Interactome Construction

1 - By localization
The localization can also be combined to a keyword, a tissue or a disease
(e.g. Extracellular molecules implicated in Alzheimer disease)

Extracellular matrix Biomolecules
Secreted Biomolecules
Membrane Biomolecules

2 - By UniProtKB/Swiss-Prot keyword(s)
Select one or several keyword(s) in the list.
All relevant proteins will be displayed with their partners.

Age-related macular degeneration Alport syndrome Alzheimer disease Amyloid Amyotrophic lateral sclerosis Angiogenesis Basement membrane Biomineralization Cell adhesion Chondrogenesis Collagen Collagen degradation Congenital muscular dystrophy Copper Disease mutation EGF-like domain Ehlers-Danlos syndrome Epidermolysis bullosa Glycation Heparan sulfate Heparin-binding Hyaluronic acid Integrin Laminin EGF-like domain Neurodegeneration Metalloprotease Metalloprotease inhibitor Mucopolysaccharidosis Osteogenesis Osteogenesis imperfecta Proteoglycan Stickler syndrome Tissue remodeling Tumor suppressor Zinc

3 - By tissue(s)
Construction of tissue specific interaction networks using mRNA expression data (EST profiles) stored in UniGene. EST (Expressed Sequence Tag) profiles are approximate gene expression inferred from EST count and the cDNA library source.
Warning: if the threshold is too high or if the molecule is not present in the tissue, no interaction network will be constructed.

A/Threshold (TPM: Transcripts per million):
≥1 TPM (low) ≥10 TPM ≥100 TPM ≥1000 TPM (high)

B/Select one or several tissue(s) in the list:
adipose_tissue adrenal_gland ascites bladder blood bone bone_marrow brain cervix connective_tissue ear embryonic_tissue esophagus eye heart intestine kidney larynx liver lung lymph lymph_node mammary_gland mouth muscle nerve ovary pancreas parathyroid pharynx pituitary_gland placenta prostate salivary_gland skin spleen stomach testis thymus thyroid tonsil trachea umbilical_cord uterus vascular

Hint: the number of TPM per tissues of the molecules are available in Cytoscape (molecule annotations).

4 - By disease(s)
Construction of disease specific interaction networks using OMIM,
Online Mendelian Inheritance in Man, a database of human genes
and genetic phenotypes.
(e.g. Extracellular molecules implied in Ostegenesis imperfecta)

Enter the EXACT OMIM identifier(s) corresponding to a disease
separated by a ",".



Hint: identifiers can be retrieved on the OMIM website
(no symbols, numbers only)
Example: 166210 for OSTEOGENESIS IMPERFECTA, TYPE IIA

1 - Interaction network of Biomolecule(s)
Enter the EXACT identifier of the Biomolecule(s):
- UniProtKB Accession Number for proteins (P39060),
- MatrixDB identifier for other biomolecules (PFRAG_1_human, GAG_2, MULT_3_human, LIP_1, CAT_2),
separated by a "," for several molecules.

Hint: identifiers can be retrieved using the BioMolecule Search. When browsing MatrixDB then can also be added one at a time to a "shopping cart" type list, which is later transferred automatically here.

1- Direct partners of the Biomolecule(s)
2- Partners of the direct partners

2 - Restricted to tissue-specific partners of Biomolecule(s)
Construction of tissue specific interaction networks using mRNA expression data (EST profiles) stored in UniGene. EST (Expressed Sequence Tag) profiles are approximate gene expression inferred from EST count and the cDNA library source.

Warning: if the threshold is too high or if the molecule is not present in the tissue, no interaction network will be constructed.

A/ Threshold:
(TPM: Transcripts per million)
≥1 TPM (low)
≥10 TPM
≥100 TPM
≥1000 TPM (high)
Hint: the number of TPM per tissues of the molecules are available in Cytoscape (molecule annotations).

B/ Select one or several tissue(s) in the list.
All relevant proteins will be displayed with their partners.

adipose_tissue adrenal_gland ascites bladder blood bone bone_marrow brain cervix connective_tissue ear embryonic_tissue esophagus eye heart intestine kidney larynx liver lung lymph lymph_node mammary_gland mouth muscle nerve ovary pancreas parathyroid pharynx pituitary_gland placenta prostate salivary_gland skin spleen stomach testis thymus thyroid tonsil trachea umbilical_cord uterus vascular