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calicost  (Spatial Transcriptomics Inc)

 
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    Spatial Transcriptomics Inc calicost
    a , Inputs to <t>CalicoST</t> are transcript counts X 0 , allele counts Y 0 and D 0 , spatial coordinates S from one or more SRT slices or a 3D alignment of slices. b , CalicoST phases input alleles in Y 0 and D 0 using a database of haplotypes. Optionally, CalicoST infers tumor proportion per spot using the BAF. CalicoST jointly models transcript counts and allele counts as functions of allele-specific copy number states within each clone. CalicoST uses an HMM to model correlations between copy number states from adjacent genomic regions and a HMRF to model correlations between the cancer clones assigned to neighboring spatial locations. c , CalicoST infers allele-specific integer copy numbers for one or more cancer clones, a phylogeny relating these clones, a clone label, an optional tumor proportion for each spot and a phylogeographic model of the spatial expansion of cancer clones.
    Calicost, supplied by Spatial Transcriptomics Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/transcriptome/calicost/pmc11621028-58-2-12
    Average 86 stars, based on 1 article reviews
    calicost - by Bioz Stars, 2026-08
    86/100 stars

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    1) Product Images from "Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics"

    Article Title: Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics

    Journal: Nature Methods

    doi: 10.1038/s41592-024-02438-9

    a , Inputs to CalicoST are transcript counts X 0 , allele counts Y 0 and D 0 , spatial coordinates S from one or more SRT slices or a 3D alignment of slices. b , CalicoST phases input alleles in Y 0 and D 0 using a database of haplotypes. Optionally, CalicoST infers tumor proportion per spot using the BAF. CalicoST jointly models transcript counts and allele counts as functions of allele-specific copy number states within each clone. CalicoST uses an HMM to model correlations between copy number states from adjacent genomic regions and a HMRF to model correlations between the cancer clones assigned to neighboring spatial locations. c , CalicoST infers allele-specific integer copy numbers for one or more cancer clones, a phylogeny relating these clones, a clone label, an optional tumor proportion for each spot and a phylogeographic model of the spatial expansion of cancer clones.
    Figure Legend Snippet: a , Inputs to CalicoST are transcript counts X 0 , allele counts Y 0 and D 0 , spatial coordinates S from one or more SRT slices or a 3D alignment of slices. b , CalicoST phases input alleles in Y 0 and D 0 using a database of haplotypes. Optionally, CalicoST infers tumor proportion per spot using the BAF. CalicoST jointly models transcript counts and allele counts as functions of allele-specific copy number states within each clone. CalicoST uses an HMM to model correlations between copy number states from adjacent genomic regions and a HMRF to model correlations between the cancer clones assigned to neighboring spatial locations. c , CalicoST infers allele-specific integer copy numbers for one or more cancer clones, a phylogeny relating these clones, a clone label, an optional tumor proportion for each spot and a phylogeographic model of the spatial expansion of cancer clones.

    Techniques Used: Clone Assay

    a , Accuracy of allele-specific copy numbers across 12 patients from HTAN (WashU cohort) inferred by CalicoST. Each bar represents an inferred cancer clone. b , Length distribution of CNAs identified by CalicoST from SRT data and identified by HATCHet2 from WES for the 9 patients with matched WES data of sufficient tumor purity. Blue bars are CalicoST, and orange bars are HATCHet2, with gray bars indicating the overlap of the two histograms. The median length is 77.4 Mb for CalicoST and 30 Mb for HATCHet2 (vertical dashed lines). c , Allele-specific integer copy numbers inferred by CalicoST from SRT data from a patient with CRC liver metastasis (HT230C1). Rows are cancer clones, and columns are genomic bins. Colors indicate allele-specific copy numbers. d , Allele-specific integer copy numbers inferred by CalicoST from SRT data from a patient with CRC liver metastasis (HT260C1). e , Observed RDR and BAF for chr8 of HT260C1. Points are colored by the inferred allele-specific copy numbers. Horizontal black lines indicate the RDR and BAF of the corresponding copy number states estimated by the HMM. f , Allele-specific integer copy numbers inferred by HATCHet2 from WES data of patient HT260C1. g , RDR and BAF values from WES data for bins from chromosome 8q and bins from other genomic regions with a value of {3,0} copy number state. Black points are expected RDR and BAF values for {3,0} and {2,1} states from HATCHet2 analysis.
    Figure Legend Snippet: a , Accuracy of allele-specific copy numbers across 12 patients from HTAN (WashU cohort) inferred by CalicoST. Each bar represents an inferred cancer clone. b , Length distribution of CNAs identified by CalicoST from SRT data and identified by HATCHet2 from WES for the 9 patients with matched WES data of sufficient tumor purity. Blue bars are CalicoST, and orange bars are HATCHet2, with gray bars indicating the overlap of the two histograms. The median length is 77.4 Mb for CalicoST and 30 Mb for HATCHet2 (vertical dashed lines). c , Allele-specific integer copy numbers inferred by CalicoST from SRT data from a patient with CRC liver metastasis (HT230C1). Rows are cancer clones, and columns are genomic bins. Colors indicate allele-specific copy numbers. d , Allele-specific integer copy numbers inferred by CalicoST from SRT data from a patient with CRC liver metastasis (HT260C1). e , Observed RDR and BAF for chr8 of HT260C1. Points are colored by the inferred allele-specific copy numbers. Horizontal black lines indicate the RDR and BAF of the corresponding copy number states estimated by the HMM. f , Allele-specific integer copy numbers inferred by HATCHet2 from WES data of patient HT260C1. g , RDR and BAF values from WES data for bins from chromosome 8q and bins from other genomic regions with a value of {3,0} copy number state. Black points are expected RDR and BAF values for {3,0} and {2,1} states from HATCHet2 analysis.

    Techniques Used: Clone Assay

    ( a ) CalicoST-inferred cancer clones in PDAC patient HT270P1. Grayscale indicates the inferred tumor proportion within each spot, where more gray indicates a higher proportion of normal cells (lower tumor proportion). ( b ) RDR and BAF along the genome for each inferred clone in HT270P1. Each point represents a genomic bin and is colored by CalicoST-inferred allele-specific copy numbers. The red box highlights a unique deletion in clone 2. ( c – d ) Corresponding plots for PDAC patient HT288P1. Red boxes highlight deletions that are unique to one of the inferred clones.
    Figure Legend Snippet: ( a ) CalicoST-inferred cancer clones in PDAC patient HT270P1. Grayscale indicates the inferred tumor proportion within each spot, where more gray indicates a higher proportion of normal cells (lower tumor proportion). ( b ) RDR and BAF along the genome for each inferred clone in HT270P1. Each point represents a genomic bin and is colored by CalicoST-inferred allele-specific copy numbers. The red box highlights a unique deletion in clone 2. ( c – d ) Corresponding plots for PDAC patient HT288P1. Red boxes highlight deletions that are unique to one of the inferred clones.

    Techniques Used: Clone Assay

    H&E images (top) and CalicoST-inferred tumor proportions (bottom) for breast cancer samples: ( a ) HT206B1, ( b ) HT339B1, ( c ) HT268B1, ( d ) HT265B1. The x- and y-axes represent spatial coordinates. The color bar indicates the inferred tumor proportions.
    Figure Legend Snippet: H&E images (top) and CalicoST-inferred tumor proportions (bottom) for breast cancer samples: ( a ) HT206B1, ( b ) HT339B1, ( c ) HT268B1, ( d ) HT265B1. The x- and y-axes represent spatial coordinates. The color bar indicates the inferred tumor proportions.

    Techniques Used:

    The plots for CalicoST include the allele-specific CNAs from all inferred cancer clones, labeled as ‘clone 1’, ‘clone 2’, etc. The plots for HATCHet2, labeled as ‘WES’, are included for the nine patients for whom matched WES data is available and has sufficient tumor purity.
    Figure Legend Snippet: The plots for CalicoST include the allele-specific CNAs from all inferred cancer clones, labeled as ‘clone 1’, ‘clone 2’, etc. The plots for HATCHet2, labeled as ‘WES’, are included for the nine patients for whom matched WES data is available and has sufficient tumor purity.

    Techniques Used: Clone Assay, Labeling

    a , b , Accuracy ( a ) and spatial coherence ( b ) comparison among CalicoST, Numbat, InferCNV and STARCH on CRC liver metastasis patient samples. Solid bars indicate predictions of allele-specific copy number states, and dotted bars indicate predictions of total copy number states. c , H&E image of a CRC liver metastasis sample HT260C1. d , Cancer clones inferred by CalicoST. x and y axes are spatial coordinates, and the grayscale represents the proportion of normal cells within each spot, as inferred by RCTD. Other colors indicate cancer clones. e , Cancer clones inferred by Numbat using the same color scheme as in d .
    Figure Legend Snippet: a , b , Accuracy ( a ) and spatial coherence ( b ) comparison among CalicoST, Numbat, InferCNV and STARCH on CRC liver metastasis patient samples. Solid bars indicate predictions of allele-specific copy number states, and dotted bars indicate predictions of total copy number states. c , H&E image of a CRC liver metastasis sample HT260C1. d , Cancer clones inferred by CalicoST. x and y axes are spatial coordinates, and the grayscale represents the proportion of normal cells within each spot, as inferred by RCTD. Other colors indicate cancer clones. e , Cancer clones inferred by Numbat using the same color scheme as in d .

    Techniques Used: Comparison, Starch, Clone Assay

    ( a ) Accuracy of the allele-specific copy number states inferred by CalicoST and Numbat on nine HTAN patients where ‘ground truth’ CNAs were inferred from matched WES data. ( b ) Spatial coherence of the cancer clones inferred by CalicoST and Numbat. The spatial coherence is evaluated by the z-score of joincount statistics, with higher values indicating a greater degree of spatial coherence. Each point represents a cancer clone within each slice of each patient (x-axis). As the two methods identify different numbers of clones, the two boxes include varying numbers of points for each patient. From left to right, the numbers of points in the boxplots are: HT112C1 (6 for CalicoST and 11 for Numbat), HT260C1 (3 for CalicoST and 6 for Numbat), HT265B1 (3 for CalicoST and 4 for Numbat), HT268B1 (10 for CalicoST and 39 for Numbat), HT270P1 (2 for CalicoST and 12 for Numbat), HT288P1 (2 for CalicoST and 6 for Numbat), HT306P1 (2 for CalicoST and 5 for Numbat). The upper and lower bounds of the box denote the 25% and 75% quantiles, the center line denotes the median, and the lower (upper) whiskers denote the smallest (largest) value within 1.5 times the IQR (interquartile range).
    Figure Legend Snippet: ( a ) Accuracy of the allele-specific copy number states inferred by CalicoST and Numbat on nine HTAN patients where ‘ground truth’ CNAs were inferred from matched WES data. ( b ) Spatial coherence of the cancer clones inferred by CalicoST and Numbat. The spatial coherence is evaluated by the z-score of joincount statistics, with higher values indicating a greater degree of spatial coherence. Each point represents a cancer clone within each slice of each patient (x-axis). As the two methods identify different numbers of clones, the two boxes include varying numbers of points for each patient. From left to right, the numbers of points in the boxplots are: HT112C1 (6 for CalicoST and 11 for Numbat), HT260C1 (3 for CalicoST and 6 for Numbat), HT265B1 (3 for CalicoST and 4 for Numbat), HT268B1 (10 for CalicoST and 39 for Numbat), HT270P1 (2 for CalicoST and 12 for Numbat), HT288P1 (2 for CalicoST and 6 for Numbat), HT306P1 (2 for CalicoST and 5 for Numbat). The upper and lower bounds of the box denote the 25% and 75% quantiles, the center line denotes the median, and the lower (upper) whiskers denote the smallest (largest) value within 1.5 times the IQR (interquartile range).

    Techniques Used: Clone Assay

    a , Spatial distribution and phylogeographic tree of three cancer clones inferred by CalicoST in two adjacent slices from patient HT112C1 with CRC liver metastasis. The grayscale indicates the inferred proportion of normal cells within each spot. Diamonds are the spatial centroid of each clone or inferred ancestor, and arrows indicate the inferred directions of tumor development. The distance between two slices in the z -coordinate is enlarged for clearer visualization. b , Allele-specific copy number profiles for the three cancer clones and the corresponding phylogeny (right) with branches in the phylogeny labeled by the number of unique large LOH events that occur on the branch. c , Spatial distribution and phylogeographic tree of two cancer clones inferred by CalicoST in five adjacent slices from patient HT268C1 with breast cancer. Color scheme is the same as a . d , Inferred allele-specific copy numbers and tumor phylogeny.
    Figure Legend Snippet: a , Spatial distribution and phylogeographic tree of three cancer clones inferred by CalicoST in two adjacent slices from patient HT112C1 with CRC liver metastasis. The grayscale indicates the inferred proportion of normal cells within each spot. Diamonds are the spatial centroid of each clone or inferred ancestor, and arrows indicate the inferred directions of tumor development. The distance between two slices in the z -coordinate is enlarged for clearer visualization. b , Allele-specific copy number profiles for the three cancer clones and the corresponding phylogeny (right) with branches in the phylogeny labeled by the number of unique large LOH events that occur on the branch. c , Spatial distribution and phylogeographic tree of two cancer clones inferred by CalicoST in five adjacent slices from patient HT268C1 with breast cancer. Color scheme is the same as a . d , Inferred allele-specific copy numbers and tumor phylogeny.

    Techniques Used: Clone Assay, Labeling

    a , Spatial distribution of cancer clones inferred jointly by CalicoST across five slices from a cancerous prostate. Positioning of five slices is according to ref. . Colors indicate inferred clones, including the normal clone in gray. Arrows represent the phylogeography of tumor evolution. b , Allele-specific copy number profiles for the five cancer clones and the corresponding phylogeny with branches in the phylogeny labeled by the number of unique large LOH events that occur on the branch. Colors indicate allele-specific copy numbers. The orientation and position of triangles indicate mirrored CNA events. c , BAF of each clone in chr6 and chr8. Colors indicate allele-specific copy numbers using the same color scheme as in b .
    Figure Legend Snippet: a , Spatial distribution of cancer clones inferred jointly by CalicoST across five slices from a cancerous prostate. Positioning of five slices is according to ref. . Colors indicate inferred clones, including the normal clone in gray. Arrows represent the phylogeography of tumor evolution. b , Allele-specific copy number profiles for the five cancer clones and the corresponding phylogeny with branches in the phylogeny labeled by the number of unique large LOH events that occur on the branch. Colors indicate allele-specific copy numbers. The orientation and position of triangles indicate mirrored CNA events. c , BAF of each clone in chr6 and chr8. Colors indicate allele-specific copy numbers using the same color scheme as in b .

    Techniques Used: Clone Assay, Labeling

    ( a ) UMAP of gene expression in spots from five slices of a multi-section prostate cancer patient (without applying any batch effect correction or integration tools). Each point represents a spot, colored by the slice location. ( b ) UMAP of gene expression from five slices, with each spot (point) colored according to the clone assignment from CalicoST. Grayscale indicates the inferred tumor proportion, with more gray representing a higher proportion of normal cells. ( c ) BAF along the genome for spots assigned to clone 5 from three slices (H1 4, H1 5, and H2 5) from the right portion of the prostate. Each point represents a genomic bin, colored by the inferred allele-specific copy numbers from CalicoST.
    Figure Legend Snippet: ( a ) UMAP of gene expression in spots from five slices of a multi-section prostate cancer patient (without applying any batch effect correction or integration tools). Each point represents a spot, colored by the slice location. ( b ) UMAP of gene expression from five slices, with each spot (point) colored according to the clone assignment from CalicoST. Grayscale indicates the inferred tumor proportion, with more gray representing a higher proportion of normal cells. ( c ) BAF along the genome for spots assigned to clone 5 from three slices (H1 4, H1 5, and H2 5) from the right portion of the prostate. Each point represents a genomic bin, colored by the inferred allele-specific copy numbers from CalicoST.

    Techniques Used: Gene Expression

    Each spot is colored by the clone inferred by CalicoST, with gray indicating normal spots. Spots containing the variant allele of the somatic SNV are marked by a black cross. Spots containing the reference allele are marked by a gray circle. The first five SNVs are inferred to be truncal SNVs present in both the left and right sides of the prostate, while the sixth SNV (bottom right) is inferred to be present in only the left side.
    Figure Legend Snippet: Each spot is colored by the clone inferred by CalicoST, with gray indicating normal spots. Spots containing the variant allele of the somatic SNV are marked by a black cross. Spots containing the reference allele are marked by a gray circle. The first five SNVs are inferred to be truncal SNVs present in both the left and right sides of the prostate, while the sixth SNV (bottom right) is inferred to be present in only the left side.

    Techniques Used: Variant Assay

    ( a ) Spatial organization of normal (clone 0) and three tumor clones (clones 1-3) inferred by CalicoST on a human melanoma sample sequenced using Slide-tags. ( b ) Compar- ison of cell type labels for each location from and clone labels inferred by CalicoST. ( c ) Allele-specific copy numbers inferred by CalicoST for each clone. ( d ) RDR and BAF along the genome for clones 1 and 2. Colors indicate the allele-specific copy number of the corresponding genomic bin. Red box highlights a LOH event on chr3q that is unique to clone 2.
    Figure Legend Snippet: ( a ) Spatial organization of normal (clone 0) and three tumor clones (clones 1-3) inferred by CalicoST on a human melanoma sample sequenced using Slide-tags. ( b ) Compar- ison of cell type labels for each location from and clone labels inferred by CalicoST. ( c ) Allele-specific copy numbers inferred by CalicoST for each clone. ( d ) RDR and BAF along the genome for clones 1 and 2. Colors indicate the allele-specific copy number of the corresponding genomic bin. Red box highlights a LOH event on chr3q that is unique to clone 2.

    Techniques Used: Clone Assay



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    Image Search Results


    Transcriptomic and TME characteristics associated with ECMSig in TCGA-GBM cohort (A) Volcano plot showing DEGs between ECMSig-high and ECMSig-low groups. Red dots: upregulated in high-risk; blue dots: upregulated in low-risk. Benjamini-Hochberg adjusted. (B) Gene set enrichment analysis (GSEA) plots showing enrichment of hallmark pathways. Pathways enriched in ECMSig-high and ECMSig-low groups are shown with their running enrichment scores (ESs) and ranked gene lists. Benjamini-Hochberg adjusted. (C) Heatmap showing the activity scores of selected oncogenic and tumor-related signaling pathways (rows) across TCGA-GBM samples (columns), annotated by ECMSig group and ECMSig score. Red indicates high activity, blue indicates low activity. ∗ p < 0.05. Wilcoxon signed-rank test. (D) Heatmap depicting the estimated infiltration levels of various immune and stromal cell types (rows) in TCGA-GBM samples (columns), stratified by ECMSig group and score. Red indicates high infiltration, blue indicates low infiltration. Cells significantly highly infiltrated in ECMSig-high are labeled in red, and those high in ECMSig-low group are in blue. ∗q < 0.05, ∗∗q < 0.01, ∗∗∗q < 0.001. Wilcoxon signed-rank test. Benjamini-Hochberg adjusted. (E and F) Scatterplots showing the spearman correlation between ECMSig score and (E) Macrophage_XCELL infiltration score and (F) immune_score_XCELL. The blue line represents the linear regression fit with 95% confidence interval bands. Spearman correlation test.

    Journal: iScience

    Article Title: Multi-omics profiling-derived signature links cellular ecosystem to glioblastoma prognosis

    doi: 10.1016/j.isci.2026.115982

    Figure Lengend Snippet: Transcriptomic and TME characteristics associated with ECMSig in TCGA-GBM cohort (A) Volcano plot showing DEGs between ECMSig-high and ECMSig-low groups. Red dots: upregulated in high-risk; blue dots: upregulated in low-risk. Benjamini-Hochberg adjusted. (B) Gene set enrichment analysis (GSEA) plots showing enrichment of hallmark pathways. Pathways enriched in ECMSig-high and ECMSig-low groups are shown with their running enrichment scores (ESs) and ranked gene lists. Benjamini-Hochberg adjusted. (C) Heatmap showing the activity scores of selected oncogenic and tumor-related signaling pathways (rows) across TCGA-GBM samples (columns), annotated by ECMSig group and ECMSig score. Red indicates high activity, blue indicates low activity. ∗ p < 0.05. Wilcoxon signed-rank test. (D) Heatmap depicting the estimated infiltration levels of various immune and stromal cell types (rows) in TCGA-GBM samples (columns), stratified by ECMSig group and score. Red indicates high infiltration, blue indicates low infiltration. Cells significantly highly infiltrated in ECMSig-high are labeled in red, and those high in ECMSig-low group are in blue. ∗q < 0.05, ∗∗q < 0.01, ∗∗∗q < 0.001. Wilcoxon signed-rank test. Benjamini-Hochberg adjusted. (E and F) Scatterplots showing the spearman correlation between ECMSig score and (E) Macrophage_XCELL infiltration score and (F) immune_score_XCELL. The blue line represents the linear regression fit with 95% confidence interval bands. Spearman correlation test.

    Article Snippet: The single-cell transcriptomic sequencing dataset utilizing technology from the 10X Genomics platform was available under the accession number GEO: GSE182109 at the Gene Expression Omnibus (GEO) repository.

    Techniques: Activity Assay, Protein-Protein interactions, Labeling

    Single-cell RNA sequencing analysis revealing ECMSig expression across cell types and identification of prognostically relevant cell states in GBM (A) UMAP visualization of major cell types identified in GBM scRNA-seq data. (B) Dot plot showing the scaled average expression (color intensity) and percentage of cells expressing (dot size) canonical marker genes for each major cell type. (C) Dot plot showing the scaled average expression and percentage of cells expressing the seven ECMSig genes across major cell types. (D) UMAP plots showing the expression levels of individual ECMSig genes and overall ECMSig score across all cells. (E–G) UMAP plots illustrating Scissor-identified prognostically unfavorable (Scissor_Pos, red dashed circle) and favorable (Scissor_Neg, blue dashed circle; Scissor_Others, gray) cell subpopulations within (E) tumor cells, (F) myeloid cells, and (G) endothelial cells. (H–K) Violin plots comparing ECMSig scores among tumor cells grouped by Scissor status (H) and tumor type (I), and myeloid cells (J) or endothelial cells (K) grouped by Scissor status. ∗∗∗∗ p < 0.0001. Wilcoxon signed-rank test. (L) Dot plot showing differentially expressed marker genes between myeloid Scissor_Pos and other myeloid cells. Dot size indicates the fraction of cells in the group expressing the gene; color indicates average expression level.

    Journal: iScience

    Article Title: Multi-omics profiling-derived signature links cellular ecosystem to glioblastoma prognosis

    doi: 10.1016/j.isci.2026.115982

    Figure Lengend Snippet: Single-cell RNA sequencing analysis revealing ECMSig expression across cell types and identification of prognostically relevant cell states in GBM (A) UMAP visualization of major cell types identified in GBM scRNA-seq data. (B) Dot plot showing the scaled average expression (color intensity) and percentage of cells expressing (dot size) canonical marker genes for each major cell type. (C) Dot plot showing the scaled average expression and percentage of cells expressing the seven ECMSig genes across major cell types. (D) UMAP plots showing the expression levels of individual ECMSig genes and overall ECMSig score across all cells. (E–G) UMAP plots illustrating Scissor-identified prognostically unfavorable (Scissor_Pos, red dashed circle) and favorable (Scissor_Neg, blue dashed circle; Scissor_Others, gray) cell subpopulations within (E) tumor cells, (F) myeloid cells, and (G) endothelial cells. (H–K) Violin plots comparing ECMSig scores among tumor cells grouped by Scissor status (H) and tumor type (I), and myeloid cells (J) or endothelial cells (K) grouped by Scissor status. ∗∗∗∗ p < 0.0001. Wilcoxon signed-rank test. (L) Dot plot showing differentially expressed marker genes between myeloid Scissor_Pos and other myeloid cells. Dot size indicates the fraction of cells in the group expressing the gene; color indicates average expression level.

    Article Snippet: The single-cell transcriptomic sequencing dataset utilizing technology from the 10X Genomics platform was available under the accession number GEO: GSE182109 at the Gene Expression Omnibus (GEO) repository.

    Techniques: Single Cell, RNA Sequencing, Expressing, Marker

    Spatial transcriptomic analysis revealing co-localization of ECMSig, hypoxia, Scissor-Positive cells, and pericytes in GBM (A) Spatial feature plots for four GBM samples. Each row represents a sample. Columns show spatial heatmaps of: ECMSig score, hypoxia signature score, tumor Scissor_Pos signature score, myeloid Scissor_Pos signature score, endothelial Scissor Pos signature score, and pericyte marker signature score. Color scale indicates scaled expression or score (low to high). Each dot represents a spatial barcoded spot.

    Journal: iScience

    Article Title: Multi-omics profiling-derived signature links cellular ecosystem to glioblastoma prognosis

    doi: 10.1016/j.isci.2026.115982

    Figure Lengend Snippet: Spatial transcriptomic analysis revealing co-localization of ECMSig, hypoxia, Scissor-Positive cells, and pericytes in GBM (A) Spatial feature plots for four GBM samples. Each row represents a sample. Columns show spatial heatmaps of: ECMSig score, hypoxia signature score, tumor Scissor_Pos signature score, myeloid Scissor_Pos signature score, endothelial Scissor Pos signature score, and pericyte marker signature score. Color scale indicates scaled expression or score (low to high). Each dot represents a spatial barcoded spot.

    Article Snippet: The single-cell transcriptomic sequencing dataset utilizing technology from the 10X Genomics platform was available under the accession number GEO: GSE182109 at the Gene Expression Omnibus (GEO) repository.

    Techniques: Marker, Expressing