apoptosis by DNA damage ; GO:0008630

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Hi,

Please could induction of apoptosis by DNA damage ; GO:0008630, be made a child of 'response to DNA damage ; GO:0006974'

Also, under response to DNA damage at the moment, there's several terms that relate to p53. Is p53-mediated response to DNA damage an exception, or could these be replaced by e.g. DNA damage induced cell arrest and 'induction of apoptosis by DNA damage' (since activation of the tumour suppressor p53 by DNA damage induces either cell cycle arrest or apoptotic cell death).

Thanks,

Becky

Reported by: beckyfoulger

Original Ticket: "geneontology/ontology-requests/535":https://sourceforge.net/p/geneontology/ontology-requests/535

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First part done.

Original comment by: jl242

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Proposed new structure:

response to DNA damage ; GO:0006974 ---%DNA repair ; GO:0006281 ---%DNA damage response, induction of apoptosis ; GO:0008630 ---%DNA damage response, induction of protein phosphorylation ; GO:0006975

---%DNA damage response, induction of cyclin-dependent protein kinase inhibitor p21 (WAF1/CIP1/SDI1) ; GO:0006978 ---%DNA damage response, induction of cell cycle arrest ; GO:new

------%DNA damage response, induction of cell cycle arrest by p53 ; GO:0006977 ------%DNA damage checkpoint ; GO:0000077 ---%DNA damage response, p53-mediated ; GO:0030330 ------<DNA damage response, activation of p53 ; GO:006976 ------<DNA damage response, induction of cell arrest by p53 ; GO:0006977 ------<DNA damage response, induction of apoptosis by p53 ; GO:new

induction of apoptosis ; GO:0006917 ---%induction of apoptosis by intracellular signals ; GO:0008629 ------%DNA damage response, induction of apoptosis ; GO:0008630 ---------%DNA damage response, induction of apoptosis by p53 ; GO:new

Definitions:

DNA damage checkpoint A signal transduction pathway, induced by DNA damage, that blocks cell cycle progression (in G1, G2 or metaphase) or slows the rate at which S phase proceeds. PMID: 11891124

DNA damage response, induction of protein phosphorylation The widespread phosphorylation of various molecules, triggering many downstream processes that occurs in response to cellular DNA damage.

DNA damage response, p53-mediated A change in the state or activity of a cell (in terms of enzyme production, gene expression etc.), mediated by the cell cycle regulator phosphoprotein p53, as a result of damage to its DNA.

DNA damage response, activation of p53 The stimulation of activity of p53 in response to cellular DNA damage, thought to be caused by it's phosphorylation by DNA damage-activated protein kinases which prevents it interacting with its repressor protein, MDM2. PMID: 11960694

DNA damage response, induction of cell cycle arrest by p53 The stopping or reduction in rate of the cell cycle, mediated by the phosphoprotein p53, in response to cellular DNA damage.

DNA damage response, induction of cyclin-dependent protein kinase inhibitor p21 (WAF1/CIP1/SDI1) Induction of the expression of the protein p21 (also known as WAF1, CIP1 and SDI1) response to cellular DNA damage. PMID: 10967424

DNA damage response, induction of apoptosis by p53 The initiation of apoptosis, programmed cell death, in response to DNA damage by the phosphoprotein p53.

Just waiting for response from list.

Original comment by: jl242

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Original comment by: jl242

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Many many emails on the mailing list!

http://www.geneontology.org/email/go-arc/go-2003/0713.html

Midori's summary: http://www.geneontology.org/email/go-arc/go-2003/0737.html

Here are some good multi-organism overview references:

Melo and Toczyski, Curr Opin Cell Bio, 14:237 McGowan, BioEssays, 24:502

I think this was the final structure proposed:

response to DNA damage; GO:0006974 > ---% DNA repair ; GO:0006281 > ---< DNA damage response, detection of DNA damage; GO:NEW > ---% DNA damage response, signal transduction; GO:NEW > --------% DNA damage response, signal transduction resulting in cell > cycle arrest; GO:NEW (synonym: GO:77) > ------------% DNA damage response, signal transduction resulting in > cell cycle arrest via a regulatory module (synonym: GO:6977) > --------% DNA damage response, signal transduction resulting in > induction of apoptosis; GO:8630 > ------------% DNA damage response, signal transduction resulting in > induction of apoptosis via a regulatory module (induction of apoptosis > by p53) > --------% DNA damage response, signal transduction resulting in > transcription; GO:NEW > ------------% DNA damage response, signal transduction resulting in > transcription via a regulatory module (synonym: GO:6978, positive > regulation of transcription by p53) > --------% DNA damage response, signal transduction via a regulatory > module (synonym: GO:6976, GO:30330) > ------------% DNA damage response, signal transduction resulting in > cell cycle arrest via a regulatory module (synonym: GO:6977) > ------------% DNA damage response, signal transduction resulting in > induction of apoptosis via a regulatory module (induction of apoptosis > by p53) > ------------% DNA damage response, signal transduction resulting in > transcription via a regulatory module (synonym: GO:6978, positive > regulation of transcription by p53) > ---% DNA damage response, protein phosphorylation; GO:0006975 > > induction of apoptosis; GO:0006917 > ---% induction of apoptosis by intracellular signals ; GO:0008629 > --------% DNA damage response, signal transduction resulting in > induction of apoptosis; GO:NEW (synonym: GO:8630)

So based on the things discussed at the GO meeting, are you planning to keep this structure?

%generic term for all organisms %term as it relates to p53-class proteins

Original comment by: eurie

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See also '[ 749828 ] true path violation?, response to DNA damage' relating to placement of 'response to DNA damage' - now covered in this item.

Original comment by: jl242

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New proposal:

existing structure:

response to external stimulus ; GO:0009605 ---%response to biotic stimulus ; GO:0009607 ------%response to DNA damage; GO:0006974 % response to stress ; GO:0006950 ---------%DNA damage checkpoint ; GO:0000077 ---------%DNA damage induced protein phosphorylation ; GO:0006975 ---------%induction of apoptosis by DNA damage ; GO:0008630 ---------%p53-mediated DNA damage response ; GO:0030330 ------------<DNA damage response, activation of p53 ; GO:0006976 ---------------<DNA damage response, induction of cell arrest by p53 ------------------DNA damage response, induction of cyclin-dependent protein kinase inhibitor p21 ; GO:0006978

induction of apoptosis; GO:0006917 ---%induction of apoptosis by intracellular signals ; GO:0008629 ------%induction of apoptosis by DNA damage ; GO:0008630

proposed new structure:

response to endogenous stimulus ; GO:0009719 ---%response to DNA damage; GO:0006974 % response to stress ; GO:0006950 ------%DNA repair ; GO:0006281 ------<DNA damage response, perception of DNA damage ; GO:new ------%DNA damage response, signal transduction ; GO:new ---------%DNA damage response, signal transduction resulting in cell cycle arrest ; GO:0000077 synonym:DNA damage checkpoint ------------%DNA damage response, signal transduction resulting in cell cycle arrest p53-class ; GO:0006977 ---------%DNA damage response, signal transduction resulting in induction of apoptosis ; GO:0008630 ------------%DNA damage response, signal transduction by p53-class resulting in induction of apoptosis ; GO:0006977 ---------%DNA damage response, signal transduction resulting in transcription ; GO:new ------------%DNA damage response, signal transduction by p53-class resulting in transcription of p21-class ; GO:0006978 ---------%DNA damage response, signal transduction by p53-class ; GO:0030330 synonym: GO:0006976 ------------%DNA damage response, signal transduction by p53-class resulting in cell cycle arrest ; GO:0006977 ------------%DNA damage response, signal transduction by p53-class resulting in induction of apoptosis ; GO:0006977 ------------%DNA damage response, signal transduction by p53-class resulting in transcription of p21-class ; GO:0006978 ------%DNA damage response, protein phosphorylation ; GO:0006975

induction of apoptosis; GO:0006917 ---%induction of apoptosis by intracellular signals ; GO:0008629 ------%DNA damage response, signal transduction resulting in induction of apoptosis ; GO:0008630 ---------%DNA damage response, signal transduction by p53-class resulting in induction of apoptosis ; GO:0006977

Defintions:

DNA damage response, perception of DNA damage The processes by which DNA damage is detected and converted to a molecular signal within a cell.

DNA damage response, signal transduction A cascade of processes induced by the detection of DNA damage within a cell.

DNA damage response, signal transduction resulting in cell cycle arrest A signal transduction pathway, induced by DNA damage, that blocks cell cycle progression (in G1, G2 or metaphase) or slows the rate at which S phase proceeds. PMID: 11891124

DNA damage response, protein phosphorylation The widespread phosphorylation of various molecules, triggering many downstream processes that occurs in response to the perception of DNA damage.

DNA damage response, signal transduction by p53-class A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the perception of DNA damage.

DNA damage response, signal transduction by p53-class resulting in cell cycle arrest A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, resulting in the stopping or reduction in rate of the cell cycle, in response to the perception of DNA damage.

DNA damage response, signal transduction by p53-class resulting in transcription of p21-class A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, resulting in the induction of the transcription of p21, or any equivalent protein (also known as WAF1, CIP1 and SDI1) in response to the perception of DNA damage. PMID: 10967424

DNA damage response, signal transduction by p53-class resulting in induction of apoptosis A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, resulting in the initiation of apoptosis (programmed cell death) in response to the perception of DNA damage.

DNA damage response, protein phosphorylation The widespread phosphorylation of various molecules, triggering many downstream processes that occurs in response to cellular DNA damage.

Original comment by: jl242

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Hi Jane -

Thanks for merging all the assorted emails to create the proposal.

Because the "p53-class" terms were created to facilitate searching & identification of appropriate processes, can the term names not have hyphens in it? ie. use "p53 class" instead of "p53-class". Using the hypen forces people to have to search using p53 in order to find the right term. Alternatively, I guess I can submit this as a feature request for AmiGO .... always wild card the keyword search term??
which would be a better approach?

Onto comments about the proposal:

1. Should the following terms have part_of relationships?

"DNA damage response, signal transduction" "DNA damage response, protein phosphorylation"

2. As for making 'DNA repair', GO:0006281 a child of 'response to DNA damage', I just want to make sure everyone is on the same page. Are you thinking the definition for 'response to DNA damage' (...damage to its DNA) include errors in the fidelity of replication and insults to the DNA that compromise the structural integrity of the molecule? If only encompasses the latter (compromise the structural integrity of the molecule) then this move would violate true path because in 'DNA repair', GO:0006281, damage is defined as both. It might be useful to expand on the definition of 'response to DNA damage', GO:0006974 to be explicit about that:

definition: A change in the state or activity of a cell (in terms of enzyme production, gene expression, etc.) as a result of damage to its DNA from environmental insults or errors during metabolism.

eurie

Original comment by: eurie

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Revised new structure and defintions:

response to endogenous stimulus ; GO:0009719 ---%response to DNA damage stimulus ; GO:0006974 % response to stress ; GO:0006950 ------%DNA repair ; GO:0006281 ------<DNA damage response, perception of DNA damage ; GO:new ------<DNA damage response, signal transduction ; GO:new ---------%DNA damage response, signal transduction resulting in cell cycle arrest ; GO:0000077 synonym:DNA damage checkpoint ------------%DNA damage response, signal transduction resulting in cell cycle arrest p53 class mediator ; GO:0006977 ---------%DNA damage response, signal transduction resulting in induction of apoptosis ; GO:0008630 ------------%DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis ; GO:0006977 ---------%DNA damage response, signal transduction resulting in transcription ; GO:new ------------%DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator ; GO:0006978 ---------%DNA damage response, signal transduction by p53 class mediator ; GO:0030330 synonym: GO:0006976 ------------%DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest ; GO:0006977 ------------%DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis ; GO:0006977 ------------%DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator ; GO:0006978 ------<DNA damage response, protein phosphorylation ; GO:0006975

induction of apoptosis; GO:0006917 ---%induction of apoptosis by intracellular signals ; GO:0008629 ------%DNA damage response, signal transduction resulting in induction of apoptosis ; GO:0008630 ---------%DNA damage response, signal transduction by p53-class resulting in induction of apoptosis ; GO:0006977

Defintions:

response to DNA damage stimulus A change in the state or activity of a cell (in terms of enzyme production, gene expression, etc.) as a result of damage to its DNA from environmental insults or errors during metabolism.

DNA damage response, perception of DNA damage The processes by which DNA damage is detected and converted to a molecular signal within a cell.

DNA damage response, signal transduction A cascade of processes induced by the detection of DNA damage within a cell.

DNA damage response, signal transduction resulting in cell cycle arrest A signal transduction pathway, induced by DNA damage, that blocks cell cycle progression (in G1, G2 or metaphase) or slows the rate at which S phase proceeds. PMID: 11891124

DNA damage response, protein phosphorylation The widespread phosphorylation of various molecules, triggering many downstream processes that occurs in response to the perception of DNA damage.

DNA damage response, signal transduction by p53 class mediator A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the perception of DNA damage.

DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, resulting in the stopping or reduction in rate of the cell cycle, in response to the perception of DNA damage.

DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, resulting in the induction of the transcription of p21, or any equivalent protein (also known as WAF1, CIP1 and SDI1) in response to the perception of DNA damage. PMID: 10967424

DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, resulting in the initiation of apoptosis (programmed cell death) in response to the perception of DNA damage.

DNA damage response, protein phosphorylation The widespread phosphorylation of various molecules, triggering many downstream processes that occurs in response to cellular DNA damage.

Original comment by: jl242

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Implemented structure below. New ids:

GO:0042769 DNA damage response, perception of DNA damage GO:0042770 DNA damage response, signal transduction GO:0042771 DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis GO:0042772 DNA damage response, signal transduction resulting in transcription

Original comment by: jl242

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Original comment by: jl242