Recent advancements in spatial transcriptomics(ST)technologies allow researchers to simultaneously measure RNA expression levels for hundreds to thousands of genes while preserving spatial information within tissues,p...Recent advancements in spatial transcriptomics(ST)technologies allow researchers to simultaneously measure RNA expression levels for hundreds to thousands of genes while preserving spatial information within tissues,providing critical insights into spatial gene expression patterns,tissue organization,and gene functionality.However,existing methods for clustering spatially variable genes(SVGs)into co-expression modules often fail to detect rare or unique spatial expression patterns.To address this,we present spatial transcriptomics iterative hierarchical clustering(stIHC),a novel method for clustering SVGs into co-expression modules,representing groups of genes with shared spatial expression patterns.Through three simulations and applications to ST datasets from technologies such as 10x Visium,10x Xenium,and Spatial Transcriptomics,stIHC outperforms clustering approaches used by popular SVG detection methods,including SPARK,SPARK-X,MERINGUE,and SpatialDE.Gene ontology enrichment analysis confirms that genes within each module share consistent biological functions,supporting the functional relevance of spatial co-expression.Robust across technologies with varying gene numbers and spatial resolution,stIHC provides a powerful tool for decoding the spatial organization of gene expression and the functional structure of complex tissues.展开更多
Folk song as a representative of traditional Chinese folk culture is the expression of landscape culture in a certain regional space.According to landscape gene theory,gene structure of folk song cultural landscape wa...Folk song as a representative of traditional Chinese folk culture is the expression of landscape culture in a certain regional space.According to landscape gene theory,gene structure of folk song cultural landscape was recognized from two dimensions:subject form and cultural environment,and quantitative data were combined to analyze spatial distribution features of folk song cultural landscape genes.According to the analysis,in terms of style,work song is mainly distributed on plains,mountain song is distributed in mountainous areas,and ditty in the eastern watershed of the Yangtze River,in terms of theme,work and production folk songs are mainly distributed in eastern regions with intensive farming,while love and marriage folk songs in regions far away from the Central Plain Culture.Folk song cultural landscape is a result of the interaction between man and geographical conditions,residents in different geographical environments have different perception spaces to create folk songs with regional cultural symbols.展开更多
From Tetrahymena thermophila （strain BF5）, the coding region of Cd-MT gene was cloned and sequenced. and identified as MTT1 isoform. A serial duplicate structure is discovered in its amino acid sequence, which separ...From Tetrahymena thermophila （strain BF5）, the coding region of Cd-MT gene was cloned and sequenced. and identified as MTT1 isoform. A serial duplicate structure is discovered in its amino acid sequence, which separates the coding region into three parts （Part 1：7-61; Part 2：64-118; Part 3：122-162）. The alignments among them and comparison with the corresponding parts of MT1 isoform suggest that MT1 and MTT1 isoforms both come from the same ancient gene that is homologous to Part 1, and Cd-MTs of Tetrahymena are aroused by such ancient gene duplication. The prediction of secondary structures and the analysis of the disulfide-bonding state of cysteine show that there are a lot of differences between MT1 and MTT1 isoforms, which maybe relate to their function mechanism.展开更多
基金Science Foundation Ireland,Grant/Award Numbers:18/CRT/6214,18/CRT/6214(S4)。
文摘Recent advancements in spatial transcriptomics(ST)technologies allow researchers to simultaneously measure RNA expression levels for hundreds to thousands of genes while preserving spatial information within tissues,providing critical insights into spatial gene expression patterns,tissue organization,and gene functionality.However,existing methods for clustering spatially variable genes(SVGs)into co-expression modules often fail to detect rare or unique spatial expression patterns.To address this,we present spatial transcriptomics iterative hierarchical clustering(stIHC),a novel method for clustering SVGs into co-expression modules,representing groups of genes with shared spatial expression patterns.Through three simulations and applications to ST datasets from technologies such as 10x Visium,10x Xenium,and Spatial Transcriptomics,stIHC outperforms clustering approaches used by popular SVG detection methods,including SPARK,SPARK-X,MERINGUE,and SpatialDE.Gene ontology enrichment analysis confirms that genes within each module share consistent biological functions,supporting the functional relevance of spatial co-expression.Robust across technologies with varying gene numbers and spatial resolution,stIHC provides a powerful tool for decoding the spatial organization of gene expression and the functional structure of complex tissues.
基金Sponsored by Anhui Provincial Tounsm Administration(SLYJKT201509/SLYJKT201504)Youth Fund for Humanistic and Social Sciences Programs of the Ministry of Education(15YJC790018)
文摘Folk song as a representative of traditional Chinese folk culture is the expression of landscape culture in a certain regional space.According to landscape gene theory,gene structure of folk song cultural landscape was recognized from two dimensions:subject form and cultural environment,and quantitative data were combined to analyze spatial distribution features of folk song cultural landscape genes.According to the analysis,in terms of style,work song is mainly distributed on plains,mountain song is distributed in mountainous areas,and ditty in the eastern watershed of the Yangtze River,in terms of theme,work and production folk songs are mainly distributed in eastern regions with intensive farming,while love and marriage folk songs in regions far away from the Central Plain Culture.Folk song cultural landscape is a result of the interaction between man and geographical conditions,residents in different geographical environments have different perception spaces to create folk songs with regional cultural symbols.
文摘From Tetrahymena thermophila （strain BF5）, the coding region of Cd-MT gene was cloned and sequenced. and identified as MTT1 isoform. A serial duplicate structure is discovered in its amino acid sequence, which separates the coding region into three parts （Part 1：7-61; Part 2：64-118; Part 3：122-162）. The alignments among them and comparison with the corresponding parts of MT1 isoform suggest that MT1 and MTT1 isoforms both come from the same ancient gene that is homologous to Part 1, and Cd-MTs of Tetrahymena are aroused by such ancient gene duplication. The prediction of secondary structures and the analysis of the disulfide-bonding state of cysteine show that there are a lot of differences between MT1 and MTT1 isoforms, which maybe relate to their function mechanism.
