Journal: Global Health, Epidemiology and Genomics

Article Title: Genetics of breast cancer in African populations: a literature review

doi: 10.1017/gheg.2018.8

Figure Lengend Snippet: Top enriched terms and biological pathways identified by functional analysis of breast cancer candidate genes studied in Northern Africa

Article Snippet: Cell Cycle: G2/M checkpoint , M8560 , MSigDB C2 BIOCARTA (v6.0) , 3.467 × 10 −6.

Techniques: Functional Assay, Northern Blot, Transduction

Journal: Global Health, Epidemiology and Genomics

Article Title: Genetics of breast cancer in African populations: a literature review

doi: 10.1017/gheg.2018.8

Figure Lengend Snippet: Top enriched terms and biological pathways identified by functional analysis of breast cancer candidate genes studied in southern Africa

Article Snippet: Cell Cycle: G2/M checkpoint , M8560 , MSigDB C2 BIOCARTA (v6.0) , 3.467 × 10 −6.

Techniques: Functional Assay, Homologous Recombination

Journal: Oncotarget

Article Title: Whole-exome sequencing of primary plasma cell leukemia discloses heterogeneous mutational patterns

doi:

Figure Lengend Snippet: Pathways significantly enriched in mutated genes by ToppGene analysis

Article Snippet: Cell Cycle G2/M Checkpoint , MSigDB C2: BioCarta (ID M8560) , 1.25E-05 , 1.02E-02 , 13/20 , ATM, ATR, BRCA1, CDC25A, CDKN1A, PRKDC, EP300, CHEK2, RPS6KA1, TP53.

Techniques:

Journal: Nature Communications

Article Title: Mechanisms of epigenomic and functional convergence between glucocorticoid- and IL4-driven macrophage programming

doi: 10.1038/s41467-024-52942-x

Figure Lengend Snippet: a Transcriptomic changes in M0 macrophages polarized with IL4 or GCs corticosterone (Cort) or dexamethasone (Dex) for 24 h were determined by RNAseq ( n = 3 biological replicates [mice]). Venn diagrams show DEGs in M2 IL4 and M2 GC relative to M0 (FC ≥ 2; FDR < 0.05); 92 of 133 genes are regulated in both M2 IL4 and M2 Dex in the same direction. b Volcano plots show DEGs in M2 IL4 (left) and M2 Dex (right) relative to M0 (LogFC ≥ 1; FDR < 0.05). Selected upregulated genes are highlighted in orange (M2 IL4 ) and green (M2 Dex ). Downregulated genes are highlighted in red in both populations. Examples of the M2 IL4 :M2 Dex shared DEGs are underlined. c RT-qPCR validation of genes upregulated selectively in M2 IL4 (top), M2 GC (middle), or both (bottom). One-tailed unpaired t test; p -values are shown; ns, non-significant ( p ≥ 0.05). n = 4 biological replicates (mice), error bars are SEM. d Differentially regulated pathways (unadjusted p < 0.01; see ref. . equations 14-15) identified using QuSAGE and MsigDB canonical pathways (c2.cp.v7.3, Broad Institute) are shown for M2 IL4 (top) and M2 Dex (bottom). Underlined are the shared pathways between M2 IL4 (upregulated, orange; downregulated, red) and M2 Dex (upregulated, green; downregulated, red). Circle size is proportional to the number of genes in the pathway, and color signifies the p -value. e Genes from indicated pathways induced or repressed in M2 IL4 , M2 Dex , or both are plotted as LogFC ± SD. Source data are provided as a Source data file.

Article Snippet: One-tailed unpaired t test; p -values are shown; ns, non-significant ( p ≥ 0.05). n = 4 biological replicates (mice), error bars are SEM. d Differentially regulated pathways (unadjusted p < 0.01; see ref. . equations 14-15) identified using QuSAGE and MsigDB canonical pathways (c2.cp.v7.3, Broad Institute) are shown for M2 IL4 (top) and M2 Dex (bottom).

Techniques: Quantitative RT-PCR, Biomarker Discovery, One-tailed Test

Journal: Nature Communications

Article Title: Mechanisms of epigenomic and functional convergence between glucocorticoid- and IL4-driven macrophage programming

doi: 10.1038/s41467-024-52942-x

Figure Lengend Snippet: a , b Expression of ( a ) GRIP1 or ( b ) IL4- (top) GC- (middle) or shared (bottom) M2 target genes in WT and GRIP1 cKO M0, M2 IL4 , M2 Cort , and M2 Dex populations as assessed by RT-qPCR. The average relative expression of each transcript in WT M0 is arbitrarily set to 1. n = 4 biological replicates [mice]; One-tailed unpaired t test; p -values are indicated; ns, non-significant (p ≥ 0.05). Error bars are SEM. c Stacked bar plot shows the number of DEGs (FC ≥ 1.5) in GRIP1 cKO as a fraction of WT M2 IL4 , M2 Dex , or shared DEGs relative to M0 (RNAseq, WT: n = 3, cKO: n = 4 biological replicates). d GRIP1 peaks from Fig. were annotated to their closest gene using ChIPseeker, and overlap with GRIP1-independent ( n = 1516) or -dependent ( n = 432) DEGs from ( c ) was determined for all unique peaks. A bar graph shows the % (and number) of genes in each subset associated with IL4- and/or Dex-induced peaks. The P -value for overrepresentation was determined by bootstrapping samples from the whole GRIP1 peak atlas to determine how often a set of N peaks would contain the observed overlap with each gene list by chance. e Volcano plot shows DEGs in GRIP1 cKO vs. WT in M2 IL4 (left) and M2 Dex (right) relative to M0 of each genotype. (FC ≥ 1.5, unadjusted p -value < 0.05). Selected inflammation-related genes expressed at higher levels in the cKO M2 IL4 and M2 Dex relative to WT are highlighted in red. Key M2 target genes downregulated in the cKO are highlighted in both M2 IL4 (orange) and M2 Dex (green). Examples of the shared M2 IL4 :M2 Dex GRIP1 target genes are underlined. f Differentially regulated pathways (unadjusted p < 0.01 defined as in Fig. ) identified using QuSAGE with MsigDB canonical pathways subset (Broad Institute) are shown for GRIP1 cKO vs. WT in M2 IL4 (left) and M2 Dex (right). Select pathways are labeled (upregulated, red; downregulated, orange for IL4 and green for Dex); M2 IL4 :M2 Dex -shared pathways are underlined. Circle size is proportional to the number of genes in the pathway, and color signifies the p -value. Source data are provided as a Source data file.

Article Snippet: One-tailed unpaired t test; p -values are shown; ns, non-significant ( p ≥ 0.05). n = 4 biological replicates (mice), error bars are SEM. d Differentially regulated pathways (unadjusted p < 0.01; see ref. . equations 14-15) identified using QuSAGE and MsigDB canonical pathways (c2.cp.v7.3, Broad Institute) are shown for M2 IL4 (top) and M2 Dex (bottom).

Techniques: Expressing, Quantitative RT-PCR, One-tailed Test, Labeling