-page: 5962 year: 2022 ident: bb0065 article-title: Elucidating tumor heterogeneity from spatially resolved transcriptomics data by multi-view graph collaborative learning publication-title: Nat. Commun. – reference: Fu, H. – volume: 7 start-page: 29306 year: 2016 end-page: 29320 ident: bb0140 article-title: Nuclear factor one B ( publication-title: Oncotarget – reference: 1 Integrating gene expression, spatial location and histology to identify spatial 2 domains and spatially variable genes by graph convolutional network. – volume: 88 start-page: 225 year: 2007 end-page: 231 ident: bb0200 article-title: Role of CA3 and CA1 subregions of the dorsal hippocampus on temporal processing of objects publication-title: Neurobiol. Learn. Mem. – volume: 29 start-page: 433 year: 1999 end-page: 439 ident: bb0025 article-title: Genetic K-means algorithm publication-title: IEEE Trans. Syst. Man Cybern. Part B Cybern. – volume: 20 start-page: 189 year: 2009 end-page: 201 ident: bb0115 article-title: Normalized mutual information feature selection publication-title: IEEE Trans. Neural Netw. – reference: Makiewicz, A. & Ratajczak, W. Principal components analysis (PCA). Princ. Compon. Anal. – year: 2016 ident: bb0080 article-title: Variational Graph Auto-Encoders – volume: 14 start-page: 8353 year: 2023 ident: bb0010 article-title: High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis publication-title: Nat. Commun. – volume: Volume 25, Issue 4 year: July 2024 ident: bb0070 article-title: A multi-view graph contrastive learning framework for deciphering spatially resolved transcriptomics data publication-title: Briefings in Bioinformatics – volume: 39 start-page: 1375 year: 2021 end-page: 1384 ident: bb0030 article-title: Spatial transcriptomics at subspot resolution with BayesSpace publication-title: Nat. Biotechnol. – volume: 28 start-page: 5007 year: 2008 end-page: 5017 ident: bb0210 article-title: Enkephalin elevations contribute to neuronal and behavioral impairments in a transgenic mouse model of Alzheimer’s disease publication-title: J. Neurosci. – volume: 19 start-page: 15 year: 2018 ident: bb0105 article-title: SCANPY: large-scale single-cell gene expression data analysis publication-title: Genome Biol. – volume: 34 start-page: 13954 year: 2014 end-page: 13962 ident: bb0225 article-title: Impact of RTN3 deficiency on expression of BACE1 and amyloid deposition publication-title: J. Neurosci. – volume: 13 start-page: 1071897 year: 2022 ident: bb0145 article-title: Molecular mechanisms of ferroptosis and the potential therapeutic targets of ferroptosis signaling pathways for glioblastoma publication-title: Front. Pharmacol. – volume: 136 start-page: 237 year: 2011 end-page: 245 ident: bb0180 article-title: Electrical cell-substrate impedance sensing as a non-invasive tool for cancer cell study publication-title: Analyst – volume: 16 start-page: 1289 year: 2019 end-page: 1296 ident: bb0050 article-title: Fast, sensitive and accurate integration of single-cell data with harmony publication-title: Nat. Methods – volume: 25 year: 2024 ident: bb0060 article-title: Spatially contrastive variational autoencoder for deciphering tissue heterogeneity from spatially resolved transcriptomics publication-title: Brief. Bioinform. – volume: 1877 year: 2022 ident: bb0155 article-title: Transcription factors in glioblastoma – molecular pathogenesis and clinical implications publication-title: Biochim. Biophys. Acta BBA - Rev. Cancer – volume: 23 start-page: 6879 year: 2022 ident: bb0150 article-title: Ferroptosis modulation: potential therapeutic target for glioblastoma treatment publication-title: Int. J. Mol. Sci. – volume: 377 year: 2024 ident: bb0205 article-title: Sevoflurane causes neurotoxicity and cognitive impairment by regulating hippo signaling pathway-mediated ferroptosis via upregulating PRKCD publication-title: Exp. Neurol. – volume: 361 start-page: 22 year: 2015 end-page: 32 ident: bb0195 article-title: CXCL8, overexpressed in colorectal cancer, enhances the resistance of colorectal cancer cells to anoikis publication-title: Cancer Lett. – volume: 2008 start-page: P10008 year: 2008 ident: bb0130 article-title: Fast unfolding of communities in large networks publication-title: J. Stat. Mech. Theory Exp. – volume: 110 start-page: 2935 year: 2014 end-page: 2944 ident: bb0185 article-title: Clinical prognostic value of combined analysis of Aldh1, Survivin, and EpCAM expression in colorectal cancer publication-title: Br. J. Cancer – volume: 8 start-page: 13998 year: 2017 ident: bb0190 article-title: Contractile forces at tricellular contacts modulate epithelial organization and monolayer integrity publication-title: Nat. Commun. – volume: 39 start-page: 313 year: 2021 end-page: 319 ident: bb0015 article-title: Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2 publication-title: Nat. Biotechnol. – volume: 50 start-page: e131 year: 2022 ident: bb0100 article-title: DeepST: identifying spatial domains in spatial transcriptomics by deep learning publication-title: Nucleic Acids Res. – year: 2019 ident: bb0075 article-title: Cluster-GCN: An Efficient Algorithm for Training Deep and Large Graph Convolutional Networks publication-title: Proceedings of the 25th ACM SIGKDD International Conference on Knowledge Discovery & Data Mining 257–266 – volume: 377 year: 2022 ident: bb0020 article-title: Single-cell stereo-seq reveals induced progenitor cells involved in axolotl brain regeneration publication-title: Science – volume: 8 year: 2012 ident: bb0135 article-title: Uncovering MicroRNA and transcription factor mediated regulatory networks in glioblastoma publication-title: PLoS Comput. Biol. – volume: 8 start-page: 14495 year: 2017 ident: bb0235 article-title: Proteolysis regulates cardiomyocyte maturation and tissue integration publication-title: Nat. Commun. – volume: 37 start-page: 395 year: 2009 end-page: 414 ident: bb0230 article-title: Histology atlas of the developing mouse heart with emphasis on E11.5 to E18.5 publication-title: Toxicol. Pathol. – volume: 24 start-page: 425 year: 2021 ident: 10.1016/j.lfs.2024.123208_bb0085 article-title: Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex publication-title: Nat. Neurosci. doi: 10.1038/s41593-020-00787-0 – volume: 37 start-page: 395 year: 2009 ident: 10.1016/j.lfs.2024.123208_bb0230 article-title: Histology atlas of the developing mouse heart with emphasis on E11.5 to E18.5 publication-title: Toxicol. Pathol. doi: 10.1177/0192623309335060 – year: 2020 ident: 10.1016/j.lfs.2024.123208_bb0035 – volume: 22 start-page: 308 year: 2008 ident: 10.1016/j.lfs.2024.123208_bb0175 article-title: Extracellular matrix protein βig-h3/TGFBI promotes metastasis of colon cancer by enhancing cell extravasation publication-title: Genes Dev. doi: 10.1101/gad.1632008 – volume: 136 start-page: 237 year: 2011 ident: 10.1016/j.lfs.2024.123208_bb0180 article-title: Electrical cell-substrate impedance sensing as a non-invasive tool for cancer cell study publication-title: Analyst doi: 10.1039/C0AN00560F – volume: 13 start-page: 1739 year: 2022 ident: 10.1016/j.lfs.2024.123208_bb0055 article-title: Deciphering spatial domains from spatially resolved transcriptomics with an adaptive graph attention auto-encoder publication-title: Nat. Commun. doi: 10.1038/s41467-022-29439-6 – ident: 10.1016/j.lfs.2024.123208_bb0125 – volume: 8 start-page: 289 year: 2016 ident: 10.1016/j.lfs.2024.123208_bb0110 article-title: E. mclust 5: clustering, classification and density estimation using Gaussian finite mixture models publication-title: R J. doi: 10.32614/RJ-2016-021 – volume: 39 start-page: 313 year: 2021 ident: 10.1016/j.lfs.2024.123208_bb0015 article-title: Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2 publication-title: Nat. Biotechnol. doi: 10.1038/s41587-020-0739-1 – volume: 88 start-page: 225 year: 2007 ident: 10.1016/j.lfs.2024.123208_bb0200 article-title: Role of CA3 and CA1 subregions of the dorsal hippocampus on temporal processing of objects publication-title: Neurobiol. Learn. Mem. doi: 10.1016/j.nlm.2007.04.013 – volume: 16 start-page: 1289 issue: 12 year: 2019 ident: 10.1016/j.lfs.2024.123208_bb0050 article-title: Fast, sensitive and accurate integration of single-cell data with harmony publication-title: Nat. Methods doi: 10.1038/s41592-019-0619-0 – volume: 7 year: 2012 ident: 10.1016/j.lfs.2024.123208_bb0165 article-title: Neuronatin in a subset of glioblastoma multiforme tumor progenitor cells is associated with increased cell proliferation and shorter patient survival publication-title: PloS One – volume: 377 year: 2022 ident: 10.1016/j.lfs.2024.123208_bb0020 article-title: Single-cell stereo-seq reveals induced progenitor cells involved in axolotl brain regeneration publication-title: Science doi: 10.1126/science.abp9444 – volume: 29 start-page: 433 year: 1999 ident: 10.1016/j.lfs.2024.123208_bb0025 article-title: Genetic K-means algorithm publication-title: IEEE Trans. Syst. Man Cybern. Part B Cybern. doi: 10.1109/3477.764879 – volume: 71 start-page: 213 year: 2019 ident: 10.1016/j.lfs.2024.123208_bb0220 article-title: SLC1A2 mediates refractory temporal lobe epilepsy with an initial precipitating injury by targeting the glutamatergic synapse pathway publication-title: IUBMB Life doi: 10.1002/iub.1956 – volume: 50 start-page: e131 year: 2022 ident: 10.1016/j.lfs.2024.123208_bb0100 article-title: DeepST: identifying spatial domains in spatial transcriptomics by deep learning publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkac901 – volume: 20 start-page: 189 year: 2009 ident: 10.1016/j.lfs.2024.123208_bb0115 article-title: Normalized mutual information feature selection publication-title: IEEE Trans. Neural Netw. doi: 10.1109/TNN.2008.2005601 – volume: 14 start-page: 1155 year: 2023 ident: 10.1016/j.lfs.2024.123208_bb0090 article-title: Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with GraphST publication-title: Nat. Commun. doi: 10.1038/s41467-023-36796-3 – volume: 25 year: 2024 ident: 10.1016/j.lfs.2024.123208_bb0060 article-title: Spatially contrastive variational autoencoder for deciphering tissue heterogeneity from spatially resolved transcriptomics publication-title: Brief. Bioinform. doi: 10.1093/bib/bbae016 – volume: 11 year: 2015 ident: 10.1016/j.lfs.2024.123208_bb0215 article-title: Postnatal loss of Hap1 reduces hippocampal neurogenesis and causes adult depressive-like behavior in mice publication-title: PLoS Genet. doi: 10.1371/journal.pgen.1005175 – ident: 10.1016/j.lfs.2024.123208_bb0040 – volume: 14 start-page: 8353 year: 2023 ident: 10.1016/j.lfs.2024.123208_bb0010 article-title: High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis publication-title: Nat. Commun. doi: 10.1038/s41467-023-43458-x – volume: 20 start-page: 59 year: 2019 ident: 10.1016/j.lfs.2024.123208_bb0120 article-title: PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells publication-title: Genome Biol. doi: 10.1186/s13059-019-1663-x – volume: 377 year: 2024 ident: 10.1016/j.lfs.2024.123208_bb0205 article-title: Sevoflurane causes neurotoxicity and cognitive impairment by regulating hippo signaling pathway-mediated ferroptosis via upregulating PRKCD publication-title: Exp. Neurol. doi: 10.1016/j.expneurol.2024.114804 – volume: 7 start-page: 29306 year: 2016 ident: 10.1016/j.lfs.2024.123208_bb0140 article-title: Nuclear factor one B ( NFIB ) encodes a subtype-specific tumour suppressor in glioblastoma publication-title: Oncotarget doi: 10.18632/oncotarget.8720 – volume: Volume 25, Issue 4 year: 2024 ident: 10.1016/j.lfs.2024.123208_bb0070 article-title: A multi-view graph contrastive learning framework for deciphering spatially resolved transcriptomics data – volume: 13 start-page: 1071897 year: 2022 ident: 10.1016/j.lfs.2024.123208_bb0145 article-title: Molecular mechanisms of ferroptosis and the potential therapeutic targets of ferroptosis signaling pathways for glioblastoma publication-title: Front. Pharmacol. doi: 10.3389/fphar.2022.1071897 – ident: 10.1016/j.lfs.2024.123208_bb0080 – volume: 8 start-page: 13998 year: 2017 ident: 10.1016/j.lfs.2024.123208_bb0190 article-title: Contractile forces at tricellular contacts modulate epithelial organization and monolayer integrity publication-title: Nat. Commun. doi: 10.1038/ncomms13998 – ident: 10.1016/j.lfs.2024.123208_bb0095 – ident: 10.1016/j.lfs.2024.123208_bb0045 – year: 2019 ident: 10.1016/j.lfs.2024.123208_bb0075 article-title: Cluster-GCN: An Efficient Algorithm for Training Deep and Large Graph Convolutional Networks – volume: 23 start-page: 6879 year: 2022 ident: 10.1016/j.lfs.2024.123208_bb0150 article-title: Ferroptosis modulation: potential therapeutic target for glioblastoma treatment publication-title: Int. J. Mol. Sci. doi: 10.3390/ijms23136879 – volume: 28 start-page: 5007 year: 2008 ident: 10.1016/j.lfs.2024.123208_bb0210 article-title: Enkephalin elevations contribute to neuronal and behavioral impairments in a transgenic mouse model of Alzheimer’s disease publication-title: J. Neurosci. doi: 10.1523/JNEUROSCI.0590-08.2008 – volume: 8 year: 2012 ident: 10.1016/j.lfs.2024.123208_bb0135 article-title: Uncovering MicroRNA and transcription factor mediated regulatory networks in glioblastoma publication-title: PLoS Comput. Biol. doi: 10.1371/journal.pcbi.1002488 – volume: 1877 year: 2022 ident: 10.1016/j.lfs.2024.123208_bb0155 article-title: Transcription factors in glioblastoma – molecular pathogenesis and clinical implications publication-title: Biochim. Biophys. Acta BBA - Rev. Cancer – volume: 34 start-page: 13954 year: 2014 ident: 10.1016/j.lfs.2024.123208_bb0225 article-title: Impact of RTN3 deficiency on expression of BACE1 and amyloid deposition publication-title: J. Neurosci. doi: 10.1523/JNEUROSCI.1588-14.2014 – volume: 19 start-page: 15 year: 2018 ident: 10.1016/j.lfs.2024.123208_bb0105 article-title: SCANPY: large-scale single-cell gene expression data analysis publication-title: Genome Biol. doi: 10.1186/s13059-017-1382-0 – volume: 39 start-page: 1375 year: 2021 ident: 10.1016/j.lfs.2024.123208_bb0030 article-title: Spatial transcriptomics at subspot resolution with BayesSpace publication-title: Nat. Biotechnol. doi: 10.1038/s41587-021-00935-2 – volume: 13 start-page: 5962 year: 2022 ident: 10.1016/j.lfs.2024.123208_bb0065 article-title: Elucidating tumor heterogeneity from spatially resolved transcriptomics data by multi-view graph collaborative learning publication-title: Nat. Commun. doi: 10.1038/s41467-022-33619-9 – volume: 7 start-page: 1360 year: 2008 ident: 10.1016/j.lfs.2024.123208_bb0160 article-title: Cancer stem cells: models, mechanisms and implications for improved treatment publication-title: Cell Cycle doi: 10.4161/cc.7.10.5953 – volume: 2008 start-page: P10008 year: 2008 ident: 10.1016/j.lfs.2024.123208_bb0130 article-title: Fast unfolding of communities in large networks publication-title: J. Stat. Mech. Theory Exp. doi: 10.1088/1742-5468/2008/10/P10008 – volume: 12 start-page: 491 year: 2008 ident: 10.1016/j.lfs.2024.123208_bb0170 article-title: ABCA2 as a therapeutic target in cancer and nervous system disorders publication-title: Expert Opin. Ther. Targets doi: 10.1517/14728222.12.4.491 – volume: 110 start-page: 2935 year: 2014 ident: 10.1016/j.lfs.2024.123208_bb0185 article-title: Clinical prognostic value of combined analysis of Aldh1, Survivin, and EpCAM expression in colorectal cancer publication-title: Br. J. Cancer doi: 10.1038/bjc.2014.226 – volume: 361 start-page: 22 year: 2015 ident: 10.1016/j.lfs.2024.123208_bb0195 article-title: CXCL8, overexpressed in colorectal cancer, enhances the resistance of colorectal cancer cells to anoikis publication-title: Cancer Lett. doi: 10.1016/j.canlet.2015.02.021 – volume: 8 start-page: 14495 year: 2017 ident: 10.1016/j.lfs.2024.123208_bb0235 article-title: Proteolysis regulates cardiomyocyte maturation and tissue integration publication-title: Nat. Commun. doi: 10.1038/ncomms14495 – volume: 19 start-page: 534 year: 2022 ident: 10.1016/j.lfs.2024.123208_bb0005 article-title: Museum of spatial transcriptomics publication-title: Nat. Methods doi: 10.1038/s41592-022-01409-2
SSID	ssj0005573
Score	2.4536886
Snippet	Advancements in Spatial Transcriptomics (ST) technologies in recent years have transformed the analysis of tissue structure and function within spatial...
SourceID	proquest pubmed crossref elsevier
SourceType	Aggregation Database Index Database Publisher
StartPage	123208
SubjectTerms	colorectal neoplasms Colorectal Neoplasms - genetics Colorectal Neoplasms - pathology Contrastive learning data collection Deep learning domain extracellular matrix Gene expression Gene Expression Profiling - methods glioblastoma Glioblastoma - genetics Glioblastoma - pathology Humans Machine Learning Neural Networks, Computer Prefrontal Cortex Spatial clustering spatial data Spatial transcriptomics therapeutics Transcriptome transcriptomics Variational graph autoencoder
Title	GraphCVAE: Uncovering cell heterogeneity and therapeutic target discovery through residual and contrastive learning
URI	https://dx.doi.org/10.1016/j.lfs.2024.123208 https://www.ncbi.nlm.nih.gov/pubmed/39488267 https://www.proquest.com/docview/3123551250 https://www.proquest.com/docview/3154266968
Volume	359
WOSCitedRecordID	wos001350528900001&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: PRVESC databaseName: ScienceDirect customDbUrl: eissn: 1879-0631 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0005573 issn: 0024-3205 databaseCode: AIEXJ dateStart: 19950106 isFulltext: true titleUrlDefault: https://www.sciencedirect.com providerName: Elsevier
link	http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwtV1bb9MwFLa6DSReEBu3cZmMhBAwZcrNsc1bNXVcVBWE2lHxYjmJQzNNabc2Y_33HMfOBcSm8cBLFEW2G-X7ap9z_B0fhF66kXSlBO-EEimdkLuhw0NPORmHe7AQlKqy-I-HdDRi0yn_0uuVdS7MxSktCnZ5yRf_FWp4BmDr1Nl_gLsZFB7APYAOV4AdrjcC_r0-gvrwuD_Qzv6kSLRGs8qs1VG6mVa_zKGv0ta3VU_WCVj7RhauN22qXuumig_45CZpy2TB6YDwstIc2aITP7o27jDP1L5dWc1BUJx247lNjPr7LP-p8jakb55qne1ZXrYh9Epv8LWcr1sif2tGgMazMu_GLvzqhESTvdnkEoRO4LukOx8HhO8vDrSp5zLnr7O8CTicHJxm-sB1P7SN2yWt3sYffRZHk-FQjAfT8avFmaOLjelNeVt5ZQNt-ZRwmAy3-h8H00-tNohYaYJ9vXo7vBIG_vGrVxk0VzksleEyvofuWo8D9w1TtlFPFTvotqlBut5B23Z2X-LX9gjyN_fRsiHRO9xSCGsK4d8ohIEQuEMhbCiEGwphSyFcU6jq0aEQrin0AE2OBuPDD44tz-EkQcBWju-pRJcrSDOfxzRSnMY0TpgnYYnI0lARmbqxH6ex8qSMogwc44SlcRK5jKuIxsFDtFnMC_UY4SR1Scp8LWFSISw60mMs9hI3JUnsyZjsorf1NxYLcwqLqOWJJwIAERoQYQDZRWGNgrBkN-ahAP5c1-1FjZiAKVZ_UVmoebkUgc4nB8OYuNe1IdrW5RGM88jA3bxpwGGV9CP65Aa9n6I77R_lGdpcnZfqObqVXKzy5fke2qBTtmfZ-gtgkLVa
linkProvider	Elsevier
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=GraphCVAE%3A+Uncovering+cell+heterogeneity+and+therapeutic+target+discovery+through+residual+and+contrastive+learning&rft.jtitle=Life+sciences+%281973%29&rft.au=Zhang%2C+Zhiwei&rft.au=Wang%2C+Mengqiu&rft.au=Dai%2C+Ruoyan&rft.au=Wang%2C+Zhenghui&rft.date=2024-12-15&rft.issn=0024-3205&rft.volume=359+p.123208-&rft_id=info:doi/10.1016%2Fj.lfs.2024.123208&rft.externalDBID=NO_FULL_TEXT
thumbnail_l	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=0024-3205&client=summon
thumbnail_m	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=0024-3205&client=summon
thumbnail_s	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=0024-3205&client=summon