The Human Protein Atlas as a proteomic resource for biomarker discovery

Pontén, Fredrik; Schwenk, Jochen M.; Asplund, Anna; Edqvist, Per‐Henrik

doi:10.1111/j.1365-2796.2011.02427.x

Cited by 240 publications

(207 citation statements)

References 95 publications

(117 reference statements)

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“…specific antibodies on a global scale combining high-throughput generation of affinity-purified polyclonal antibodies with immunohistochemistry-based protein profiling on tissue and cell microarrays (Ponten et al, 2011). All protein expression data, are published on the free and publically available Human Protein Atlas portal (www.proteinatlas.org; Uhlen et al, 2005Uhlen et al, , 2010.…”

Section: Discussionmentioning

confidence: 99%

Paladin (X99384) is expressed in the vasculature and shifts from endothelial to vascular smooth muscle cells during mouse development

Wallgard

Nitzsche

Larsson

et al. 2012

Developmental Dynamics

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Background: Angiogenesis is implicated in many pathological conditions. The role of the proteins involved remains largely unknown, and few vascular‐specific drug targets have been discovered. Previously, in a screen for angiogenesis regulators, we identified Paladin (mouse: X99384, human: KIAA1274), a protein containing predicted S/T/Y phosphatase domains. Results: We present a mouse knockout allele for Paladin with a β‐galactosidase reporter, which in combination with Paladin antibodies demonstrate that Paladin is expressed in the vasculature. During mouse embryogenesis, Paladin is primarily expressed in capillary and venous endothelial cells. In adult mice Paladin is predominantly expressed in arterial pericytes and vascular smooth muscle cells. Paladin also displays vascular‐restricted expression in human brain, astrocytomas, and glioblastomas. Conclusions: Paladin, a novel putative phosphatase, displays a dynamic expression pattern in the vasculature. During embryonic stages it is broadly expressed in endothelial cells, while in the adult it is selectively expressed in arterial smooth muscle cells. Developmental Dynamics 241:770–786, 2012. © 2012 Wiley Periodicals, Inc.

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Section: Discussionmentioning

confidence: 99%

Paladin (X99384) is expressed in the vasculature and shifts from endothelial to vascular smooth muscle cells during mouse development

Wallgard

Nitzsche

Larsson

et al. 2012

Developmental Dynamics

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“…The need for a wider range of less expensive affinity reagents is the subject of several large development programs. The Human Protein Atlas Project has developed a genecentered pipeline for the systematic generation and validation of affinity-purified polyclonal antibodies [41,101]. The starting point for this pipeline is the identification in silico of 80-100 amino acid epitope tags that have low homology with other proteins.…”

Section: The Systematic Generation Of More Affinity Moleculesmentioning

confidence: 99%

Sensitivity and specificity: twin goals of proteomics assays. Can they be combined?

Wilson¹

2013

Expert Review of Proteomics

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“…Immunohistochemistry plays vital role in histological diagnosis, and the immunohistochemical markers could be used for estimating prognosis and predicting therapy response (Ordóñez, 2013). The HPA is built based on immunohistochemistry data, and provides a reliable proteomic resource for biomarker discovery (Pontén et al, 2011). It is a powerful platform not only to provide immunohistochemical mapping but also to provide quantitative protein expression profiles across different tissues.…”

Section: Introductionmentioning

confidence: 99%

Novel bioinformatic identification of differentially expressed tissue-specific and cancer-related proteins from the Human Protein Atlas for biomarker discovery

2015

Genet. Mol. Res.

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ABSTRACT. Identification of cancer-associated and tissue-specific proteins is important for research on carcinogenesis mechanisms and biomarker discovery. Here we performed a new strategy to identify candidate cancer proteins by mining immunohistochemistry protein profiles. Proteins with quantitative values from 14 normal tissues and their corresponding cancer tissues were compared and analyzed using bioinformatics. The final results included identification of tissue-specific proteins and differentially expressed proteins in different cancer types that are primarily involved in energy metabolism and cell invasion. From the tissue-specific proteins, secreted and membrane proteins were further screened and functionally clustered. These primarily belonged to the gene families of endogenous ligands, cluster of differentiation molecules, and solute carriers, and were mainly involved in the processes of cell motility, hormone metabolism, adhesion, and transport. Further studies are warranted to validate the candidates identified herein and substantiate the suggested enriched functions. The results 4557-4565 (2015) from this study might provide a reliable resource to study underlying carcinogenesis mechanisms and discover potential cancer targets for the development of therapeutic targets and of early diagnosis and disease response markers.

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The Human Protein Atlas as a proteomic resource for biomarker discovery

Abstract: Abstract. Pontén F, Schwenk JM, Asplund A, Edqvist P-HD

Cited by 240 publications

References 95 publications

Paladin (X99384) is expressed in the vasculature and shifts from endothelial to vascular smooth muscle cells during mouse development

Paladin (X99384) is expressed in the vasculature and shifts from endothelial to vascular smooth muscle cells during mouse development

Sensitivity and specificity: twin goals of proteomics assays. Can they be combined?

Novel bioinformatic identification of differentially expressed tissue-specific and cancer-related proteins from the Human Protein Atlas for biomarker discovery

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