HumanPSD

HumanPSDTM release 2017.3 is available now

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.

New release

PROTEOME (HumanPSD+TRANSPATH®) release 2017.3

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

  • Integration of new clinical trial (CT) data sources

Integration of new data on clinical trials from clinicaltrials.gov and OpenTrials (https://opentrials.net/), covering studies from, among others, European, Japanese and Australian registries. The number of CT-Disease-Drug assignments increases from 227,170 to 349,417, while the CT-Disease assignments increase from 316,785 to 641,872.

  • Improved user data management

The “storage” link in the “my data” menu loads an overview page with usage space statistics for each stored user data file or result list. Obsolete files can be deleted directly to stay within the allotted user space.

  • Quick search for disease and drug entries

The quick search menu includes now options to search for diseases or drugs by external identifiers, such as MeSH ID, Drugbank ID, or Pubchem CID.

  • Link-out to BRENDA professional – the comprehensive enzyme information system

Locus reports of genes/proteins with enzymatic function now contain links to BRENDA, which can be accessed by users with a valid BRENDA subscription.

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

  • New phosphorylation targets content

1,000 new phosphorylation reactions have been added, describing substrates and their phosphosites for key kinases such as ERK1, SYK, Plk1, and Aurora-A/B.

Free trial

Thank you very much for your interest in our programs!

Please contact us and you will be provided with your free trial version.

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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 2017.3 (download; pdf, 0.72 MB)
HumanPSDTM Features 2017.3 (download; pdf, 0.72 MB)

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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