with the precrec R package (https://github.com/evalclass/precrec) using the corresponding “gold standard” and sorting DREEP drug/cell line pairs according to the estimated median cell line enrichment score multiplied by minus one in order to have drugs predicted to be sensitive at the top...
The structural similarity S was computed by one minus dissimilarity measure D. Manifold and classification learning of intercellular communication networks The manifold learning of the inferred intercellular communication networks consists of three steps. First, we built a shared nearest neighbor (SNN) ...
CellBender (v0.2.0)61 was used on ‘raw_feature_bc_matrix’ to remove empty droplets and ambient RNA; scDblFinder (v1.5.11)62 was applied to exclude potential doublets. Downstream analyses were performed as all other included studies (see below)....
In the case of the proliferation assays with genetic knockdowns, proliferation was calculated similarly by normalizing the L of each clone at the end of the experiment minus L at day 0 relative to the L of NTC cells at the end of the experiment minus L at day 0.IC50 was calculated with...
Anchorage of microtubule minus ends to adherens junctions regulates epithelial cell-cell contacts. Cell 135, 948-959 (2008) 90 A. Chausovsky, A. D. Bershadsky and G. G. Borisy: Cadherin-mediated regulation of microtubule dynamics. Nat Cell Biol... W Meng,Y Mushika,T Ichii,... - 《...
In general, integrins mediate cell-matrix or cell-cell adhesion and are involved in transducing signals to regulate transcription and cell growth. The subunit β4 associates with α6, and the resulting integrin α6β4 is a receptor for the laminin family of extracellular matrix proteins. Integrin...
Impaired neurite outgrowth of src-minus cerebellar neurons on the cell adhesion molecule L1. The nonreceptor tyrosine protein kinases pp60 c- src , p590 fyn , and pp62 c- yes are localized in growth cones of developing neurons, but their function ... MA Ignelzi,DR Miller,P Soriano,......
Next, we excluded any nuclei that did not have sufficient TSS enrichment in a sample adaptive fashion by excluding any nuclei with TSS enrichment lower than median TSS enrichment in the sample minus 1 standard deviation. This resulted in the removal of 6,011 nuclei across all samples (Table ...
Head and neck squamous cell carcinoma (HNSCC) is characterized by complex relations between stromal, epithelial, and immune cells within the tumor microenvironment (TME). To enable the development of more efficacious therapies, we aim to study the hetero
92% of matched same minus different correlations were positive. Wilcoxon signed-rank p-value < 0.0001. Full size image We next aimed at extending our computational analysis of simulated data to distinguishing between pairs of communicating cells in experimental data. Our analysis pipeline was ...