overview
Species -
Disease -
Technology -
Number of spots -
Number of microbiota (genus) -
Number of markers -
Number of spatial neighborhood -
Paired single-cell data -
Publication
Slice annotation
  • Spot annotation
  • Spatial co-occurred module
  • Spot deconvolution
  • SVG

H&E Stain

H&E image
The number of cell across transcriptome clusters

Markers of spatial transcriptome clusters

Cluster Gene Pct.1 Pct.2 FC P Value FDR
The number of marker gene number across transcriptome clusters
Expression of marker gene across transcriptome clusters
Marker

Spatial co-expression module in slices

Source Target Corr Module View
Click a spot below

SVG in spatial transcriptome clusters

Gene Moran's I P Value FDR Enriched Spot Cluster View
Abundance of microbiota in slice
  • Microbiota distribution
  • Microbiota expression
Taxonomy

Abundance of microbiota in spots

The UMI across microbiota
Microbiota
Spatial neighborhood of microbiota
  • Neighborhood Annotation
  • Distribution of microbiota
  • Differentially expressed microbiota

H&E Stain

H&E image
The number of spots across different regions

Differently expressed genes of neighborhood

Neighborhood Gene Pct.1 Pct.2 FC P Value FDR
The marker gene across different regions
Marker
Microbiota
The number of microbe-containing spots across different regions

Expression of gene in neighborhood

Gene
Taxonomy
Metagenome type Mean exp1 Mean exp2 LogFC P value FDR Group
V. Function of high microbiota abundance region
  • Malignant region
  • Boundary region

Differential expression of microbiota enriched in malignant region

Gene Mean exp1 Mean exp2 LogFC P value FDR State

Enriched cancer Hallmark in high microbiota abundance region

Hallmark GSVA score P value FDR Gene
Functions of microbiota enriched region

note* for hypergeometric test between differential expression gene of microbiota in malignant region and signatures for each cancer hallmarks (FDR < 0.05 )


Differential expression of microbiota enriched in boundary region

Gene Mean exp1 Mean exp2 LogFC P value FDR State

Enriched immune pathway in high microbiota abundance region

Pathway GSVA Score P value FDR Gene
Functions of microbiota enriched region

* for hypergeometric test between differential expression gene of microbiota in boundary region and signatures for each immune pathway (FDR < 0.05 )


Cell types within high microbiota abundance region
Microbiota (genus)

Spot deconvolution

Cell types associated with microbiota (genus)

Host microbiota co-expression module

Co-expression module of microbiota and gene

To evaluate the potential impact of microbiota on gene expression, Spearman correlation was calculated for the microbiota UMI count and gene expression within the corresponding spots. Gene co-expression module of the selected microbiota was used to perform pathway(GO-BP) enrichment analysis to investigate the potential impact of microbiota on the biological functions.

Neighborhood
Microbiota Gene Corr P value FDR View
Host microbiota co-expression module

Enriched GO-BP functions in co-expression modules

Microbiota Pathway P value FDR Gene
Top 5 enriched functions
Clinical relevance

To evaluate the potential impact of microbiota on prognosis, survival analysis was performed based on the microbiota abundance.

Microbiota
Microbiota beta HR Cox P value
Univariate 1 2 3 4
     
Multivariate 5 6 7 8
gender 9 10 11
age AgebetaMulti AgeHRMulti AgepvalueMulti
Survival curve