Journal: Nucleic Acids Research

Article Title: Gene set selection via LASSO penalized regression (SLPR)

doi: 10.1093/nar/gkx291

Figure Lengend Snippet: TCGA gene expression results

Article Snippet: For the mutation data, only MGSA selected the EGFR-related pathways PID_TCPTP_PATHWAY, BIOCARTA_TEL_PATHWAY and BIOCARTA_HER2_PATHWAY or the Interleukin signaling pathways REACTOME_IL_2_SIGNALING, BIOCARTA_IL7_PATHWAY and REACTOME_IL_7_SIGNALING.

Techniques: Expressing

Journal: Nucleic Acids Research

Article Title: Gene set selection via LASSO penalized regression (SLPR)

doi: 10.1093/nar/gkx291

Figure Lengend Snippet: TCGA mutation results

Article Snippet: For the mutation data, only MGSA selected the EGFR-related pathways PID_TCPTP_PATHWAY, BIOCARTA_TEL_PATHWAY and BIOCARTA_HER2_PATHWAY or the Interleukin signaling pathways REACTOME_IL_2_SIGNALING, BIOCARTA_IL7_PATHWAY and REACTOME_IL_7_SIGNALING.

Techniques: Mutagenesis

Journal: Experimental Hematology & Oncology

Article Title: Identifying ADGRG1 as a specific marker for tumor-reactive T cells in acute myeloid leukemia

doi: 10.1186/s40164-024-00560-0

Figure Lengend Snippet: The identification and characteristics of tumor-reactive T cells in AML. A The schema plot for identification of pTRTs. This figure is edited by BioRender.com. B The scatter plot of the tumor enrichment index and clonal expansion index in each CD8 + T cell cluster. The proliferation index is shown in gradient color and the color bar is annotated on the right margin. C Heatmap showing the TCR downstream signal activation level of different clusters. TCR-signaling-related genesets were obtained from https://www.gsea-msigdb.org/gsea/msigdb/ . TCR_sgnl: REACTOME_TCR_SIGNALING, Downstream_TCR_sgnl: REACTOME_DOWNSTREAM_ TCR_SIGNALING, pCD3_and_TCRZ: REACTOME_PHOSPHORYLATION_OF_CD3_AND_TCR_ZETA_CHAINS, Second_messenger: REACTOME_GENERATION_OF_SECOND_MESSENGER_MOLECULES, TCRa_pathway: BIOCARTA_TCRA_PATHWAY, ZAP70_to_immuosynapse: REACTOME_TRANSLOCATION_OF_ZAP_70_TO_IMMUNOLOGICAL_SYNAPSE. D UMAP visualization of clusters annotated by TCR repertoire. Red represents pTRT, blue represents pTRT-relavant cells and the rest of the cells are annotated as pTRT-irrelevant cells in grey. E Bar plot of pTRT-relevant cell frequency in each cluster. F The UMAP plot of tumor-reactive T cells. C0_stem: stem-like cluster, C1_transitory: transitory cluster, C2_TD: terminally differentiated cluster. G Dot plot showing the relative expression of marker genes across different tumor-reactive T cell clusters. Bubble size is proportional to the percentage of cells expressing a gene and color intensity is proportional to average scaled gene expression. H The diffusion map of tumor-reactive T cells. The color annotations are on the right margin. The differential trajectory is indicated by the grey arrow

Article Snippet: TCR_sgnl: REACTOME_TCR_SIGNALING, Downstream_TCR_sgnl: REACTOME_DOWNSTREAM_ TCR_SIGNALING, pCD3_and_TCRZ: REACTOME_PHOSPHORYLATION_OF_CD3_AND_TCR_ZETA_CHAINS, Second_messenger: REACTOME_GENERATION_OF_SECOND_MESSENGER_MOLECULES, TCRa_pathway: BIOCARTA_TCRA_PATHWAY, ZAP70_to_immuosynapse: REACTOME_TRANSLOCATION_OF_ZAP_70_TO_IMMUNOLOGICAL_SYNAPSE.

Techniques: Activation Assay, Translocation Assay, Expressing, Marker, Diffusion-based Assay

Journal:

Article Title: Pathway analysis of breast cancer genome wide association study highlights three pathways and one canonical signaling cascade

doi: 10.1158/0008-5472.CAN-09-4502

Figure Lengend Snippet: A list of pathways associated with breast cancer susceptibility at the p ≤ 0.05 level

Article Snippet: Red broken boxes outline the genes of the RAS/RAF/MAPK canonical signaling cascade table ft1 table-wrap mode="anchored" t5 caption a7 Rank Source Pathway name # genes * P ES † FDR 1 PID Syndecan-1-mediated signaling events 13 0.00053 0.118 2 BioCarta Signaling of hepatocyte growth factor receptor 33 0.00063 0.118 3 BioCarta Growth hormone signaling 22 0.00084 0.118 4 BioCarta Insulin signaling 19 0.00642 0.442 5 KEGG Basal cell carcinoma 53 0.00674 0.487 6 BioCarta Eicosanoid metabolism 19 0.00695 0.515 7 PID Signaling events mediated by Stem cell factor receptor (c-Kit) 50 0.00779 0.515 8 KEGG Tryptophan metabolism 57 0.01516 0.664 9 BioCarta ADP-ribosylation factor 16 0.01800 0.842 10 PID FGF signaling pathway 52 0.02189 0.871 11 KEGG ErbB signaling 86 0.02379 0.871 12 BioCarta ALK in cardiac myocytes 33 0.02747 0.871 13 BioCarta IL-2 receptor beta chain in T cell activation 34 0.03389 0.881 14 BioCarta Intrinsic prothrombin activation 16 0.03600 0.881 15 KEGG Streptomycin biosynthesis 10 0.03600 0.881 16 BioCarta Angiotensin II mediated activation of JNK pathway via Pyk2 dependent signaling 27 0.03663 0.881 17 BioCarta Sprouty regulation of tyrosine kinase signals 15 0.04095 0.881 18 KEGG Maturity onset diabetes of the young 24 0.04547 0.881 19 BioCarta Regulation of hematopoiesis by cytokines 15 0.04568 0.881 20 KEGG Phosphatidylinositol signaling system 75 0.04674 0.881 21 KEGG Melanogenesis 98 0.04747 0.881 Open in a separate window * p-values are computed for the pathway’s enrichment scores (ES) using 10,000 permutations.

Techniques: Activation Assay