Human Gene Set: NABA_PROTEOGLYCANS

For the Mouse gene set with the same name, see NABA_PROTEOGLYCANS

Standard name NABA_PROTEOGLYCANS
Systematic name M5882
Brief description Genes encoding proteoglycans
Full description or abstract One hallmark of ECM proteins is their domain-based structure. Exploiting this characteristic, we established a list of diagnostic InterPro domains commonly found in ECM proteins. This domain list was used to screen the UniProt protein database. We know that some of the domains used to select positively for ECM proteins are also found in transmembrane receptors and proteins involved in cell adhesion (growth factor receptors, integrins, etc) that do not belong to the ECM. These families of proteins also display a subset of specific domains and transmembrane domains incompatible with definition as ?extracellular matrix? proteins. Therefore, a second step comprised a negative selection using another set of domains and a transmembrane domain prediction. Manual curation of the matrisome lists also allowed us to add a very few known ECM proteins that do not contain any known domains. Protein-centric predictions were then converted to gene-centric lists. Finally, knowledge-based annotation of these gene lists allowed us to define subcategories within the core matrisome; namely, ECM glycoproteins, collagens, and proteoglycans. We also defined separate lists of domains commonly found in 1) ECM-affiliated proteins (proteins that share either some architectural similarities with ECM proteins or that are known to be associated with ECM proteins; 2) ECM regulators: ECM-remodeling enzymes, crosslinkers, proteases, regulators etc.; 3) secreted factors, many of which are known to bind to ECM and others that may. As for the core matrisome list, we also defined lists of domains that excluded mis-assigned proteins from these categories. Using similar bioinformatic pipelines as for the core matrisome, we defined three categories of ?matrisome-associated? proteins: ECM-affiliated proteins, ECM regulators, and secreted factors.
Collection C2: Curated
      CGP: Chemical and Genetic Perturbations
Source publication Pubmed 22159717   Authors: Naba A,Clauser KR,Hoersch S,Liu H,Carr SA,Hynes RO
Exact source  
Related gene sets (show 13 additional gene sets from the source publication)

(show 53 gene sets from any of these authors)
External links http://matrisome.org
Filtered by similarity ?
Source species Homo sapiens
Contributed by Alexandra Naba (Massachusetts Institute of Technology)
Source platform or
identifier namespace		 HGNC_ID
Dataset references  
Download gene set format: grp | gmt | xml | json | TSV metadata
Compute overlaps ? (show collections to investigate for overlap with this gene set)
Compendia expression profiles ? NG-CHM interactive heatmaps
(Please note that clustering takes a few seconds)
GTEx compendium
Human tissue compendium (Novartis)
Global Cancer Map (Broad Institute)
NCI-60 cell lines (National Cancer Institute)

Legacy heatmaps (PNG)
GTEx compendium
Human tissue compendium (Novartis)
Global Cancer Map (Broad Institute)
NCI-60 cell lines (National Cancer Institute)
Advanced query Further investigate these 35 genes
Gene families ? Categorize these 35 genes by gene family
Show members (show 35 source identifiers mapped to 35 genes)
Version history 5.0: First introduced

See MSigDB license terms here. Please note that certain gene sets have special access terms.