transcriptome data of human cancer cell lines (ccls)  (Broad Institute Inc)

Journal: International Journal of Clinical Practice

Article Title: Machine Learning-Based Integrated Analysis of PANoptosis Patterns in Acute Myeloid Leukemia Reveals a Signature Predicting Survival and Immunotherapy

doi: 10.1155/2024/5113990

Figure Lengend Snippet: Identification of the diverse patterns based on the PANoptosis gene list. (a) A total of 226 PANoptosis-related genes belonging to necroptosis, apoptosis, and pyroptosis were collected for downstream analysis. (b) The univariate Cox regression analysis and Spearman's sum rank test were performed in the HOVON cohort, which was set as the training cohort. 28 genes with prognostic prediction were screened out with p value <0.05. (c) An interaction network of prognostic PANoptosis-related genes. (d) The 618 patients in HOVON cohort were divided into three clusters, according to the consensus clustering analysis based on the transcriptome profile of PANoptosis-related genes. (e) The KM curves showing the differential overall survival among the three subgroups. (f) A heat map showing the expression of the prognostic PANoptosis related genes in different subgroups. The two-sided p value <0.05 was considered significant for all statistical analyses and shown as ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001, and ∗∗∗∗ p < 0.0001.

Article Snippet: Transcriptome data of human cancer cell lines (CCLs) were downloaded from the Broad Institute-Cancer Cell Line Encyclopedia project (CCLE, https://sites.broadinstitute.org/ccle/ ) and the CERES scores, the score to evaluate the dependency of the certain gene in the CCL, which indicated that the score was negative correlation with the possible significance of the gene in cell proliferation of the certain CCL, were downloaded from the dependency map portal (DepMap, https://depmap.org/portal/ ).

Techniques: Expressing

Journal: Scientific Reports

Article Title: Evolution from adherent to suspension: systems biology of HEK293 cell line development

doi: 10.1038/s41598-020-76137-8

Figure Lengend Snippet: Comparisons of genomic and transcriptomic profiles of HEK293 cells showed taxonomic divergence between parental HEK293 and progeny cell lines. ( a ) A schematic overview of the lineage relationship of the six HEK293 cell lines used in this study. Blue dots represent adherent cells whereas grey dots represent suspension cell lines. ( b ) Genomic comparison between HEK293 cell lines based on Spearman correlation coefficients of read counts. Darker blue color indicates higher correlation. ( c ) Sample-to-sample comparison between transcriptomes illustrated by a heatmap and hierarchical clustering of taxonomical divergence between samples. Darker blue color indicates shorter Euclidean distance between samples and more similarity. ( d ) PCA plot showing the separation in expression pattern between samples. ( e ) RNA expression levels (in DESeq2 median of ratios) and standard deviations (n = 3) of stably integrated viral genes (EBNA-1, Large T, E1A and E1B) in HEK293 cell lineages determined by RNA sequencing.

Article Snippet: Figure 6 Gene expression validation of the 38 previously identified differentially expressed genes in 63 human cell lines, identified nine significantly differentially expressed genes between suspension and adherent cell lines. ( a ) PCA transcriptomic data of 63 human cell-lines from the Human Protein Atlas shows a clear separation of suspension and adherent cell lines from different tissues. ( b ) Range of normalized counts in HPA cell lines for each of the previously identified 38 genes, differentially expressed between all adherent and suspension HEK293 cell lines.

Techniques: Suspension, Comparison, Expressing, RNA Expression, Stable Transfection, RNA Sequencing

Journal: Scientific Reports

Article Title: Evolution from adherent to suspension: systems biology of HEK293 cell line development

doi: 10.1038/s41598-020-76137-8

Figure Lengend Snippet: Gene expression validation of the 38 previously identified differentially expressed genes in 63 human cell lines, identified nine significantly differentially expressed genes between suspension and adherent cell lines. ( a ) PCA transcriptomic data of 63 human cell-lines from the Human Protein Atlas shows a clear separation of suspension and adherent cell lines from different tissues. ( b ) Range of normalized counts in HPA cell lines for each of the previously identified 38 genes, differentially expressed between all adherent and suspension HEK293 cell lines. The black line in each box shows median of normalized counts for the gene. ( c ) Genes that are differentially expressed between adherent and suspension cells using a Mann–Whitney U-test, with p-values < 0.01, are highlighted in purple, where length of bars shows logarithmic fold change of median between two groups and the color of bars denotes degree of significance of p-value. Non-significant genes have gray bars.

Article Snippet: Figure 6 Gene expression validation of the 38 previously identified differentially expressed genes in 63 human cell lines, identified nine significantly differentially expressed genes between suspension and adherent cell lines. ( a ) PCA transcriptomic data of 63 human cell-lines from the Human Protein Atlas shows a clear separation of suspension and adherent cell lines from different tissues. ( b ) Range of normalized counts in HPA cell lines for each of the previously identified 38 genes, differentially expressed between all adherent and suspension HEK293 cell lines.

Techniques: Gene Expression, Biomarker Discovery, Suspension, MANN-WHITNEY