Journal: BMC Cancer

Article Title: Genomic analysis of DNA repair genes and androgen signaling in prostate cancer

doi: 10.1186/s12885-018-4848-x

Figure Lengend Snippet: Androgen-dependent transcriptional responses of prostate cancer cell lines. a RT-qPCR shows androgen treatment (2 nM R1881, 12 h) induces FKBP5 , ABCC4 , EAF2 , and PIAS1 expression in PC3-AR cells. b Eigengene expression plots from WGCNA of PC3-AR RNA-sequencing. c Venn diagram of all differentially expressed transcripts in PC3-AR, LNCaP, and VCaP cell lines after 2 nM R1881 androgen treatment. Differential fold change was set to the following parameters: > 1.5-fold or < 0.67-fold; adj. p ≤ 0.01. LNCaP and VCaP treatments were conducted for 24 h while PC3-AR data was taken from a 12 h treatment. d Heatmap displaying normalized enrichment scores (NES) generated from a pre-ranked Gene Set Enrichment Analysis (GSEA) of androgen-treated prostate cancer cell lines. Standard GSEA methods were limited to the MSigDB hallmarks. e Principal component analysis (PCA) plot of mRNA expression data generated from RNA-sequencing. Data derived from LNCaP, VCaP, and PC3-AR cells before and after androgen treatment

Article Snippet: GSEA (Broad Institute, Inc., release v. 3.0) was used to calculate gene set enrichments [ , ].

Techniques: Quantitative RT-PCR, Expressing, RNA Sequencing, Generated, Derivative Assay

Journal: BMC Cancer

Article Title: Genomic analysis of DNA repair genes and androgen signaling in prostate cancer

doi: 10.1186/s12885-018-4848-x

Figure Lengend Snippet: Reduced expression of multiple DNA repair genes occurs in response to androgen treatment. a Heatmap of DNA damage repair genes in prostate cancer cell line models. RNA-sequencing from untreated and androgen-treated cells were Z-score normalized for the 32 DNA damage repair genes reported by Polkinghorn et al. (2013) and 28 control AR-target genes reported by Hieronymus et al. (2006) . Genes in bold indicate differential regulation across all three cell lines. b Heatmap of DESeq2 log2 fold changes of DNA damage repair genes in prostate cancer cell line models. c GSEA of the RNA-seq data from prostate cancer lines, limited to the 32- DNA repair gene set signature

Article Snippet: GSEA (Broad Institute, Inc., release v. 3.0) was used to calculate gene set enrichments [ , ].

Techniques: Expressing, RNA Sequencing, Control

Journal: Journal of Oncology

Article Title: Expression Profiles of HOXC6 Predict the Survival of Glioblastoma Patients and Correlate with Cell Cycle

doi: 10.1155/2022/8656865

Figure Lengend Snippet: GO cellular component analysis and KEGG pathway enrichment analysis. (a) Merged top 5 GO terms enriched either in DEGs or genes highly correlated with HOXC6. (b) Merged top 5 KEGG pathways enriched either in DEGs or genes highly correlated with HOXC6. (c) Yellow circles represent the top 5 GO cellular components enriched in genes highly correlated with HOXC6, whereas brown circles represent the enriched genes. (d) KEGG pathway analysis based on genes highly correlated with HOXC6. Colored rectangles represent the highly correlated genes, and the color bar indicates the log2-fold change of genes between the high-expression group and the low-expression group of HOXC6. GSEA and heat map represents GSEA results. (e) GSEA was performed in patients sorted by HOXC6 expression value. Above: biological process, genes associated with positive regulation of cell cycle process, cell cycle, and mitotic cell cycle are enriched in patients with high levels of HOXC6 expression; center: cellular component, genes associated with spindle midzone, condensed nuclear chromosome, and condensed chromosome are enriched in patients with high levels of HOXC6 expression; below: KEGG pathway, genes associated with cell cycle, mismatch repair, and proteasome pathways are enriched in patients with high levels of HOXC6 expression. The horizontal bar in graded color from red to blue represents the rank ordering of patients based on decreasing levels of HOXC6 expression. Vertical black lines represent the projection of individual genes constituting relevant gene sets. (f) Heat map showing enriched genes from the GSEA gene sets of in combination with the HOXC6 expression value. DEG: differentially expressed gene; COR: highly correlated gene.

Article Snippet: The GSEA (gene set enrichment analysis) was performed using Gene Set Enrichment Analysis v3.0 software downloaded from the Broad Institute ( http://www.broadinstitute.org/gsea ).

Techniques: Expressing

Journal: PLoS Pathogens

Article Title: Ablation of non-coding RNAs affects bovine leukemia virus B lymphocyte proliferation and abrogates oncogenesis

doi: 10.1371/journal.ppat.1008502

Figure Lengend Snippet: (A) Enrichment map of Gene Set Enrichment Analysis (GSEA) generated by Cytoscape. Displayed sets contain between 15 and 500 genes that are enriched with a false discovery rate less than 0.001 (FDR < 0.001). Red nodes symbolize enriched GO gene sets. Node size indicates the total number of genes in each gene set. Edge thickness (blue line) indicates the number of overlapping genes between gene sets computed based on Jaccard coefficient. (B) Chord diagram of enriched gene sets in B cells from pBLV-WT-infected sheep based on family wise-error rate less than 0.001 (FWER < 0.001). The segment represents the GO gene sets and the ribbon highlights the similarity between them.

Article Snippet: For the identification of enriched transcriptomic signatures, differential gene expression list was loaded on the gene set enrichment analysis (GSEA) tool (v3.0) from the Broad Institute at MIT [ ].

Techniques: Generated, Infection

Journal: Journal for Immunotherapy of Cancer

Article Title: Respiratory complex I regulates dendritic cell maturation in explant model of human tumor immune microenvironment

doi: 10.1136/jitc-2023-008053

Figure Lengend Snippet: Complex 1 inhibition contributes to DC activation and CD4+T cell proliferation. (A) Representative flow cytometry histogram of median fluorescence intensity of CD163 of monocyte-derived macrophages following treatment. (B) Quantification of (A) from monocyte-derived macrophages of four biologically independent PBMC donors. (C) Representative flow cytometry histogram of median fluorescence intensity of CD206 of monocyte-derived macrophages following treatment. (D) Quantification of (C) from monocyte-derived macrophages of four biologically independent PBMC donors. (E) Gene Set Enrichment Analysis comparison of differentially expressed genes between 10 mM metformin and control-treated PBMC-derived dendritic cells from n=6 biologically independent PBMC donors. (F) Flow cytometry gating guide of HLA-DR and CD86 high-expressing DCs which are referred to as “activated DCs”. (G) Quantification of the percentage of activated DCs following treatment from n=4 monocyte-derived DC samples with significant increase in surface expression of CD86 and HLA-DR following metformin (p=0.0226) and venetoclax+metformin (p=0.0014) treatments (H) seahorse extracellular flux assay of monocyte-derived DCs (n=3, referred to as P1, P2, P3). Data points with the same label are technical repeats. Data shows that 24 hours metformin treatment shifts the energy requirements of DCs from aerobic to glycolytic. (I) Quantification of DC activation following a larger panel of treatments with significant DC activation following 2.5 nM IACS-010759 (p=0.0287), 10 nM rotenone (p=0.0105), and 30 nM rotenone (p=0.0309 (J) representative T-cell proliferation plot. G0 refers to the undivided generation, with each increasing G number referring to the number of proliferative cycles (K) flow cytometry analysis of CD4+T cell proliferation index indicating the proportion of the proliferating samples that keep proliferating (G1–G4) with significant increases in CD4+T cell proliferation following 5 mM metformin (p=0.0043) and 10 nM rotenone (p=0.0161) treatments. All data are presented as mean values±SD. Statistical significance was tested with a one-way analysis of variance with Fisher’s exact test. DC, dendritic cell; FDR, false discovery rate; FSC-A, forward scatter area; GSEA, gene set enrichment analysis; HLA-DR, human leukocyte antigen- DR isotype; MFI, median fluorescence intensity;PBMC, peripheral blood mononuclear cells; PDEC, patient-derived explant culture; SSC-a, side scatter area.

Article Snippet: The Gene Set Enrichment Analysis (GSEA) V.3.0 (Broad Institute) was used to analyze the differences in the gene expression profiles.

Techniques: Inhibition, Activation Assay, Flow Cytometry, Fluorescence, Derivative Assay, Comparison, Control, Expressing, XF Assay

Journal: eLife

Article Title: Identification of functionally distinct fibro-inflammatory and adipogenic stromal subpopulations in visceral adipose tissue of adult mice

doi: 10.7554/eLife.39636

Figure Lengend Snippet:

Article Snippet: Software, algorithm , Gene Set Enrichment Analysis v3.0 , Broad Institute , RRID: SCR_003199 , .

Techniques: Blocking Assay, Membrane, Recombinant, SYBR Green Assay, Multiplex Assay, Isolation, Software