gsea java desktop application  (Broad Institute Inc)

Journal: Cells

Article Title: Identification of the Inner Cell Mass and the Trophectoderm Responses after an In Vitro Exposure to Glucose and Insulin during the Preimplantation Period in the Rabbit Embryo

doi: 10.3390/cells11233766

Figure Lengend Snippet: Significantly enriched gene sets (FDR < 0.05) in ICM and TE transcriptomes of in vitro-developed blastocysts with HI compared to CNTRL. Significantly enriched gene sets were identified by GSEA with the Molecular Signature Database (MSigDB) gene set collections: Hallmarks, KEGG, Reactome, and GO BP. GSEA was followed by SUMER analysis for gene set condensation. ( A ). Pie charts showing the enriched gene sets in HI ICM versus CNTRL ICM. ( B ). Pie charts showing the enriched gene sets in HI TE versus CNTRL TE. ICM, inner cell mass. TE, trophectoderm.

Article Snippet: Gene Set Enrichment Analysis (GSEA) [ ] was performed using the GSEA Java Desktop application (v4.0.3) from the Broad Institute.

Techniques: In Vitro

Journal: Cells

Article Title: Identification of the Inner Cell Mass and the Trophectoderm Responses after an In Vitro Exposure to Glucose and Insulin during the Preimplantation Period in the Rabbit Embryo

doi: 10.3390/cells11233766

Figure Lengend Snippet: Significantly enriched gene sets (FDR < 0.05) in ICM and TE transcriptomes of in vitro-developed blastocysts with HG compared to CNTRL. Significantly enriched gene sets were identified by GSEA with the Molecular Signature Database (MSigDB) gene set collections: Hallmarks, KEGG, Reactome, and GO BP. GSEA was followed by SUMER analysis for gene set condensation. ( A ). Pie charts showing the enriched gene sets in HG ICM versus CNTRL ICM. ( B ). Pie charts showing the enriched gene sets in HG TE versus CNTRL TE. ICM, inner cell mass. TE, trophectoderm.

Article Snippet: Gene Set Enrichment Analysis (GSEA) [ ] was performed using the GSEA Java Desktop application (v4.0.3) from the Broad Institute.

Techniques: In Vitro

Journal: Cells

Article Title: Identification of the Inner Cell Mass and the Trophectoderm Responses after an In Vitro Exposure to Glucose and Insulin during the Preimplantation Period in the Rabbit Embryo

doi: 10.3390/cells11233766

Figure Lengend Snippet: Significantly enriched gene sets (FDR < 0.05) in the ICM and TE transcriptomes of in vitro-developed blastocysts with HGI compared to CNTRL. Significantly enriched gene sets were identified by GSEA with the Molecular Signature Database (MSigDB) gene set collections: Hallmarks, KEGG, Reactome, and GO BP. GSEA was followed by SUMER analysis for gene set condensation. ( A ). Pie charts showing the enriched gene sets in HGI ICM versus CNTRL ICM. ( B ). Pie charts showing the enriched gene sets in HGI TE versus CNTRL TE. ICM, inner cell mass. TE, trophectoderm.

Article Snippet: Gene Set Enrichment Analysis (GSEA) [ ] was performed using the GSEA Java Desktop application (v4.0.3) from the Broad Institute.

Techniques: In Vitro

Journal: International Journal of Molecular Sciences

Article Title: Downregulation of Methionine Cycle Genes MAT1A and GNMT Enriches Protein-Associated Translation Process and Worsens Hepatocellular Carcinoma Prognosis

doi: 10.3390/ijms23010481

Figure Lengend Snippet: Searching for the potential biological processes associated with low expression of MAT1A and GNMT . ( A ) MAT1A and GNMT expressions in paired tumor and adjacent normal tissues in the HCC cases ( n = 42). ( B ) Pearson’s correlation for MAT1A and GNMT expression in the 42 HCC cases. ( C ) Flow chart for searching the candidate biological processes that could be driven by low expression of MAT1A and GNMT ; GSEA was used to process the 42 HCC RNA-seq data. REACTOME_TRANSLATION gene set was found to be significantly enriched in HCC with low MAT1A. The median of mRNA expression level was used as the cutoff point for the dichotomization of MAT1A and GNMT. A score greater than median was defined as “high” expression, whereas a score of less than or equal to median was defined as “low” expression, and the categories further were mapped into GSEA databases. ( D ) and in HCC with low GNMT ( E ). ( F ) Heatmaps of the REACTOME_ TRANSLATION enrichment genes in HCC with high and low MAT1A and GNMT categories ( G ) A total of 71 overlapped genes of the REACTOME_ TRANSLATION gene set that are enriched in both low MAT1A and low GNMT HCC samples.

Article Snippet: This was performed using java GSEA Desktop Application from the Broad Institute at MIT.

Techniques: Expressing, RNA Sequencing

Journal: iScience

Article Title: Intercellular cGAMP transmission induces innate immune activation and tissue inflammation in Trex1 deficiency

doi: 10.1016/j.isci.2021.102833

Figure Lengend Snippet: Delivery of cGAMP from radioresistant cells to immune cells induces tonic IFN and NF-κB signaling in Trex1 deficiency (A) Global gene expression analysis by 3′-mRNA seq. Gene and sample-wise hierarchical clustering based on differentially expressed genes (non-adjusted p value <0.05, n = 660) within the dataset of spleen tissue from Cgas −/− BM and dKO BM mice. Gene expression values are Z score standardized. For visualization purposes Z scores were limited to numbers between −2 and 2. (B) PCA plot of spleen tissue data from Cgas −/− BM and dKO BM mice. PCA is based on differentially expressed genes (non-adjusted p value <0.05, n = 684). (C) Volcano plot indicating transcriptomic changes between Cgas −/− BM and dKO BM mice. Genes with a non-adjusted p value <0.05 and a signed fold change >2 are colored in red (upregulated in Cgas −/− KO BM mice) and blue (upregulated in dKO BM mice). Differentially expressed genes with an adjusted p value < 0.05 are labeled. (D) Normalized Enrichment Scores (NES) of Hallmark gene sets significantly upregulated (FDR q value <0.01) in spleen tissue from Cgas −/− BM mice compared with that from dKO BM mice in a pre-ranked Gene Set Enrichment Analysis (GSEA) based on a metric score calculated by log 2 (fold change) x (-log 10 (p value)). n = 5 mice per group. (E) Percentage of splenic classical monocytes and red pulp macrophages with high expression of IκBα (n = 7 for Cgas −/− BM mice, n = 6 for dKO BM mice). (F) Fold change of p-RelA mean fluorescence intensity (MFI) of classical monocytes and red pulp macrophages in instantly fixed spleens from Cgas −/− BM (n = 7) and dKO BM (n = 6) mice. Individual fold change values were calculated as ΔMFI i = (MFI i , untreated – MFI i , λPP ) divided by the average of ΔMFI i values obtained from dKO BM mice. (G) Histograms display representative results for IκBα staining of gated classical monocytes and red pulp macrophages. Data in bar graphs are represented as mean + SEM. Data in (E-G) are pooled from two independent experiments. Statistically significant differences were determined by two-tailed unpaired Mann-Whitney U test ( ∗ p < 0.05, ∗∗ p < 0.01). See also Figure S2 .

Article Snippet: For gene set enrichment analysis (GSEA) a pre-ranked list was generated based on a metric score calculated by: l o g 2 ( f o l d c h a n g e ) x ( − l o g 10 ( p v a l u e ) ) and applied to the GSEA java desktop application (version 4.0.3) provided by the Broad Institute ( ).

Techniques: Gene Expression, Labeling, Expressing, Fluorescence, Staining, Two Tailed Test, MANN-WHITNEY

Journal: Vaccines

Article Title: A Senescence-Like Cellular Response Inhibits Bovine Ephemeral Fever Virus Proliferation

doi: 10.3390/vaccines9060601

Figure Lengend Snippet: The GSEA results show enriched gene subsets in KEGG pathway with senescence related gene subsets. The data demonstrate FDR value (<0.25) in KEGG pathway at least significance in one experiment group. Side bar in left shows categories of gene subsets.

Article Snippet: To evaluate the biological pathways altered between BEFV-infected BHK-21 cell and mock-infected BHK-21, the Gene Set Enrichment Analysis (GSEA) (Broad Institute, Cambridge, MA, USA, java GSEA Desktop Application version 4.1.0) [ , ] tool was employed.

Techniques: