Integrin activation terms

[gocentral]

I need some new terms to describe integrin activation, the process of activating an alpha-beta integrin complex to exhibit enhanced binding to specific ligands, and integrin-mediated cell adhesion. The terms are needed for annotation of the reference genome gene Cd24a (PMID:7534304) and will find applicability in annotation of many other genes.

Thanks,

Alex

Ontology structure first, then term definitions.

cellular protein metabolic process ; GO:0044267 --% integrin activation ; GO:NewTer1 ----< regulation of integrin activation ; GO:NewTer2 ------% negative regulation of integrin activation ; GO:NewTer3 ------% positive regulation of integrin activation ; GO:NewTer4

cell surface receptor linked signal transduction ; GO:0007166 --% cell surface receptor linked signal transduction leading to integrin activation ; GO:NewTer5

cell adhesion ; GO:0007155 --% cell adhesion mediated by integrin ; GO:NewTer6 ----< regulation of cell adhesion mediated by integrin ; GO:NewTer7 ------% negative regulation of cell adhesion mediated by integrin ; GO:NewTer8 ------% positive regulation of cell adhesion mediated by integrin ; GO:NewTer9 --% cell-cell adhesion ; GO:0016337 ----% cell-cell adhesion mediated by integrin ; GO:NewTe10 ------< regulation of cell-cell adhesion mediated by integrin ; GO:NewTe11 --------% negative regulation of cell-cell adhesion mediated by integrin ; GO:NewTe12 --------% postive regulation of cell-cell adhesion mediated by integrin ; GO:NewTe13

Of course, you'll have to make all the complicated regulation relationships that I am too lazy to spell out.

Term definitions [Term] id: GO:NewTer1 name: integrin activation exact_synonym: integrin complex activation def: The chemical reactions and pathways involving an integrin, a heterodimeric adhesion receptor formed by the non-covalent association of particular alpha and beta subunits, that lead to the increased affinity of the integrin for its extracellular ligands. [PMID:12213832, PMID:14754902, GOC:add]

[Term] id: GO:NewTer2 name: regulation of integrin activation exact_synonym: regulation of integrin complex activation def: Any process that modulates the frequency, rate, or extent of integrin activation. [GOC:add]

[Term] id: GO:NewTer3 name: negative regulation of integrin activation exact_synonym: negative regulation of integrin complex activation def: Any process that stops, prevents or reduces the frequency, rate, or extent of integrin activation. [GOC:add]

[Term] id: GO:NewTer4 name: positive regulation of integrin activation exact_synonym: positive regulation of integrin complex activation def: Any process that activates or increases the frequency, rate, or extent of integrin activation. [GOC:add]

[Term] id: GO:NewTer5 name: cell surface receptor linked signal transduction leading to integrin activation exact_synonym: cell surface receptor linked signal transduction leading to integrin complex activation def: Any series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell that lead to the increased affinity of an integrin, a heterodimeric adhesion receptor formed by the non-covalent association of particular alpha and beta subunits, for its extracellular ligands. [PMID:12213832, PMID:14754902, GOC:add]

[Term] id: GO:NewTer6 name: cell adhesion mediated by integrin exact synonym: cell adhesion mediated by integrin complex def: The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via an integrin, a heterodimeric adhesion receptor formed by the non-covalent association of particular alpha and beta subunits. [PMID:12213832, PMID:14754902, GOC:add]

[Term] id: GO:NewTer7 name: regulation of cell adhesion mediated by integrin exact synonym: regulation of cell adhesion mediated by integrin complex def: Any process that modulates the frequency, rate, or extent of cell adhesion mediated by integrin. [GOC:add]

[Term] id: GO:NewTer8 name: negative regulation of cell adhesion mediated by integrin exact synonym: negative regulation of cell adhesion mediated by integrin complex def: Any process that stops, prevents or reduces the frequency, rate, or extent of cell adhesion mediated by integrin. [GOC:add]

[Term] id: GO:NewTer9 name: positive regulation of cell adhesion mediated by integrin exact synonym: positive regulation of cell adhesion mediated by integrin complex def: Any process that activates or increases the frequency, rate, or extent of cell adhesion mediated by integrin. [GOC:add]

[Term] id: GO:NewTe10 name: cell-cell adhesion mediated by integrin exact synonym: cell-cell adhesion mediated by integrin complex def: The attachment of one cell to another cell via an integrin, a heterodimeric adhesion receptor formed by the non-covalent association of particular alpha and beta subunits. [PMID:12213832, PMID:14754902, GOC:add]

[Term] id: GO:NewTe11 name: regulation of cell-cell adhesion mediated by integrin exact synonym: regulation of cell-cell adhesion mediated by integrin complex def: Any process that modulates the frequency, rate, or extent of cell-cell adhesion mediated by integrin. [GOC:add]

[Term] id: GO:NewTe12 name: negative regulation of cell-cell adhesion mediated by integrin exact synonym: negative regulation of cell-cell adhesion mediated by integrin complex def: Any process that stops, prevents or reduces the frequency, rate, or extent of cell-cell adhesion mediated by integrin. [GOC:add]

[Term] id: GO:NewTe13 name: positive regulation of cell-cell adhesion mediated by integrin exact synonym: positive regulation of cell-cell adhesion mediated by integrin complex def: Any process that activates or increases the frequency, rate, or extent of cell-cell adhesion mediated by integrin. [GOC:add]

Reported by: addiehl

Original Ticket: "geneontology/ontology-requests/4504":https://sourceforge.net/p/geneontology/ontology-requests/4504

[gocentral]

Logged In: YES user_id=436423 Originator: NO

> Of course, you'll have to make all the complicated regulation relationships > that I am too lazy to spell out.

lucky me!

Original comment by: mah11

[gocentral]

• assigned_to: nobody --> gomidori

Original comment by: mah11

[gocentral]

Logged In: YES user_id=865072 Originator: YES

Midori,

I see that 'regulation of cell-cell adhesion ; GO:0022407' is not a part_of to 'cell-cell adhesion ; GO:0016337' as one would expect. Can you fix this as well, as part of your exercise in linking up all the require regulation terms.

Thanks,

Alex

Original comment by: addiehl

[gocentral]

Logged In: YES user_id=436423 Originator: NO

added integrin activation GO:0033622 regulation of integrin activation GO:0033623 negative regulation of integrin activation GO:0033624 positive regulation of integrin activation GO:0033625 cell surface receptor linked signal transduction leading to integrin activation GO:0033626 cell adhesion mediated by integrin GO:0033627 regulation of cell adhesion mediated by integrin GO:0033628 negative regulation of cell adhesion mediated by integrin GO:0033629 positive regulation of cell adhesion mediated by integrin GO:0033630 cell-cell adhesion mediated by integrin GO:0033631 regulation of cell-cell adhesion mediated by integrin GO:0033632 negative regulation of cell-cell adhesion mediated by integrin GO:0033633 positive regulation of cell-cell adhesion mediated by integrin GO:0033634

added relationship regulation of cell-cell adhesion GO:0022407 part_of cell-cell adhesion GO:0016337

will close after you check for typos, and the west coast folks have a chance to see it

Original comment by: mah11

[gocentral]

• status: open --> open-accepted

Original comment by: mah11

[gocentral]

Logged In: YES user_id=865072 Originator: YES

Midori,

It appears there are several relationship errors:

'cell-cell adhesion mediated by integrin ; GO:0033631' is missing one of its two is_a parents. The term should have an is_a relationship to both 'cell adhesion mediated by integrin ; GO:0033627' and 'cell-cell adhesion ; GO:0016337'; it is lacking the latter relationship.

'regulation of cell adhesion mediated by integrin ; GO:0033628' should be an is_a to 'regulation of cell adhesion ; GO:0030155' and not an is_a to 'regulation of cell-cell adhesion ; GO:0022407'.

'negative regulation of cell adhesion mediated by integrin ; GO:0033629' should be an is_a to 'negative regulation of cell adhesion ; GO:0007162' and not to 'negative regulation of cell-cell adhesion ; GO:0022408'.

'positive regulation of cell adhesion mediated by integrin ; GO:0033630' should be an is_a to 'positive regulation of cell adhesion ; GO:0045785' and not to 'positive regulation of cell-cell adhesion ; GO:0022409'.

Thanks,

Alex

Original comment by: addiehl

[gocentral]

Logged In: YES user_id=436423 Originator: NO

Alex,

Thanks for checking closely -- it's all too easy to make relationship errors when one's been staring at the tangles for too long. I've corrected them.

midori

Original comment by: mah11

[gocentral]

• status: open-accepted --> closed-accepted

Original comment by: mah11

[gocentral]

• milestone: 192945 --> PAINT

Original comment by: addiehl