Journal: The Journal of Biological Chemistry

Article Title: The oxidoreductase CLIC4 is required to maintain mitochondrial function and resistance to exogenous oxidants in breast cancer cells

doi: 10.1016/j.jbc.2022.102275

Figure Lengend Snippet: Loss of CLIC4 in 6DT1 cells is associated with major transcriptional rewiring associated with response to oxidative stress. A , principal component analysis (PCA) using global expression profiles (∼13K genes selected as described in the ) of CLIC4-WT and KO clone sg# 1 untreated (NT) cells or treated with 1 μM H 2 O 2 for 24 h separated by genotype and treatment. B , Venn diagram showing the numbers of overlapping and distinct sets of differentially expressed genes (DEGs) in CLIC4-WT or KO clone sg# 1 6DT1 cells with or without H 2 O 2 treatment. C , gene ontology (GO) circle plot for DEGs between CLIC4-WT and CLIC4-KO 6DT1 cells without treatment and the over-represented GO terms. The outer ring shows a scatter plot of the log2 fold change for each gene under the GO term; red dots indicate the upregulated and blue the downregulated genes. The inner ring is a bar plot, where the height of the bar indicates the significance of the GO term enrichment (−log10 p -value), and the color corresponds to the z-score: blue , decreased; red , increased; and white , unchanged. D , Differentially Expressed Mitochondrial Genes (DEMGs, p < 0.05, >1.5 fold) in CLIC4-KO compared to CLIC4-WT 6DT1 cells without treatment (NT) or treated with 1 μM H 2 O 2 for 24 h. E – G , GSEA leading edge enrichment plot of three significantly regulated hallmark pathways in untreated CLIC4-KO clone sg# 1 compared to CLIC4-WT 6DT1 cells untreated. p value of 0.0 indicates an actual p value of less than 0.01. CLIC4, chloride intracellular channel-4; GSEA, gene set enrichment analysis.

Article Snippet: The analyses were performed using the R programming language [ https://cran.r-project.org/ ], where the Venn diagram and PCA plot were generated using R version 3.5.1 and the NIDAP environment (the NIH Integrative Analysis Platform) [ https://nidap.nih.gov ], and the GO circle plots were generated using R 3.6.3 and RStudio [ https://www.rstudio.com/ ].

Techniques: Expressing

Journal: Data in Brief

Article Title: Transcriptomic dataset of the development and maturation of the Rhipicephalus microplus ovary

doi: 10.1016/j.dib.2024.110661

Figure Lengend Snippet: Representation of homologue genes in different databases, CDS size distribution and transcription factor family classification. A) Venn diagram of the NR, KOG, KEGG, SwissProt, and Interpro databases. Extensive functional overlap can be found among the different databases; however, some genes are only represented in unique databases. B) Length distribution of all unigene CDSs. C) Transcription Factor family classification of unigenes. D) Heatmap showing the distribution of transcription factor expression levels according to tissue. Transcription factor expression clearly clusters ovarian tissue regardless of its maturity (C = Carcass; Male = Undissected intact males; PIO = Preingurgitated Ovary; IO = Ingurgitated ovary; FMIO = Fully Matured Ingurgitated Ovary) separately from males, which are also clearly differentiated from gonadless somatic tissue (carcasses).

Article Snippet: A) Venn diagram of the NR, KOG, KEGG, SwissProt, and Interpro databases.

Techniques: Functional Assay, Expressing

Journal: Virology Journal

Article Title: Performance of BioFire array or QuickVue influenza A + B test versus a validation qPCR assay for detection of influenza A during a volunteer A/California/2009/H1N1 challenge study

doi: 10.1186/s12985-021-01516-0

Figure Lengend Snippet: Venn diagram of BioFire performance versus qPCR. Number of samples positive by qPCR (blue), positive by BioFire (green), or positive by both qPCR and BioFire (yellow). Samples negative for both qPCR and BioFire (grey). Size of circles is proportional to n

Article Snippet: Fig. 1 Venn diagram of BioFire performance versus qPCR.

Techniques:

Journal: G3: Genes|Genomes|Genetics

Article Title: Glucose or Altered Ceramide Biosynthesis Mediate Oxygen Deprivation Sensitivity Through Novel Pathways Revealed by Transcriptome Analysis in Caenorhabditis elegans

doi: 10.1534/g3.116.031583

Figure Lengend Snippet: Venn diagram depicts the number of (A) upregulated transcripts or (B) downregulated transcripts identified between N2 and hyl-2(tm2031) animals fed a glucose diet. (C) Venn diagram depicts the transcripts that are differentially expressed and predicted to produce lipid metabolism proteins. (D) Venn diagram depicts that 199 transcripts are common between the anoxia sensitive animals (N2 glucose-fed and hyl-2(tm2031) animals).

Article Snippet: We used the Gene List Venn Diagram program ( http://genevenn.sourceforge.net ) to identify and compare the lipid metabolism genes that were differentially regulated in hyl-2 ( tm2031 ) animals, glucose-fed hyl-2 ( tm2031 ) animals, and glucose-fed wild-type animals ( , Table S1 , and Table S2 ).

Techniques: