robust multiarray averaging (rma) function Search Results


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Robust Multiarray Average Algorithm, supplied by Partek, 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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dAKAP1 expression is inversely related to mesenchymal markers. A, Pearson's r values quantifying the correlation of AKAPs mRNA and 36 mesenchymal markers from gene array analysis data of <t>CCLE</t> breast cancer cell lines (n = 59) (29). Median and interquartile ranges (red bars) are indicated. B, heat map displaying r values of correlation of AKAP and mesenchymal gene mRNA expression. The rows (mesenchymal genes) are organized with hierarchical clustering, and columns (AKAPs) are organized by mean r value. Intensity scale indicates r values ranging from high (yellow) to low (teal). C, Pearson's r values as in A but with mitochondrion-related proteins as columns. D, heat map of r values as in B with mitochondrial proteins as columns. Note that repeated genes from previous panels display the same data with new clustering applied. E, heat map of dAKAP1 mRNA intensity and mean mesenchymal marker mRNA across each individual breast cancer cell line (of 59 total) used in this data set, organized by ascending dAKAP1 mRNA expression. F, scatter plot of dAKAP1 mRNA against mean mesenchymal marker mRNA. Error bars represent S.E. Breast cancer cell lines MCF7, BT474, MDA231 (also called MDA-MB-231), and HS578T used later in this study are highlighted in magenta. G and H, heat maps depicting correlation of mesenchymal marker expression with dAKAP1 mRNA (G) and dAKAP1 protein expression (H) in patient samples (32) from four clinically defined breast cancer subtypes (indicated above each lane). I, immunoblot analysis of patient samples from breast cancer tumors monitoring dAKAP1 expression (top), E-cadherin epithelial marker (second from top), N-cadherin (middle) and Snail mesenchymal markers (second from bottom), and Eif2α loading control (bottom). Individual patients are designated A–D at the bottom of the panel (see Table S1 for patient sample details).
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dAKAP1 expression is inversely related to mesenchymal markers. A, Pearson's r values quantifying the correlation of AKAPs mRNA and 36 mesenchymal markers from gene array analysis data of <t>CCLE</t> breast cancer cell lines (n = 59) (29). Median and interquartile ranges (red bars) are indicated. B, heat map displaying r values of correlation of AKAP and mesenchymal gene mRNA expression. The rows (mesenchymal genes) are organized with hierarchical clustering, and columns (AKAPs) are organized by mean r value. Intensity scale indicates r values ranging from high (yellow) to low (teal). C, Pearson's r values as in A but with mitochondrion-related proteins as columns. D, heat map of r values as in B with mitochondrial proteins as columns. Note that repeated genes from previous panels display the same data with new clustering applied. E, heat map of dAKAP1 mRNA intensity and mean mesenchymal marker mRNA across each individual breast cancer cell line (of 59 total) used in this data set, organized by ascending dAKAP1 mRNA expression. F, scatter plot of dAKAP1 mRNA against mean mesenchymal marker mRNA. Error bars represent S.E. Breast cancer cell lines MCF7, BT474, MDA231 (also called MDA-MB-231), and HS578T used later in this study are highlighted in magenta. G and H, heat maps depicting correlation of mesenchymal marker expression with dAKAP1 mRNA (G) and dAKAP1 protein expression (H) in patient samples (32) from four clinically defined breast cancer subtypes (indicated above each lane). I, immunoblot analysis of patient samples from breast cancer tumors monitoring dAKAP1 expression (top), E-cadherin epithelial marker (second from top), N-cadherin (middle) and Snail mesenchymal markers (second from bottom), and Eif2α loading control (bottom). Individual patients are designated A–D at the bottom of the panel (see Table S1 for patient sample details).
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guanine cytosine robust multiarray analysis (gcrma) background subtraction  (Partek)
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dAKAP1 expression is inversely related to mesenchymal markers. A, Pearson's r values quantifying the correlation of AKAPs mRNA and 36 mesenchymal markers from gene array analysis data of <t>CCLE</t> breast cancer cell lines (n = 59) (29). Median and interquartile ranges (red bars) are indicated. B, heat map displaying r values of correlation of AKAP and mesenchymal gene mRNA expression. The rows (mesenchymal genes) are organized with hierarchical clustering, and columns (AKAPs) are organized by mean r value. Intensity scale indicates r values ranging from high (yellow) to low (teal). C, Pearson's r values as in A but with mitochondrion-related proteins as columns. D, heat map of r values as in B with mitochondrial proteins as columns. Note that repeated genes from previous panels display the same data with new clustering applied. E, heat map of dAKAP1 mRNA intensity and mean mesenchymal marker mRNA across each individual breast cancer cell line (of 59 total) used in this data set, organized by ascending dAKAP1 mRNA expression. F, scatter plot of dAKAP1 mRNA against mean mesenchymal marker mRNA. Error bars represent S.E. Breast cancer cell lines MCF7, BT474, MDA231 (also called MDA-MB-231), and HS578T used later in this study are highlighted in magenta. G and H, heat maps depicting correlation of mesenchymal marker expression with dAKAP1 mRNA (G) and dAKAP1 protein expression (H) in patient samples (32) from four clinically defined breast cancer subtypes (indicated above each lane). I, immunoblot analysis of patient samples from breast cancer tumors monitoring dAKAP1 expression (top), E-cadherin epithelial marker (second from top), N-cadherin (middle) and Snail mesenchymal markers (second from bottom), and Eif2α loading control (bottom). Individual patients are designated A–D at the bottom of the panel (see Table S1 for patient sample details).
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robust multiarray analysis  (Iobion Informatics)
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dAKAP1 expression is inversely related to mesenchymal markers. A, Pearson's r values quantifying the correlation of AKAPs mRNA and 36 mesenchymal markers from gene array analysis data of <t>CCLE</t> breast cancer cell lines (n = 59) (29). Median and interquartile ranges (red bars) are indicated. B, heat map displaying r values of correlation of AKAP and mesenchymal gene mRNA expression. The rows (mesenchymal genes) are organized with hierarchical clustering, and columns (AKAPs) are organized by mean r value. Intensity scale indicates r values ranging from high (yellow) to low (teal). C, Pearson's r values as in A but with mitochondrion-related proteins as columns. D, heat map of r values as in B with mitochondrial proteins as columns. Note that repeated genes from previous panels display the same data with new clustering applied. E, heat map of dAKAP1 mRNA intensity and mean mesenchymal marker mRNA across each individual breast cancer cell line (of 59 total) used in this data set, organized by ascending dAKAP1 mRNA expression. F, scatter plot of dAKAP1 mRNA against mean mesenchymal marker mRNA. Error bars represent S.E. Breast cancer cell lines MCF7, BT474, MDA231 (also called MDA-MB-231), and HS578T used later in this study are highlighted in magenta. G and H, heat maps depicting correlation of mesenchymal marker expression with dAKAP1 mRNA (G) and dAKAP1 protein expression (H) in patient samples (32) from four clinically defined breast cancer subtypes (indicated above each lane). I, immunoblot analysis of patient samples from breast cancer tumors monitoring dAKAP1 expression (top), E-cadherin epithelial marker (second from top), N-cadherin (middle) and Snail mesenchymal markers (second from bottom), and Eif2α loading control (bottom). Individual patients are designated A–D at the bottom of the panel (see Table S1 for patient sample details).
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Image Search Results


dAKAP1 expression is inversely related to mesenchymal markers. A, Pearson's r values quantifying the correlation of AKAPs mRNA and 36 mesenchymal markers from gene array analysis data of CCLE breast cancer cell lines (n = 59) (29). Median and interquartile ranges (red bars) are indicated. B, heat map displaying r values of correlation of AKAP and mesenchymal gene mRNA expression. The rows (mesenchymal genes) are organized with hierarchical clustering, and columns (AKAPs) are organized by mean r value. Intensity scale indicates r values ranging from high (yellow) to low (teal). C, Pearson's r values as in A but with mitochondrion-related proteins as columns. D, heat map of r values as in B with mitochondrial proteins as columns. Note that repeated genes from previous panels display the same data with new clustering applied. E, heat map of dAKAP1 mRNA intensity and mean mesenchymal marker mRNA across each individual breast cancer cell line (of 59 total) used in this data set, organized by ascending dAKAP1 mRNA expression. F, scatter plot of dAKAP1 mRNA against mean mesenchymal marker mRNA. Error bars represent S.E. Breast cancer cell lines MCF7, BT474, MDA231 (also called MDA-MB-231), and HS578T used later in this study are highlighted in magenta. G and H, heat maps depicting correlation of mesenchymal marker expression with dAKAP1 mRNA (G) and dAKAP1 protein expression (H) in patient samples (32) from four clinically defined breast cancer subtypes (indicated above each lane). I, immunoblot analysis of patient samples from breast cancer tumors monitoring dAKAP1 expression (top), E-cadherin epithelial marker (second from top), N-cadherin (middle) and Snail mesenchymal markers (second from bottom), and Eif2α loading control (bottom). Individual patients are designated A–D at the bottom of the panel (see Table S1 for patient sample details).

Journal: The Journal of Biological Chemistry

Article Title: Depletion of dAKAP1–protein kinase A signaling islands from the outer mitochondrial membrane alters breast cancer cell metabolism and motility

doi: 10.1074/jbc.RA118.006741

Figure Lengend Snippet: dAKAP1 expression is inversely related to mesenchymal markers. A, Pearson's r values quantifying the correlation of AKAPs mRNA and 36 mesenchymal markers from gene array analysis data of CCLE breast cancer cell lines (n = 59) (29). Median and interquartile ranges (red bars) are indicated. B, heat map displaying r values of correlation of AKAP and mesenchymal gene mRNA expression. The rows (mesenchymal genes) are organized with hierarchical clustering, and columns (AKAPs) are organized by mean r value. Intensity scale indicates r values ranging from high (yellow) to low (teal). C, Pearson's r values as in A but with mitochondrion-related proteins as columns. D, heat map of r values as in B with mitochondrial proteins as columns. Note that repeated genes from previous panels display the same data with new clustering applied. E, heat map of dAKAP1 mRNA intensity and mean mesenchymal marker mRNA across each individual breast cancer cell line (of 59 total) used in this data set, organized by ascending dAKAP1 mRNA expression. F, scatter plot of dAKAP1 mRNA against mean mesenchymal marker mRNA. Error bars represent S.E. Breast cancer cell lines MCF7, BT474, MDA231 (also called MDA-MB-231), and HS578T used later in this study are highlighted in magenta. G and H, heat maps depicting correlation of mesenchymal marker expression with dAKAP1 mRNA (G) and dAKAP1 protein expression (H) in patient samples (32) from four clinically defined breast cancer subtypes (indicated above each lane). I, immunoblot analysis of patient samples from breast cancer tumors monitoring dAKAP1 expression (top), E-cadherin epithelial marker (second from top), N-cadherin (middle) and Snail mesenchymal markers (second from bottom), and Eif2α loading control (bottom). Individual patients are designated A–D at the bottom of the panel (see Table S1 for patient sample details).

Article Snippet: Cancer Cell Line Encyclopedia (CCLE) data ( 29 ) RMA (robust multiarray average)–normalized mRNA expression data were downloaded from the Broad Institute ( https://portals.broadinstitute.org/ccle ).

Techniques: Expressing, Marker, Western Blot, Control