MatrixDB Tutorial

• UniProtKB/Swiss-Prot accession numbers, entry names, common names, synonyms and gene names for the proteins
• MatrixDB accession numbers, common names and synonyms for the others
• ChEBI identifiers for cations, lipids and inorganic compounds and EBI identifiers of complexes for multimers

IMEx IDentifier (IMEx-ID) search

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Biomolecule data:

Protein data

• Entry Name from UniProtKB/Swiss-Prot: another type of identifier for a protein entry (Example: PGBM_HUMAN for P98160). A link to the UniProtKB/Swiss-Prot protein page is provided.
• Common Name: UniProtKB/Swiss-Prot recommended name of the protein (Example: Basement membrane-specific heparan sulfate proteoglycan core protein for P98160).
• Other name(s) or identifier(s) indicated in UniProtKB/Swiss-Prot: alternative names of the protein (Example: HSPG, Perlecan, PLC for P98160).
• Species: NCBI taxonomy identifier for species, followed by the scientific and the common names (Example: 9606, Homo sapiens, Human).
• Gene Name: name(s) of the gene(s) coding for the protein (Example: HSPG2 for P98160).
• Bound covalently to: this term indicates the existence of a covalent link between two biomolecules (e.g. glycosaminoglycan chains are covalently bound to a core protein to form a proteoglycan). Example: Heparan sulfate (HS) for P98160.
• Multimer: clicking on the multimer identifier (MULT_x_species or MULT_x_VARy_species) displays the list of proteins comprising the multimer.
  
• Interaction(s): the data provided are the identifier of the interaction (identifier of the interacting molecules in alphabetical order separated by an underscore), the common name of the partner and the number of experiments showing the interaction. Example: P14543_P98160, Nidogen-1, 5 description(s) for P98160). The identifier of the interaction provides a link to interaction data.
• Protein Data Bank: Protein Data Bank (PDB) identifier of the 3D structure of the protein (Example: 1BNL for Endostatin), and a link to the PDB Web Site.
  
• Bibliography: PubMed IDentifier (PMID) and link to the abstract in PubMed.
• Molecular Weight: calculated according to the amino acid sequence.
• Number of amino acids
• Keywords: UniProtKB/Swiss-Prot keywords (click here to see the complete list). Example: Angiogenesis, Basement membrane, Complete proteome, Direct protein sequencing Disease mutation, Disulfide bond, EGF-like domain, Extracellular matrix, Glycoprotein, Heparan sulfate Immunoglobulin domain, Laminin EGF-like domain, Polymorphism, Proteoglycan, Repeat, Secreted, Signal for P98160.
  Click on the link to see the definition and the category of the keyword, the number of molecules annotated with this keyword and the correspondence to Gene Ontology terms when available.
• MatrixDB Keywords: additional annotations related to localization (example: missing extracellular matrix annotations)
• Protein fragment(s): released by proteolytic cleavage of a full-length molecule, displaying biological activities of their own (Example: Endorepellin (PFRAG_6_human) for P98160). Link to the fragment data in MatrixDB.
• UniGene expression profile(s): UniGene identifier and link to the UniGene Web Site (Example: Hs.517356 for P39060). Each UniGene entry is a set of transcript sequences that come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location. EST profiles show approximate gene expression patterns as inferred from EST counts and the cDNA library sources. Click on the identifier link to see the expression data of a protein.
• OMIM disorder(s): Online Mendelian Inheritance in Man database of human genes and genetic disorders identifier and link to the OMIM Web Site (Example: 166200, OSTEOGENESIS IMPERFECTA, TYPE I, for P02452).
• Human Protein Atlas: The Human Protein Atlas database shows expression and localization of proteins in a large variety of normal human tissues, cancer cells and cell lines. Link to the Human Protein Atlas Web Site (Example: CAB000126 for P02751). The data of the Human Protein Atlas are not available for downloading.
• Gene Ontology: Gene Ontology identifier, term, category, determination method (link available for details), source of the annotation and link to the Gene Ontology Web Site (Example: GO:0001525, angiogenesis (biological_process), IEA, UniProtKB-KW for P98160). Gene Ontology provides a controlled vocabulary to describe proteins according to their molecular function, biological process, and cellular component. Click on the identifier link to see the number of molecules annotated with a GO term and the corresponding UniProtKB/Swiss-Prot keyword.
• InterPro: InterPro identifier, entry name and link to the InterPro Web Site (Example: IPR006210, EGF-like for P98160). InterPro is a database of protein families, domains, repeats and sites in which identifiable features found in known proteins can be applied to new protein sequences. Click on the identifier link to see the number of molecules annotated with the selected term.
• Pfam: Pfam identifier, entry name, number of repetitions and link to the Pfam Web Site (Example : PF00008, EGF, 2 for P98160). The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models. Click on the identifier link to access the number and name of the molecules annotated with this selected term.
  
• KEGG Glycan Binding Protein: KEGG identifier, group, type and link to the KEGG Glycan Binding Protein or Orthology Web Site (Example : K06793, Group 1: Proteoglycan core proteins, C-Type lectins for P13611). The KEGG Glycan Binding Protein database stores different types of glycan binding proteins, organized as KEGG Orthology groups and classified as a functional hierarchy of KEGG BRITE. KEGG BRITE is a collection of hierarchical classifications representing knowledge on various aspects of biological systems. Click on the identifier link to see the number of molecules annotated with the selected term.
  
• Tissue: Description of the tissue where mRNA(s) or the protein(s) is expressed (UniProtKB/Swiss-Prot data).

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Glycosaminoglycan data

• Name of the glycosaminoglycan: Common name given to the glycosaminoglycan (Example: Dermatan_Sulfate).
• Other Name: alternative name(s) given to the glycosaminoglycan (Example: Chondroitin_Sulfate_B for Dermatan Sulfate).
• Chemical structure:  names of the constituent monosaccharides of glycosaminoglycans (Example: Linear repeating units containing D-galactosamine and either L-iduronic acid or D-glucuronic acid for Dermatan Sulfate).
• Tissue(s): tissues containing the glycosaminoglycan (Example: Abundant in skin and is also found in heart valves, tendons and arterial walls for Dermatan Sulfate).
• Bound covalently to: this term indicates the existence of a covalent link between two biomolecules (e.g. glycosaminoglycan chains are covalently bound to a core protein to form a proteoglycan). Example: Heparan sulfate (HS) for P98160.
• MatrixDB Keywords: additional annotations related to localization (example: missing extracellular matrix annotations)
• ChEBI identifier: ChEBI (Chemical Entities of Biological Interest) identifier, and link to the Web Site of CheBI (Example: CHEBI:18376 for Dermatan Sulfate, GAG_3).
• KEGG Compound identifier: KEGG (Kyoto Encyclopedia of Genes and Genomes) Compound identifier, and link to the Web Site of KEGG Compound (Example: C00426 for Dermatan Sulfate, GAG_3). KEGG COMPOUND is a collection of small molecules, biopolymers, and other chemical substances that are relevant to biological systems.
• Interaction(s): the data provided are the identifier of the interaction (identifier of the interacting molecules in alphabetical order separated by an underscore), the common name of the partner and the number of experiments showing the interaction. Example: GAG_1_P35555, Fibrillin-1, 2 description(s) for GAG_1). The identifier of the interaction provides a link to interaction data.
• Bibliography: PubMed IDentifier (PMID) and link to the abstract in PubMed.

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Protein Fragment data

• Name of the fragment: Common name given to the protein fragment (Example: Endostatin for PFRAG_1_human)
• Other name of the fragment: alternative name(s) given to the protein fragment.
• Parent biomolecule(s): biomolecule(s) giving rise to the fragment by proteolytic cleavage (Example: P39060 and NC1-XVIII for PFRAG_1_human). Click on the identifier of the parent molecule to display data its data.
  
• Description of the fragment: Example: C-terminal globular domain NC1 of collagen XVIII for Endostatin.
• Species: NCBI taxonomy identifier for species, followed by the scientific and the common names (Example: 9606, Homo sapiens, Human).
• MatrixDB Keywords: additional annotations related to localization (example: missing extracellular matrix annotations)
• UniProtKB Feature Identifier: UniProtKB identifier of the processed fragment (Example: PRO_0000391621 for Endorepellin) from a protein, and a link to the UniProt Web Site.
  
• Molecular Weight: experimental molecular weight (kDa)
  
• Other information
• Number of amino acids
• Interaction(s): the data provided are the identifier of the interaction (identifier of the interacting molecules in alphabetical order separated by an underscore), the common name of the partner and the number of experiments showing the interaction. Example: P07996_PFRAG_1_human, Thrombospondin-1, 2 description(s) for PFRAG_1_human). The identifier of the interaction provides a link to interaction data.
• Bibliography: PubMed IDentifier (PMID) and link to the abstract in PubMed.

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Cation data

• Name of the Cation: Common name of the cation (Example: Calcium).
• ChEBI: ChEBI (Chemical Entities of Biological Interest) identifier (Example: CHEBI:29108 for Calcium, CAT_3), and a link to ChEBI Web Site.
  
• KEGG Compound identifier: KEGG (Kyoto Encyclopedia of Genes and Genomes) Compound identifier, and link to the Web Site of KEGG Compound (Example: C00076 for Calcium, CAT_3). KEGG COMPOUND is a collection of small molecules, biopolymers, and other chemical substances that are relevant to biological systems.
• MatrixDB Keywords: additional annotations related to localization (example: missing extracellular matrix annotations)
• Interaction(s): the data provided are the identifier of the interaction (identifier of the interacting molecules in alphabetical order separated by an underscore), the common name of the partner and the number of experiments showing the interaction. Example: CAT_3_P09486, SPARC, 6 description(s) for CAT_3). The identifier of the interaction provides a link to interaction data.
• Bibliography: PubMed IDentifier (PMID) and link to the abstract in PubMed.

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Lipid data

• Name of the Lipid: Common name of the lipid (Example: Sulfatide).
• Category: Category of the lipid (Example: Cerebroside for Sulfatide)
• ChEBI: ChEBI (Chemical Entities of Biological Interest) identifier (Example: CHEBI:18318 for Sulfatide, LIP_1), and link to the ChEBI Web Site.
  
• KEGG Compound identifier: KEGG (Kyoto Encyclopedia of Genes and Genomes) Compound identifier, and link to the Web Site of KEGG Compound (Example: C06125 for Sulfatide, LIP_1). KEGG COMPOUND is a collection of small molecules, biopolymers, and other chemical substances that are relevant to biological systems.
• Lipid Maps identifier: Lipid Maps identifier, and link to the "Lipidomics gateway" Web Site formed collaboratively between Nature Publishing Group and the LIPID MAPS consortium (Example: LMSP06020000 for Sulfatide, LIP_1). The LIPID MAPS (Lipid Metabolites and Pathways Strategy) consortium is a multi-institutional effort to further our understanding of lipid metabolism and the role lipids play in diseases such as diabetes, stroke, and cancer.
• MatrixDB Keywords: additional annotations related to localization (example: missing extracellular matrix annotations)
• Interaction(s): the data provided are the identifier of the interaction (identifier of the interacting molecules in alphabetical order separated by an underscore), the common name of the partner and the number of experiments showing the interaction. Example: LIP_1_PFRAG_1_human, Endostatin, 3 description(s) for LIP_1). The identifier of the interaction provides a link to interaction data.
• Bibliography: PubMed IDentifier (PMID) and link to the abstract in PubMed.

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Inorganic compound data

• Name of the compound: Common name of the inorganic compound (Example: Hydroxyapatite).
• Synonym: other name of the inorganic compound (Example: Hydroxylapatite for Hydroxyapatite)
• Definition: definition of the inorganic compound (Example: A phosphate mineral with the formula Ca5(PO4)3(OH) for Hydroxyapatite)
• ChEBI: ChEBI (Chemical Entities of Biological Interest) identifier (Example: CHEBI:52255 for Hydroxyapatite, INORG_1), and link to the ChEBI Web Site.
  
• MatrixDB Keywords: additional annotations related to localization (example: missing extracellular matrix annotations)
• Interaction(s): the data provided are the identifier of the interaction (identifier of the interacting molecules in alphabetical order separated by an underscore), the common name of the partner and the number of experiments showing the interaction. Example: INORG_1_P09486, SPARC, 2 description(s) for INORG_1). The identifier of the interaction provides a link to interaction data.
• Bibliography: PubMed IDentifier (PMID) and link to the abstract in PubMed.

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Multimer data

• Name of the Multimer: Common name of the multimer (Example: Laminin-111).
• Biomolecules involved: UniProtKB/Swiss-Prot identifiers of the individual polypeptides of the multimer (Example: P25391, P07942, P11047 for MULT_1_human).
• Species: NCBI taxonomy identifier for species, followed by the scientific and the common names (Example: 9606, Homo sapiens, Human).
• EBI complex identifier: EBI identifier of complexes corresponding to stable multimers (Example: EBI-2529702 for Laminin-111, MULT_1_human), and a link to the EBI Web Site.
  
• MatrixDB Keywords: additional annotations related to localization (example: missing extracellular matrix annotations)
• Interaction(s): the data provided are the identifier of the interaction (identifier of the interacting molecules in alphabetical order separated by an underscore), the common name of the partner and the number of experiments showing the interaction. Example: GAG_1_MULT_1_human, Heparin, 2 description(s) for MULT_1_human). The identifier of the interaction provides a link to interaction data.
• Bibliography: PubMed IDentifier (PMID) and link to the abstract in PubMed.
• More information

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Interaction data:

• Participants: UniProtKB/Swiss-Prot or MatrixDB identifiers of the biomolecules participating in the interaction, and their common name.
• Interaction/Complex from : HPRD, DIP, IntAct, MINT, BioGRID, MatrixDB curation or SPR experiments.
  
• Experiment(s) : experiments reporting an interaction (one interaction might be reported in several experiments using different detection methods) associated to the data  (HPRD, BioGRID, DIP, IntAct, MINT, MatrixDB curations, SPR experiments). Click on the Experiment link, to obtain more data.
  
• Bibliography: PubMed IDentifier (PMID) of the publication and a link to the abstract in PubMed. Click on the link to display the authors, the title, the journal and date of the publication.

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Experiment data:

HPRD data

• Participant(s): UniProtKB/Swiss-Prot or MatrixDB identifiers of the biomolecules participating in the interaction, and their common names.
• Interaction: Interaction corresponding to the experiment, and a link to the interaction data.
• HPRD Association determined by :  in vitro, in vivo and two hybrid (Human Protein Reference Database). According to HPRD two proteins interact in vivo when proteins are truly interacting in a mammalian cell. An interaction occurs in vitro when the experiment was not performed in the context of a mammalian cell. Yeast 2-hybrid was not annotated as in vivo but two hybrid because the interaction was detected in yeast cells.
• HPRD cross-reference: Link to the HPRD website, with the list of interactions established by the biomolecule.
  
• Bibliography: PubMed IDentifier (PMID) of the publication and a link to the abstract in PubMed.

MatrixDB and other IMEx partners data (MINT, DIP, IntAct, BioGRID)

• Participant(s): UniProtKB/Swiss-Prot or MatrixDB identifiers of the biomolecules participating in the interaction, and their common names.
• Interaction: Interaction corresponding to the experiment, and a link to the interaction data.
• Partner details: biological role, experimental role, participant detection method and experimental species of the biomolecules involved in the interaction.
  Biological role: particular role of the interaction in a biological context (example: an enzyme or an inhibitor).
  Experimental role: role played by the participant in the experiment (example: bait, prey or neutral component).
  Participant detection method: method used to identify the molecules in the experiment (example: identification by antibody, or by protein sequence).
  Experimental species: the NCBI Taxonomy identifier of the species.
  Experimental Molecule: the UniProtKB/Swiss-Prot identifier of the molecule used in the experiment.
  Feature(s): binding sites, mutations modifying the interaction strength, post-traductional modifications required for the interaction, and experimental tags. Feature types are reported with a controlled vocabulary. Start and end positions, status and detection methods of the features are also indicated. Domain names are indicated using InterPro database.
• Host(s) organism(s): organism in which the experiment has been performed. The organism is identified by the NBCI taxonomy identifier (in vitro: -1). Tissue types are identified using controlled vocabulary of BRENDA database (BTO: BRENDA Tissue Ontology), cell types using Cabri database identifiers and Compartments using Gene Ontology.
• IMEx ID of the experiment:  a common identifier allocated by IMEx Central, to the publication (IMEX-x) and to the experiment (IMEX-x-y)
• Experiment modification:  Modifications of the standard experimental method described in the controlled vocabulary
• Positive control:  to be indicated for an interaction used as a positive control.
• Caution:  warning about errors or confusion.
• Confidence:  confidence classification assigned by the author of the publication to a specific interaction.
• [MatrixDB literature curation | MINT | DIP | BioGRID | IntAct], determined by: method used to demonstrate the interaction, respecting the controlled vocabulary. Definitions of the vocabulary terms are available here.
• Interaction type:  physical association, colocalization, direct interaction. Definitions of the vocabulary are available here.
• Binding site(s): free text reporting domains, amino acids involved or post-translational modifications for a protein or a protein fragment, length and sulfation positions for a glycosaminoglycan.
• Affinity (KD)
• Kinetics (ka and kd)
• [MINT | DIP | IntAct | BioGRID] cross-reference: Link to the websites, with additional data on the experiment.
• Figure(s): reporting the interaction in the publication.
• Table(s):  reporting the interaction in the publication.
• Bibliography: PubMed IDentifier (PMID) of the publication and a link to the abstract in PubMed.
• First author and title: of the publication.
• Contact email:  of the corresponding author of the publication.

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Download MatrixDB data:

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Interactome Construction:

• Building complete interaction networks : all the interactome construction modes described below can be combined together. The combinations are restrictive and may in some cases fail to build an interaction network because there is no interaction left during the selection process.
  By cell localization: select "Extracellular matrix biomolecules" to display the interaction network involving all the extracellular biomolecules. Secreted biomolecules and membrane biomolecules can be added to the extracellular matrix interaction network by selecting the corresponding checkboxes.
  By UniProtKB/Swiss-Prot keyword(s): keyword and localization can be combined to build specific networks. Hold down the Ctrl key on the keyboard while clicking to select / deselect keywords.
  By tissues(s): Tissue-specific networks are constructed using UniGene EST (Expressed Sequence Tag) profiles data. EST profiles show approximate gene expression patterns as inferred from EST counts and the cDNA library sources. The threshold (the minimum number of transcripts per million present in a tissue) can be adjusted. Hold down the Ctrl key on the keyboard while clicking to select / deselect tissues.
  By disease(s): The building of disease-specific interaction networks is based on the disease identifier provided by the OMIM database of human genes and genetic disorders. A list of OMIM identifier separated by a "," can also be used to build interaction network of several diseases. Alternatively disease-specific interaction networks are build using UniProtKB keywords when available.
  

• Molecule interaction networks :
  Interaction network of Biomolecule(s): UniProtKB/Swiss-Prot or MatrixDB identifiers (but NOT the common name of the biomolecule) must be used. This data can be retrieven using data on the "Biomolecule report" page, using either the direct link or the cart (see the above explanation). Select either the direct partners of the biomolecule or the direct partners of the biomolecule plus the partners of the direct partners.
  Restricted to tissue-specific partners of Biomolecule(s) : Partners of biomolecule(s) restricted to those present in a tissue above a defined threshold, determinated using UniGene EST profiles.

Upon launching Cytoscape a first message asks which program to use to open the file. This file must be opened with Java Web Start, which is available in the Java Runtime Environment. If this program is not available on your computer, download it here. To run Cytoscape, the execution of the application in the warning panel needs to be accepted (click on run). The certificate issued by the CNRS (french National Scientific Research Institute) is unfortunately not recognized as a trusted source by default.
















The interaction network is displayed using the default visual style, with specific colors for each class of molecules: green for proteins, teal for protein fragments, yellow for lipids, magenta for cations, orange for multimers, and purple for glycosaminoglycans.
Dashed lines ended by an arrow: covalent link between two molecules.
Dashed lines ended by a diamond: link between the protein fragment and its parent biomolecule.
Dashed lines ended by a circle: link between a monomer and a multimer.











Several representations can be selected, including the Organic (Layout->yFiles->Organic), or the Force-Directed (Layout->Cytoscape Layouts->Force-Directed Layout->unweighted) layouts. The force-directed style gives the following graphs for the interaction network of perlecan (level 2)

Visual attributes can be selected in the left panel, in the VizMapper part, or created de novo. Default and localization visual styles have been developped by MatrixDB. For cell localization, extracellular molecules are colored in: blue, secreted molecules

teal: extracellular matrix + membrane.













On the graphs, molecules are identified by UniProtKB/Swiss-Prot or MatrixDB identifiers. Information on the molecules can be displayed by selecting one or several items: GO term - biological process, UniProtKB/Swiss-Prot Common name,

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