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ProteomicsINKA, an integrative analysis pipeline for inference of hyperactive phosphokinases in mass spectrometry-based phosphoproteomics data
As a large proportion of current targeted cancer therapies is based on specific (tyrosine) kinase inhibitors, uncovering the identity of hyperactive kinases at work in tumors is crucial for proper treatment selection. A major challenge in phosphoproteomic data analysis is to relate kinases to the ex...
ORGANISM(S): Homo sapiens (Human) 
2019-04-18 | PXD006616 | Pride
Human Single-shot Tyrosine kinase Phosphokinase ranking Label-free Phosphoproteomics 
ProteomicsThe phosphoproteomic landscape of 16 Acute Myeloid Leukemia (AML) cell lines
Acute myeloid leukemia (AML) is a clonal hematopoietic malignancy, characterized by expansion of immature leukemic blasts in the bone marrow. In AML, specific tyrosine kinases have been implicated in leukemogenesis, and are associated with poor treatment outcome. However, targeted therapy using kina...
ORGANISM(S): Homo sapiens (Human) 
2019-11-11 | PXD007237 | Pride
Human Single-shot Tyrosine kinase Phosphokinase ranking Label-free Phosphoproteomics Acute myeloid leukemia Aml 
ProteomicsHuman testis phosphoproteome reveals kinases as potential targets in spermatogenesis and testicular cancer
Spermatogenesis is a complex cell differentiation process that includes marked genetic, cellular functional and structural changes. It requires tight regulation, since disturbances in any of the spermatogenic stages would lead to fertility deficiencies. In order to increase our knowledge of signal t...
ORGANISM(S): Homo sapiens (Human) 
2019-02-01 | PXD010246 | Pride
Human Testis Single-shot Phosphokinase ranking Label-free Phosphoproteomics 
ProteomicsINKA, an integrative analysis pipeline for inference of hyperactive phosphokinases in mass spectrometry-based phosphoproteomics data: CRC Organoids
CRC Organoid and corresponding PDX data are part of a larger project that includes proteomeXchange accessions PXD006616, PXD008032, and PXD009995. We present a computational pipeline called Integrative Inferred Kinase Activity (INKA) scoring that integrates the observed abundance of phosphopeptides ...
ORGANISM(S): Homo sapiens (Human) 
2019-04-18 | PXD012565 | Pride
Human Single-shot Organoids Phosphokinase ranking Crc Label-free Pdx Phosphoproteomics 
ProteomicsINKA, an integrative analysis pipeline for inference of hyperactive phosphokinases in mass spectrometry-based phosphoproteomics data
this data upload is part of PXD006616. The new data is acquired from human-in-mouse PDX tumor tissue. The data uploaded as PXD006616 was cell line data. The two data sets can be merged into a single PXD accession. The Sample processing and Data processing sections are updated and the corresponding s...
ORGANISM(S): Homo sapiens (Human) 
2019-04-18 | PXD009995 | Pride
Human Single-shot Tyrosine kinase Phosphokinase ranking Label-free Pdx Phosphoproteomics Clinical 
ProteomicsIntegrating phenotypic search and phosphoproteomic profiling of active kinases for optimization of drug mixtures for renal cell carcinoma treatment
Renal cell carcinoma (RCC) is one of the ten most common malignancies. Even though recent paradigm changes led to inclusion of immune checkpoint inhibitor combination therapy in treatment of naive metastatic RCC, insight in the biology and management of RCC would still favour the use of a combinatio...
ORGANISM(S): Homo sapiens (Human) 
2021-09-09 | PXD016475 | Pride
Human Renal cell carcinoma Combination therapy Single-shot Drug selection Phosphokinase ranking Label-free Phosphoproteomics 
ProteomicsOptimized high-order drug mixtures improve colorectal carcinoma treatment via inactivationof MAP kinase signaling pathway and cell cycle alteration
Colorectal carcinoma is currently treated with a combination of chemotherapeutic drugs supplemented with targeted drugs. Since there is an eminent need to improved therapeutic success we employed the phenotypically-driven therapeutically guided multidrug optimization (TGMO) technology to identify pe...
ORGANISM(S): Homo sapiens (Human) 
2021-09-09 | PXD016604 | Pride
Human Combination therapy Ptyr ip Single-shot Phosphoproteomics Drug selection Colorectal carcinoma Phosphokinase ranking Label-free 
ProteomicsUnveiling signaling pathways inducing MHC class II expression in neutrophils
Gram-negative bacillary bacteremia poses a significant threat, ranking among the most severe infectious diseases capable of triggering life-threatening sepsis. Despite the unambiguous involvement of neutrophils in this potentially fatal disease, there are limited data about the molecular signaling m...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
MSV000095939 | MassIVE
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