HumanPSD

HumanPSD

 

The Human Proteome Survey Database (HumanPSDTM) is a catalog of proteins and their complexes from human cells, plus their orthologs from mouse and rat sources.
Its main focus is on the association of human proteins with diseases as well as on their potential use as biomarkers.

Drugs targeting human proteins are reported. In addition, information can be retrieved on the molecular functions, biological roles, localization, and modifications of proteins, expression patterns across cells, tissues, organs, and tumors, consequences of gene mutations in mice, and the physical and regulatory interactions between proteins and genes. The TRANSPATH® database on signal transduction and metabolic pathways is an integral part of HumanPSDTM.

Picture of HumanPSD

TP53_HumanPSD
Contents of a standard locus report of HumanPSD

Introduction
Description
Synonyms
Biomarker Associations
Diseases associated with MYC
Inherit MYC mutations
Drug Interactions
Drug(s) targeting MYC
Gene Ontology
Molecular function
Biological process
Cellular component
Expression
Tissue expression

Regulation of MYC expression

Mutant Phenotype

Mutant phenotype of closely related homolog(s)

Pathways & interactions
Pathways
Protein-protein interactions
Events acting on MYC
Events triggered by MYC
Transcriptional Regulation
Add a subscription to TRANSFAC® and this report will display additional information
RNA Features
Overview of RNA sequence
Protein Features
Overview of protein sequence and structure
Post-translational modifications of MYC protein
View complex containing MYC protein
Identifiers
Accessions mapped to this record
Annotations
Description
Editor’s Notes
Disease related

Biomarker / disease associations

A tabular summary of literature-derived relationships between human genes and gene products with human diseases is given.
These associations are clearly sorted according to their type, e.g. whether a gene/protein has a causal relationship with a disease to develop, or whether it is merely correlative, etc.
Disease association MYC

Tabulated summary of disease associations of the human MYC gene.

Key features

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Reports about more than 53,000 proteins and 5000 microRNAs.
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More than 110,000 gene-disease assignments extracted from original scientific literature and evaluated by experts, referring to more than 3,800 diseases (human) or disease models (mouse).
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More than 14,000 drug-protein interactions, referring to more than 8,200 drugs.
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More than 580,000 assignments to Gene Ontology (GO), manually annotated and quality-checked.
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More than 460,000 gene expression assignments.
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More than 950,000 annotation statements given.
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More than 370,000 references to peer-reviewed scientific publications provided.
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An integrated Ontology Browser supports easy selection of defined sets of gene/molecules.
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A tool for functional analysis allows to identify shared characteristics in a set of genes/proteins or miRNAs.
TRANSPATH included!

Benefits

Quickly access detailed reports for individual genes, proteins, miRNAs, diseases,
and drugs without time-consuming literature search.
Uncover biologically relevant connections between seemingly disparate genes,
diseases, and drugs.
Identify and rank potential therapeutic targets based on known functional
characteristics.
Explore canonical pathways and build custom protein networks, overlaying
known disease and drug associations.

Current HumanPSD release

HumanPSD™+TRANSPATH® release 2020.1

The Human Proteome Survey Database (HumanPSDTM) with focus on human proteins as disease biomarkers and drug targets contains these new features:

• External disease identifiers added
External identifiers and hyperlinks to disease classifications and ontologies such as ICD10, Snomed CT or NCI thesaurus have been included based on data from the Mondo Disease Ontology and the Disease Ontology (DO).
In total, 26,615 external references have been added to 2,817 distinct disease reports.

• More Clinical Trial and Biomarker data
New data from clinicaltrials.gov and manual disease biomarker curation by experts have increased the number of CT-Disease-Drug assignments to 424,169 and the number of disease annotations to 333,184.

The TRANSPATH® database on mammalian signal transduction and metabolic pathways contains these new data features:

• Increase in number of reactions
1,450 new binding reactions between proteins in human and in mouse have been added, among them e.g. reactions of the human KRAB zinc finger protein or the mouse GAP/GEF protein interactome.

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Reports

The basic information unit is a “locus report”, which summarizes the existing knowledge about the product(s) of a gene. It is part of a hierarchy, with individual proteins (isoforms such as splice variants) encoded by a gene at a level under the locus report, and summarizing features of the orthologs of human, mouse and rat origin at a higher level.

Information downloads

HumanPSDTM Statistics (download)
HumanPSDTM Features (download)
HumanPSD FlyerTM (download)

Publications

Stegmaier, P., Krull, M., Voss, N., Kel, A.E., Wingender, E. (2010) Molecular mechanistic associations of human diseases. BMC Syst Biol. 4, 124. doi: 10.1186/1752-0509-4-124. PubMed.

Michael, H., Hogan, J., Kel, A., Kel-Margoulis, O., Schacherer, F., Voss, N., Wingender, E. (2008) Building a knowledge base for systems pathology. Brief. Bioinform. 9, 518-531. doi: 10.1093/bib/bbn038. PubMed.

Wingender, E., Crass, T., Hogan, J.D., Kel, A.E., Kel-Margoulis, O.V., Potapov, A.P. (2007) Integrative content-driven concepts for bioinformatics “beyond the cell”. J Biosci. 32, 169-180. PubMed.

Hodges PE, Carrico, P.M., Hogan, J.D., O’Neill, K.E., Owen, J.J., Mangan, M., Davis, B.P., Brooks, J.E., Garrels, J.I. (2002) Annotating the human proteome: the Human Proteome Survey Database (HumanPSD) and an in-depth target database for G protein-coupled receptors (GPCR-PD) from Incyte Genomics. Nucleic Acids Res. 30:137-141. PubMed.

HumanPSD is a trademark of QIAGEN GmbH.
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