SMORE: spatial motifs reveal patterns in cellular architecture of complex tissues
Abstract Deciphering the link between tissue architecture and function requires methods to identify and interpret patterns in spatial arrangement of cells. We present SMORE, an approach to detect patterns in sequential arrangements of cells and examine their associated gene expression specialization...
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| Format: | Article |
| Language: | English |
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BMC
2025-01-01
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| Series: | Genome Biology |
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| Online Access: | https://doi.org/10.1186/s13059-024-03467-5 |
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| _version_ | 1841559351653826560 |
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| author | Zainalabedin Samadi Kai Hao Amjad Askary |
| author_facet | Zainalabedin Samadi Kai Hao Amjad Askary |
| author_sort | Zainalabedin Samadi |
| collection | DOAJ |
| description | Abstract Deciphering the link between tissue architecture and function requires methods to identify and interpret patterns in spatial arrangement of cells. We present SMORE, an approach to detect patterns in sequential arrangements of cells and examine their associated gene expression specializations. Applied to retina, brain, and embryonic tissue maps, SMORE identifies novel spatial motifs, including one that offers a new mechanism of action for type 1b bipolar cells. Structural signatures detected by SMORE also form a basis for classifying tissues. Together, our method provides a new framework for uncovering spatial complexity in tissue organization and offers novel insights into tissue function. |
| format | Article |
| id | doaj-art-3c33ba76419b4c8d9e6e179292f8e9a9 |
| institution | Kabale University |
| issn | 1474-760X |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj-art-3c33ba76419b4c8d9e6e179292f8e9a92025-01-05T12:31:59ZengBMCGenome Biology1474-760X2025-01-0126113010.1186/s13059-024-03467-5SMORE: spatial motifs reveal patterns in cellular architecture of complex tissuesZainalabedin Samadi0Kai Hao1Amjad Askary2Department of Molecular, Cell and Developmental Biology, University of CaliforniaDepartment of Molecular, Cell and Developmental Biology, University of CaliforniaDepartment of Molecular, Cell and Developmental Biology, University of CaliforniaAbstract Deciphering the link between tissue architecture and function requires methods to identify and interpret patterns in spatial arrangement of cells. We present SMORE, an approach to detect patterns in sequential arrangements of cells and examine their associated gene expression specializations. Applied to retina, brain, and embryonic tissue maps, SMORE identifies novel spatial motifs, including one that offers a new mechanism of action for type 1b bipolar cells. Structural signatures detected by SMORE also form a basis for classifying tissues. Together, our method provides a new framework for uncovering spatial complexity in tissue organization and offers novel insights into tissue function.https://doi.org/10.1186/s13059-024-03467-5Spatial transcriptomicsNeighborhood graphsUniform path samplingNetwork motifs |
| spellingShingle | Zainalabedin Samadi Kai Hao Amjad Askary SMORE: spatial motifs reveal patterns in cellular architecture of complex tissues Genome Biology Spatial transcriptomics Neighborhood graphs Uniform path sampling Network motifs |
| title | SMORE: spatial motifs reveal patterns in cellular architecture of complex tissues |
| title_full | SMORE: spatial motifs reveal patterns in cellular architecture of complex tissues |
| title_fullStr | SMORE: spatial motifs reveal patterns in cellular architecture of complex tissues |
| title_full_unstemmed | SMORE: spatial motifs reveal patterns in cellular architecture of complex tissues |
| title_short | SMORE: spatial motifs reveal patterns in cellular architecture of complex tissues |
| title_sort | smore spatial motifs reveal patterns in cellular architecture of complex tissues |
| topic | Spatial transcriptomics Neighborhood graphs Uniform path sampling Network motifs |
| url | https://doi.org/10.1186/s13059-024-03467-5 |
| work_keys_str_mv | AT zainalabedinsamadi smorespatialmotifsrevealpatternsincellulararchitectureofcomplextissues AT kaihao smorespatialmotifsrevealpatternsincellulararchitectureofcomplextissues AT amjadaskary smorespatialmotifsrevealpatternsincellulararchitectureofcomplextissues |