PLOD2 [The Human Chemical-Genetic Interaction Map Project]

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======= PLOD2 =======


== Gene Information ==
  * **<color #00a2e8>Official Symbol</color>**: PLOD2
  * **<color #00a2e8>Official Name</color>**: procollagen-lysine,2-oxoglutarate 5-dioxygenase 2
  * **<color #00a2e8>Aliases and Previous Symbols</color>**: N/A
  * **<color #00a2e8>Entrez ID</color>**: [[https://www.ncbi.nlm.nih.gov/gene/?term=5352|5352]]
  * **<color #00a2e8>UniProt</color>**: [[https://www.uniprot.org/uniprot/O00469|O00469]]
  * **<color #00a2e8>Interactions</color>**: [[https://thebiogrid.org/search.php?search=PLOD2&organism=9606|BioGRID]]
  * **<color #00a2e8>PubMed articles</color>**: [[https://www.ncbi.nlm.nih.gov/pubmed/?term=gene%20PLOD2|Open PubMed]]
  * **<color #00a2e8>OMIM</color>**: [[https://omim.org/entry/601865|Open OMIM]]

== Function Summary ==
  * **<color #00a2e8>Entrez Summary</color>**:  The protein encoded by this gene is a membrane-bound homodimeric enzyme that is localized to the cisternae of the rough endoplasmic reticulum. The enzyme (cofactors iron and ascorbate) catalyzes the hydroxylation of lysyl residues in collagen-like peptides. The resultant hydroxylysyl groups are attachment sites for carbohydrates in collagen and thus are critical for the stability of intermolecular crosslinks. Some patients with Ehlers-Danlos syndrome type VIB have deficiencies in lysyl hydroxylase activity. Mutations in the coding region of this gene are associated with Bruck syndrome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]. 
  * **<color #00a2e8>UniProt Summary</color>**:  Forms hydroxylysine residues in -Xaa-Lys-Gly- sequences in collagens. These hydroxylysines serve as sites of attachment for carbohydrate units and are essential for the stability of the intermolecular collagen cross-links. {ECO:0000250|UniProtKB:P24802}.

<button type='primary' size='sm' modal='Pfam_Domains'>Pfam Domains</button>
<button type='primary' size='sm' modal='GO_terms'>GO Terms</button>


<modal id='Pfam_Domains' size='lg' title='Pfam Domains'>
|2OG-FeII Oxy|
</modal>

<modal id='GO_terms' size='lg' title='GO Terms'>
|procollagen glucosyltransferase activity|
|hydroxylysine biosynthetic process|
|hydroxylysine metabolic process|
|procollagen-lysine 5-dioxygenase activity|
|peptidyl-lysine hydroxylation|
|rough endoplasmic reticulum membrane|
|L-ascorbic acid binding|
|protein hydroxylation|
|aspartate family amino acid biosynthetic process|
|cellular modified amino acid biosynthetic process|
|collagen fibril organization|
|aspartate family amino acid metabolic process|
|alpha-amino acid biosynthetic process|
|collagen metabolic process|
|cellular amino acid biosynthetic process|
|protein O-linked glycosylation|
|iron ion binding|
|cellular modified amino acid metabolic process|
|alpha-amino acid metabolic process|
|protein glycosylation|
|macromolecule glycosylation|
|glycosylation|
|carboxylic acid biosynthetic process|
|organic acid biosynthetic process|
|cellular amino acid metabolic process|
|peptidyl-lysine modification|
|glycoprotein biosynthetic process|
|extracellular matrix organization|
|response to hypoxia|
|response to decreased oxygen levels|
|response to oxygen levels|
|extracellular structure organization|
|glycoprotein metabolic process|
|supramolecular fiber organization|
|small molecule biosynthetic process|
|carbohydrate derivative biosynthetic process|
|peptidyl-amino acid modification|
|carboxylic acid metabolic process|
|endoplasmic reticulum membrane|
|oxidation-reduction process|
|oxoacid metabolic process|
|endoplasmic reticulum|
|organic acid metabolic process|
|carbohydrate derivative metabolic process|
|response to abiotic stimulus|
|organonitrogen compound biosynthetic process|
|cellular macromolecule biosynthetic process|
|small molecule metabolic process|
|macromolecule biosynthetic process|
|protein-containing complex subunit organization|
</modal>
\\

 === CRISPR Data ===
<button type='primary' size='small' modal='Compound_Hit'>Compound Hit</button>
<button type='default' size='small' modal='Most_Correlated_Genes'>Most Correlated Genes in Chemogenomics</button>
<button type='primary' size='small' modal='Essential_Avana'>Tissues where Essential in the Avana Dataset (DepMap 20Q1)</button>

<modal id='Compound_Hit' size='lg' title='Compound Hit'>
^Screen^Score^
|[[:results:exp230|Epigallocatechin gallate 20μM R05 exp230]]|-1.74|
|[[:results:exp379|MSC2530818 10μM R07 exp379]]|1.72|
|[[:results:exp317|Geldanamycin 0.015 to 0.05μM on day4 R07 exp317]]|1.9|
</modal>

<modal id='Most_Correlated_Genes' size='lg' title='Most Correlated Genes in Chemogenomics'>
No correlation found to any other genes in chemogenomics.
</modal>

<modal id='Essential_Avana' size='lg' title='Tissues where Essential in the Avana Dataset (DepMap 20Q1)'>
Global Fraction of Cell Lines Where Essential: 0/726
^Tissue^Fraction Of Cell Lines Where Essential^
|1290807.0|0/1|
|909776.0|0/1|
|bile duct|0/28|
|blood|0/28|
|bone|0/25|
|breast|0/33|
|central nervous system|0/56|
|cervix|0/4|
|colorectal|0/17|
|esophagus|0/13|
|fibroblast|0/1|
|gastric|0/15|
|kidney|0/21|
|liver|0/20|
|lung|0/75|
|lymphocyte|0/14|
|ovary|0/26|
|pancreas|0/24|
|peripheral nervous system|0/16|
|plasma cell|0/15|
|prostate|0/1|
|skin|0/24|
|soft tissue|0/7|
|thyroid|0/2|
|upper aerodigestive|0/22|
|urinary tract|0/29|
|uterus|0/5|
</modal>

== Essentiality in NALM6  ==
    * **<color #00a2e8>Essentiality Rank</color>**: 13412
    * **<color #00a2e8>Expression level (log2 read counts)</color>**: 1.61 
<button type='primary' size='small' modal='Dist_expr'>Expression Distribution</button>
<modal id='Dist_expr' size='lg' title='PLOD2 Expression in NALM6 Cells: 1.61'>
{{:chemogenomics:nalm6 dist.png?nolink |}}
</modal>