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tcga gene expression data for skin cutaneous melanoma (skcm) and breast carcinoma (brca)  (Broad Institute Inc)

 
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    Broad Institute Inc tcga gene expression data for skin cutaneous melanoma (skcm) and breast carcinoma (brca)
    a , b cDC1 scores based on the expression of CLNK , BATF3 , XCR1 and CLEC9A (cDC1 gene signature established in ref. ) and CD4 + Trm scores based on the expression of the genes included in the cDC1-induced CD4 + Trm signature and the human <t>BRCA</t> CD4 + Trm signature (Table ) were calculated for breast carcinoma (BRCA) ( a ) or human skin melanoma (SKCM) ( b ) from <t>the</t> <t>TCGA.</t> The Pearson’s correlations of cDC1 and CD4 + Trm scores normalized by percentile rank and the linear regression with a 95% confidence region are shown. c Uniform Manifold Approximation and Projection (UMAP) representing CD4 + T cells from 22 human BRCA patients (GSE176078 ,). The newly identified sub-clusters after re-clustering are shown. d Heatmap showing the scaled signature score of the cDC1-induced CD4 + Trm signature and the human BRCA CD4 + Trm signature (Table ) of cells contained in each of the 17 CD4 + T cell sub-clusters in human BRCA identified in ( c ). e UMAPs depicting the single cell expression of CXCR6 (left panel) and CCR7 (right panel) by cells contained within the CD4 + T cell clusters in human BRCA. Grey dots show the outline for the CD4 + T cell clusters and brown-colored dots indicate the level of expression for the respective gene by a cell. A black circle indicates the location of the CD4 + Trm sub-cluster C16. f The frequency of cells contained in the CD4 + Trm sub-cluster C16 ( c – e ) and the cDC1:CLEC9A cluster (identified in ref. ) within all tumor cells was calculated for each BRCA patient ( n = 22). The Pearson’s correlation of intratumoral CD4 + Trm and cDC1 frequencies and the linear regression with a 95% confidence region are shown. g – n Survival curves of BRCA ( g , i , k ) and SKCM ( h , j , l ) patients from the TGCA with high or low (top and bottom tertiles, respectively) intratumoral cDC1 ( g , h ) or CD4 + Trm ( j – l ) scores calculated using gene signatures as in ( a , b ). Hazard ratio and 95% coefficient interval are indicated ( j , n ). Statistical analysis by Mantel-Cox test.
    Tcga Gene Expression Data For Skin Cutaneous Melanoma (Skcm) And Breast Carcinoma (Brca), supplied by Broad Institute Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Immunotherapy with conventional type-1 dendritic cells induces immune memory and limits tumor relapse"

    Article Title: Immunotherapy with conventional type-1 dendritic cells induces immune memory and limits tumor relapse

    Journal: Nature Communications

    doi: 10.1038/s41467-025-58289-1

    a , b cDC1 scores based on the expression of CLNK , BATF3 , XCR1 and CLEC9A (cDC1 gene signature established in ref. ) and CD4 + Trm scores based on the expression of the genes included in the cDC1-induced CD4 + Trm signature and the human BRCA CD4 + Trm signature (Table ) were calculated for breast carcinoma (BRCA) ( a ) or human skin melanoma (SKCM) ( b ) from the TCGA. The Pearson’s correlations of cDC1 and CD4 + Trm scores normalized by percentile rank and the linear regression with a 95% confidence region are shown. c Uniform Manifold Approximation and Projection (UMAP) representing CD4 + T cells from 22 human BRCA patients (GSE176078 ,). The newly identified sub-clusters after re-clustering are shown. d Heatmap showing the scaled signature score of the cDC1-induced CD4 + Trm signature and the human BRCA CD4 + Trm signature (Table ) of cells contained in each of the 17 CD4 + T cell sub-clusters in human BRCA identified in ( c ). e UMAPs depicting the single cell expression of CXCR6 (left panel) and CCR7 (right panel) by cells contained within the CD4 + T cell clusters in human BRCA. Grey dots show the outline for the CD4 + T cell clusters and brown-colored dots indicate the level of expression for the respective gene by a cell. A black circle indicates the location of the CD4 + Trm sub-cluster C16. f The frequency of cells contained in the CD4 + Trm sub-cluster C16 ( c – e ) and the cDC1:CLEC9A cluster (identified in ref. ) within all tumor cells was calculated for each BRCA patient ( n = 22). The Pearson’s correlation of intratumoral CD4 + Trm and cDC1 frequencies and the linear regression with a 95% confidence region are shown. g – n Survival curves of BRCA ( g , i , k ) and SKCM ( h , j , l ) patients from the TGCA with high or low (top and bottom tertiles, respectively) intratumoral cDC1 ( g , h ) or CD4 + Trm ( j – l ) scores calculated using gene signatures as in ( a , b ). Hazard ratio and 95% coefficient interval are indicated ( j , n ). Statistical analysis by Mantel-Cox test.
    Figure Legend Snippet: a , b cDC1 scores based on the expression of CLNK , BATF3 , XCR1 and CLEC9A (cDC1 gene signature established in ref. ) and CD4 + Trm scores based on the expression of the genes included in the cDC1-induced CD4 + Trm signature and the human BRCA CD4 + Trm signature (Table ) were calculated for breast carcinoma (BRCA) ( a ) or human skin melanoma (SKCM) ( b ) from the TCGA. The Pearson’s correlations of cDC1 and CD4 + Trm scores normalized by percentile rank and the linear regression with a 95% confidence region are shown. c Uniform Manifold Approximation and Projection (UMAP) representing CD4 + T cells from 22 human BRCA patients (GSE176078 ,). The newly identified sub-clusters after re-clustering are shown. d Heatmap showing the scaled signature score of the cDC1-induced CD4 + Trm signature and the human BRCA CD4 + Trm signature (Table ) of cells contained in each of the 17 CD4 + T cell sub-clusters in human BRCA identified in ( c ). e UMAPs depicting the single cell expression of CXCR6 (left panel) and CCR7 (right panel) by cells contained within the CD4 + T cell clusters in human BRCA. Grey dots show the outline for the CD4 + T cell clusters and brown-colored dots indicate the level of expression for the respective gene by a cell. A black circle indicates the location of the CD4 + Trm sub-cluster C16. f The frequency of cells contained in the CD4 + Trm sub-cluster C16 ( c – e ) and the cDC1:CLEC9A cluster (identified in ref. ) within all tumor cells was calculated for each BRCA patient ( n = 22). The Pearson’s correlation of intratumoral CD4 + Trm and cDC1 frequencies and the linear regression with a 95% confidence region are shown. g – n Survival curves of BRCA ( g , i , k ) and SKCM ( h , j , l ) patients from the TGCA with high or low (top and bottom tertiles, respectively) intratumoral cDC1 ( g , h ) or CD4 + Trm ( j – l ) scores calculated using gene signatures as in ( a , b ). Hazard ratio and 95% coefficient interval are indicated ( j , n ). Statistical analysis by Mantel-Cox test.

    Techniques Used: Expressing

    Related Articles

    Gene Expression:

    Article Title: Clinical relevance of CERK and SPHK1 in breast cancer and their association with metastasis and drug resistance.
    Article Snippet: .. Gene expression data pertaining to breast invasive carcinoma (TCGA abbreviation BRCA ) was retrieved from the Firehose portal of Broad Institute (gdac.broadinstitute.org); this dataset comprises lowest-normalized level-3 microarray data (Agilent 244 K [G4502A]) from 529 tumor and 61 adjacent normal tissues. ..

    Microarray:

    Article Title: Clinical relevance of CERK and SPHK1 in breast cancer and their association with metastasis and drug resistance.
    Article Snippet: .. Gene expression data pertaining to breast invasive carcinoma (TCGA abbreviation BRCA ) was retrieved from the Firehose portal of Broad Institute (gdac.broadinstitute.org); this dataset comprises lowest-normalized level-3 microarray data (Agilent 244 K [G4502A]) from 529 tumor and 61 adjacent normal tissues. ..



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    a , b cDC1 scores based on the expression of CLNK , BATF3 , XCR1 and CLEC9A (cDC1 gene signature established in ref. ) and CD4 + Trm scores based on the expression of the genes included in the cDC1-induced CD4 + Trm signature and the human <t>BRCA</t> CD4 + Trm signature (Table ) were calculated for breast carcinoma (BRCA) ( a ) or human skin melanoma (SKCM) ( b ) from <t>the</t> <t>TCGA.</t> The Pearson’s correlations of cDC1 and CD4 + Trm scores normalized by percentile rank and the linear regression with a 95% confidence region are shown. c Uniform Manifold Approximation and Projection (UMAP) representing CD4 + T cells from 22 human BRCA patients (GSE176078 ,). The newly identified sub-clusters after re-clustering are shown. d Heatmap showing the scaled signature score of the cDC1-induced CD4 + Trm signature and the human BRCA CD4 + Trm signature (Table ) of cells contained in each of the 17 CD4 + T cell sub-clusters in human BRCA identified in ( c ). e UMAPs depicting the single cell expression of CXCR6 (left panel) and CCR7 (right panel) by cells contained within the CD4 + T cell clusters in human BRCA. Grey dots show the outline for the CD4 + T cell clusters and brown-colored dots indicate the level of expression for the respective gene by a cell. A black circle indicates the location of the CD4 + Trm sub-cluster C16. f The frequency of cells contained in the CD4 + Trm sub-cluster C16 ( c – e ) and the cDC1:CLEC9A cluster (identified in ref. ) within all tumor cells was calculated for each BRCA patient ( n = 22). The Pearson’s correlation of intratumoral CD4 + Trm and cDC1 frequencies and the linear regression with a 95% confidence region are shown. g – n Survival curves of BRCA ( g , i , k ) and SKCM ( h , j , l ) patients from the TGCA with high or low (top and bottom tertiles, respectively) intratumoral cDC1 ( g , h ) or CD4 + Trm ( j – l ) scores calculated using gene signatures as in ( a , b ). Hazard ratio and 95% coefficient interval are indicated ( j , n ). Statistical analysis by Mantel-Cox test.
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    a , b cDC1 scores based on the expression of CLNK , BATF3 , XCR1 and CLEC9A (cDC1 gene signature established in ref. ) and CD4 + Trm scores based on the expression of the genes included in the cDC1-induced CD4 + Trm signature and the human BRCA CD4 + Trm signature (Table ) were calculated for breast carcinoma (BRCA) ( a ) or human skin melanoma (SKCM) ( b ) from the TCGA. The Pearson’s correlations of cDC1 and CD4 + Trm scores normalized by percentile rank and the linear regression with a 95% confidence region are shown. c Uniform Manifold Approximation and Projection (UMAP) representing CD4 + T cells from 22 human BRCA patients (GSE176078 ,). The newly identified sub-clusters after re-clustering are shown. d Heatmap showing the scaled signature score of the cDC1-induced CD4 + Trm signature and the human BRCA CD4 + Trm signature (Table ) of cells contained in each of the 17 CD4 + T cell sub-clusters in human BRCA identified in ( c ). e UMAPs depicting the single cell expression of CXCR6 (left panel) and CCR7 (right panel) by cells contained within the CD4 + T cell clusters in human BRCA. Grey dots show the outline for the CD4 + T cell clusters and brown-colored dots indicate the level of expression for the respective gene by a cell. A black circle indicates the location of the CD4 + Trm sub-cluster C16. f The frequency of cells contained in the CD4 + Trm sub-cluster C16 ( c – e ) and the cDC1:CLEC9A cluster (identified in ref. ) within all tumor cells was calculated for each BRCA patient ( n = 22). The Pearson’s correlation of intratumoral CD4 + Trm and cDC1 frequencies and the linear regression with a 95% confidence region are shown. g – n Survival curves of BRCA ( g , i , k ) and SKCM ( h , j , l ) patients from the TGCA with high or low (top and bottom tertiles, respectively) intratumoral cDC1 ( g , h ) or CD4 + Trm ( j – l ) scores calculated using gene signatures as in ( a , b ). Hazard ratio and 95% coefficient interval are indicated ( j , n ). Statistical analysis by Mantel-Cox test.

    Journal: Nature Communications

    Article Title: Immunotherapy with conventional type-1 dendritic cells induces immune memory and limits tumor relapse

    doi: 10.1038/s41467-025-58289-1

    Figure Lengend Snippet: a , b cDC1 scores based on the expression of CLNK , BATF3 , XCR1 and CLEC9A (cDC1 gene signature established in ref. ) and CD4 + Trm scores based on the expression of the genes included in the cDC1-induced CD4 + Trm signature and the human BRCA CD4 + Trm signature (Table ) were calculated for breast carcinoma (BRCA) ( a ) or human skin melanoma (SKCM) ( b ) from the TCGA. The Pearson’s correlations of cDC1 and CD4 + Trm scores normalized by percentile rank and the linear regression with a 95% confidence region are shown. c Uniform Manifold Approximation and Projection (UMAP) representing CD4 + T cells from 22 human BRCA patients (GSE176078 ,). The newly identified sub-clusters after re-clustering are shown. d Heatmap showing the scaled signature score of the cDC1-induced CD4 + Trm signature and the human BRCA CD4 + Trm signature (Table ) of cells contained in each of the 17 CD4 + T cell sub-clusters in human BRCA identified in ( c ). e UMAPs depicting the single cell expression of CXCR6 (left panel) and CCR7 (right panel) by cells contained within the CD4 + T cell clusters in human BRCA. Grey dots show the outline for the CD4 + T cell clusters and brown-colored dots indicate the level of expression for the respective gene by a cell. A black circle indicates the location of the CD4 + Trm sub-cluster C16. f The frequency of cells contained in the CD4 + Trm sub-cluster C16 ( c – e ) and the cDC1:CLEC9A cluster (identified in ref. ) within all tumor cells was calculated for each BRCA patient ( n = 22). The Pearson’s correlation of intratumoral CD4 + Trm and cDC1 frequencies and the linear regression with a 95% confidence region are shown. g – n Survival curves of BRCA ( g , i , k ) and SKCM ( h , j , l ) patients from the TGCA with high or low (top and bottom tertiles, respectively) intratumoral cDC1 ( g , h ) or CD4 + Trm ( j – l ) scores calculated using gene signatures as in ( a , b ). Hazard ratio and 95% coefficient interval are indicated ( j , n ). Statistical analysis by Mantel-Cox test.

    Article Snippet: TCGA gene expression data for skin cutaneous melanoma (SKCM) and breast carcinoma (BRCA) are available in the Broad Institute Firehose portal ( https://gdac.broadinstitute.org/ ) and summarized pan-cancer clinical data are available in the synapse database under the accession code syn12026747. are provided with this paper.

    Techniques: Expressing

    Survival analysis showed the prognostic effect of MultiK derived reproducible T cell gene signatures compared to other T cell signatures as well as single gene expression (indicated on the Y -axis) in external breast cancer datasets. Forest plots show hazard ratio (circles) and 95% confidence intervals (horizontal ranges) derived from the Cox proportional hazards model for overall survival in univariate analysis. Red indicates significant hazard ratio estimate ( p value < 0.05) whereas blue indicates non-significant estimate ( p value ≥ 0.05). The first two vertical panels show results from combining all patients (first panel) and ER+HER2− patients (second panel) from the METABRIC, Harrell 855, TCGA BRCA, and SCAN-B datasets. The third vertical panel shows results from combining HER2+ patients from the Harrell 855, TCGA BRCA, SCAN-B, and CALGB40601 datasets. The fourth vertical panel shows results from combining TNBC patients from the METABRIC, Harrell 855, TCGA BRCA, and SCAN-B datasets

    Journal: Genome Biology

    Article Title: MultiK: an automated tool to determine optimal cluster numbers in single-cell RNA sequencing data

    doi: 10.1186/s13059-021-02445-5

    Figure Lengend Snippet: Survival analysis showed the prognostic effect of MultiK derived reproducible T cell gene signatures compared to other T cell signatures as well as single gene expression (indicated on the Y -axis) in external breast cancer datasets. Forest plots show hazard ratio (circles) and 95% confidence intervals (horizontal ranges) derived from the Cox proportional hazards model for overall survival in univariate analysis. Red indicates significant hazard ratio estimate ( p value < 0.05) whereas blue indicates non-significant estimate ( p value ≥ 0.05). The first two vertical panels show results from combining all patients (first panel) and ER+HER2− patients (second panel) from the METABRIC, Harrell 855, TCGA BRCA, and SCAN-B datasets. The third vertical panel shows results from combining HER2+ patients from the Harrell 855, TCGA BRCA, SCAN-B, and CALGB40601 datasets. The fourth vertical panel shows results from combining TNBC patients from the METABRIC, Harrell 855, TCGA BRCA, and SCAN-B datasets

    Article Snippet: The TCGA BRCA gene expression data were downloaded from the Broad Institute TCGA GDAC Firehose ( https://gdac.broadinstitute.org/ ), and the clinical data were downloaded from the Genomic Data Commons Data portal ( https://portal.gdc.cancer.gov/projects/TCGA-BRCA ).

    Techniques: Derivative Assay, Gene Expression