links

Find on this page a selection of METAcancer relevant links:

 


Projects supported by the Framework Programmes of the European Commission:

METAcancer is in excellent complementarity with a number of European research projects. For example, large scale biomarker consortia in breast cancer research, such as TRANSBIG or MetaBre have their main focus on predictive transcriptomics. The publicly available data from these projects will be used by METAcancer and linked to our new metabolomic data. Similarly, the consortium "TCAC in Cancer" is investigating the role of the TCA cycle in cancer and thus forms the hypotheses for the translational studies of our consortium. The FP6 project eTUMOUR investigates a decision support system for brain cancer diagnosis based on in-vivo metabolomics by NMR. Our project covers the area of breast cancer and thus translates the comparably well established use of NMR to brain tumor diagnosis to a different type of tumor with the additional use of other complementary techniques, such as GC-MS and LCMS.


Further FP7 projects currently in execution:

 

BASIS
Breast
Cancer
Somatic Genetics Study (BASIS)

COMBINE
From flies to humans combining whole genome screens and tissue specific gene targeting to identify novel pathways involved in cancer and metastases

DDRESPONSE
The DNA damage response and breast cancer

EUROCANPLATFORM
A European Platform for Translational Cancer Research

MAMMASTEM
Molecular mechanisms of the regulation of mammary stem cell homeostasis and their subversion in cancer

RATHER
Rational Therapy for Breast Cancer: Individualized Treatment for Difficult-to-Treat Breast Cancer Subtypes

FLUODIAMON
Ultra-high resolution and ultra-sensitive fluorescence methods for objective sub-cellular diagnosis of early disease and disease progression in breast and prostate cancer

 

 

 

Activities funded by other resources:

The Human Metabolome Project

The Human Metabolome Project is a $7.5 million Genome Canada funded project launched in January 2005. The purpose of the project is to facilitate metabolomics research through several objectives to improve disease identification, prognosis and monitoring; provide insight into drug metabolism and toxicology; provide a linkage between the human metabolome and the human genome; and to develop software tools for metabolomics. 

The project mandate is to identify, quantify, catalogue and store all metabolites that can potentially be found in human tissues and biofluids at concentrations greater than one micromolar. This data will be freely accessible in an electronic format to all researchers through the Human Metabolome Database (www.hmdb.ca). In addition, all compounds will be publicly available through our Human Metabolome Library (www.metabolibrary.ca).  

 

The Human Metabolome Database (HMDB)

The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. It is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education. The database is designed to contain or link three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data. The database currently contains nearly 2500 metabolite entries including both water-soluble and lipid soluble metabolites as well as metabolites that would be regarded as either abundant (> 1 uM) or relatively rare (< 1 nM). Additionally, approximately 5500 protein (and DNA) sequences are linked to these metabolite entries. Each MetaboCard entry contains more than 90 data fields with half of the information being devoted to chemical/clinical data and the other half devoted to enzymatic or biochemical data. Many data fields are hyperlinked to other databases (KEGG, PubChem, MetaCyc, ChEBI, PDB, Swiss-Prot, and GenBank) and a variety of structure and pathway viewing applets. The HMDB database supports extensive text, sequence, chemical structure and relational query searches. Two additional databases, DrugBank and FooDB are also part of the HMDB. DrugBank contains equivalent information on 1500 drugs while FooDB contains equivalent information on 3500 food components and food additives.

 

The Metabolomics Standards Initiative (MSI)

The Metabolomics Society has appointed an Oversight Committee to monitor, coordinate and review the efforts of working groups (WG) in specialist areas that will examine standardization and make recommendations. The overall chair of this committee is Oliver Fiehn. The five MSI WGs, some of which are divided into further subgroups, are listed here:

  • Biological context metadata WGChemical analysis WG
  • Data processing WG
  • Ontology WG
  • Exchange format WG

 

Fiehn databases : SetupX and BinBase

SetupX and BinBase are two different databases that work together in an integrated way. SetupX is used to define experimental designs and also serves as user front end to download results. BinBase filters GC-TOF mass spectrometric data files and annotates compounds either as one of over 713 unique identified compounds with more than 1,100 spectra (http://fiehnlab.ucdavis.edu/Metabolite-Library-2007) or as unknowns, capturing these by database identifier numbers, retention index, mass spectra and further metadata. BinBase is administered by the front end GUI 'Bellerophon' which is only locally accessible in the Fiehn laboratory. BinBase results can therefore only be queried via SetupX.


The Metabolic Portal

  • Company news
  • New products and services
  • Upcoming events
  • Posters from recent meetings
  • Specialist company contacts
  • Latest jobs
  • Links to additional resources
  • Audio presentations from recent conferences

 

The Metabolomics Society

 

 

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