OncoboxPD: human 51 672 molecular pathways database with tools for activity calculating and visualization

Activation of the ERK1/2 molecular pathways and its relation to the pathogenicity of human malignant tumors

“… Schematic representation of the composition of algorithmically built molecular pathways centered around the ERK1 ( A ) and ERK2 ( B ) proteins. The gene products participating in the ERK1 and ERK2 signaling pathways are highlighted in the context of the model of human interactome encompassing 361 654 protein–protein interactions across 64 095 molecular players [ 35 ]. Red dots represent the central nodes of the pathways (ERK1 or ERK2); projections of pathway members are shown in blue and green for the ERK1 and ERK2 molecular pathways, respectively.…”

“…Other nodes are shown in grey, with the rest of the interactome graph shown as a background. Visualized using the Gephi software and ForceAtlas2 algorithm [ 35 ]…”

Activation of the ERK1/2 molecular pathways and its relation to the pathogenicity of human malignant tumors

“… Schematic representation of the composition of algorithmically built molecular pathways centered around the ERK1 ( A ) and ERK2 ( B ) proteins. The gene products participating in the ERK1 and ERK2 signaling pathways are highlighted in the context of the model of human interactome encompassing 361 654 protein–protein interactions across 64 095 molecular players [ 35 ]. Red dots represent the central nodes of the pathways (ERK1 or ERK2); projections of pathway members are shown in blue and green for the ERK1 and ERK2 molecular pathways, respectively.…”

“…Other nodes are shown in grey, with the rest of the interactome graph shown as a background. Visualized using the Gephi software and ForceAtlas2 algorithm [ 35 ]…”

Biomarkers of success of anti-PD-(L)1 immunotherapy for non-small cell lung cancer derived from RNA- and whole-exome sequencing: results of a prospective observational study on a cohort of 85 patients

“…The pathway activation level (PAL) is the metric that reflects the extent of up/downregulation of a pathway in tumor samples under analysis compared to the corresponding normal samples. Positive PAL indicates upregulation of a pathway, zero PAL means no changes in pathway activation, and negative PAL means downregulation ( 30 ). PAL values were previously reported as the biomarkers for various types on non-ICI targeted therapeutics in human cancers such as ramucirumab, trastuzumab, bevacizumab, cetuximab and sorafenib ( 41 – 46 ).…”

Forced Overexpression and Knockout Analysis of SLC30A and SLC39A Family Genes Suggests Their Involvement in Establishing Resistance to Cisplatin in Human Cancer Cells

“…Among them, there was only one differential gene commonly regulated in both cell types—the upregulation of the SLC30A3 gene itself. We also calculated the pathway activation level (PAL) values for 3044 intracellular molecular pathways using the OncoboxPD (Oncobox pathway databank) [ 47 ]. We found 26/127 and 89/125 significantly differentially up/downregulated pathways for the HCT-15 and HuTu80 cell types, respectively.…”

Activation of the ERK1/2 molecular pathways and its relation to the pathogenicity of human malignant tumors

“… Schematic representation of the composition of algorithmically built molecular pathways centered around the ERK1 ( A ) and ERK2 ( B ) proteins. The gene products participating in the ERK1 and ERK2 signaling pathways are highlighted in the context of the model of human interactome encompassing 361 654 protein–protein interactions across 64 095 molecular players [ 35 ]. Red dots represent the central nodes of the pathways (ERK1 or ERK2); projections of pathway members are shown in blue and green for the ERK1 and ERK2 molecular pathways, respectively.…”

“…Other nodes are shown in grey, with the rest of the interactome graph shown as a background. Visualized using the Gephi software and ForceAtlas2 algorithm [ 35 ]…”

Biomarkers of success of anti-PD-(L)1 immunotherapy for non-small cell lung cancer derived from RNA- and whole-exome sequencing: results of a prospective observational study on a cohort of 85 patients

“…The pathway activation level (PAL) is the metric that reflects the extent of up/downregulation of a pathway in tumor samples under analysis compared to the corresponding normal samples. Positive PAL indicates upregulation of a pathway, zero PAL means no changes in pathway activation, and negative PAL means downregulation ( 30 ). PAL values were previously reported as the biomarkers for various types on non-ICI targeted therapeutics in human cancers such as ramucirumab, trastuzumab, bevacizumab, cetuximab and sorafenib ( 41 – 46 ).…”

Forced Overexpression and Knockout Analysis of SLC30A and SLC39A Family Genes Suggests Their Involvement in Establishing Resistance to Cisplatin in Human Cancer Cells

“…Among them, there was only one differential gene commonly regulated in both cell types—the upregulation of the SLC30A3 gene itself. We also calculated the pathway activation level (PAL) values for 3044 intracellular molecular pathways using the OncoboxPD (Oncobox pathway databank) [ 47 ]. We found 26/127 and 89/125 significantly differentially up/downregulated pathways for the HCT-15 and HuTu80 cell types, respectively.…”

Activation of the ERK1/2 molecular pathways and its relation to the pathogenicity of human malignant tumors

“… Schematic representation of the composition of algorithmically built molecular pathways centered around the ERK1 ( A ) and ERK2 ( B ) proteins. The gene products participating in the ERK1 and ERK2 signaling pathways are highlighted in the context of the model of human interactome encompassing 361 654 protein–protein interactions across 64 095 molecular players [ 35 ]. Red dots represent the central nodes of the pathways (ERK1 or ERK2); projections of pathway members are shown in blue and green for the ERK1 and ERK2 molecular pathways, respectively.…”

“…Other nodes are shown in grey, with the rest of the interactome graph shown as a background. Visualized using the Gephi software and ForceAtlas2 algorithm [ 35 ]…”

Biomarkers of success of anti-PD-(L)1 immunotherapy for non-small cell lung cancer derived from RNA- and whole-exome sequencing: results of a prospective observational study on a cohort of 85 patients

“…The pathway activation level (PAL) is the metric that reflects the extent of up/downregulation of a pathway in tumor samples under analysis compared to the corresponding normal samples. Positive PAL indicates upregulation of a pathway, zero PAL means no changes in pathway activation, and negative PAL means downregulation ( 30 ). PAL values were previously reported as the biomarkers for various types on non-ICI targeted therapeutics in human cancers such as ramucirumab, trastuzumab, bevacizumab, cetuximab and sorafenib ( 41 – 46 ).…”

Forced Overexpression and Knockout Analysis of SLC30A and SLC39A Family Genes Suggests Their Involvement in Establishing Resistance to Cisplatin in Human Cancer Cells

“…Among them, there was only one differential gene commonly regulated in both cell types—the upregulation of the SLC30A3 gene itself. We also calculated the pathway activation level (PAL) values for 3044 intracellular molecular pathways using the OncoboxPD (Oncobox pathway databank) [ 47 ]. We found 26/127 and 89/125 significantly differentially up/downregulated pathways for the HCT-15 and HuTu80 cell types, respectively.…”