Cascades: Difference between revisions

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[[Category:Signaling]]
Return to [[Main_Page|GOC Main Page]]
Return to [[Main_Page|GOC Main Page]]


Return to Signaling Main Page [[http://wiki.geneontology.org/index.php/Signaling]]
Return to Signaling Main Page [[http://wiki.geneontology.org/index.php/Signaling]]
==Cascade Examples==
[[phosphatidylinositol 3-kinase cascade ; GO:0014065]]
[[protein kinase A signaling cascade ; GO:0010737]]
[[protein kinase B signaling cascade ; GO:0043491]]
[[protein kinase C signaling cascade ; GO:0070528]]
[[JAK-STAT signaling cascade ; GO:0007259]]
[[TOR signaling cascade ; GO:0031929]]
[[hippo signaling cascade ; GO:0035329]]
[[PKR signal transduction ; GO:0039585]]
[[stress-activated protein kinase signaling cascade ; GO:0031098]]
[[cAMP-mediated signaling ; GO:0019933]]




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*From the GO signaling workshop and the LA 2011 GO meeting, it was agreed that 'VIA' (and HAS_PART relationships) was the most appropriate syntax for these terms.
*From the GO signaling workshop and the LA 2011 GO meeting, it was agreed that 'VIA' (and HAS_PART relationships) was the most appropriate syntax for these terms.
*For the current discussions on representing the regulatory nature of signaling pathways, see [http://gocwiki.geneontology.org/index.php/Regulation]




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==[http://www.sabiosciences.com/pathway.php?sn=GPCR_Pathway GPCR] signaling==
'''There are multiple problems with the GPCR terms (Sept 11),'''
*1. The GPCR terms use 'by' in their name. This doesn't seem correct as it implies that activation of AC activity is downstream of the pathway. In GO, the pathway begins with receptor-ligand binding and ends with regulation of a downstream cellular effect (normally transcription), so I think AC, PLC etc are all part of the GPCR signaling pathway.
*2. GO isn't consistent in calling them 'G-protein coupled receptor protein signaling pathway' vs 'G-protein signaling' vs 'G-protein signaling pathway'.
*3. The current is_a relationships between all the GPCR pathway terms don't convey the connection of the receptors, the G-proteins and the downstream signaling events well.
'''Current terms (Sept 2011) are:'''
positive regulation of adenylate cyclase activity by G-protein signaling pathway ; GO:0010579
activation of adenylate cyclase activity by G-protein signaling pathway ; GO:0007189
activation of adenylate cyclase activity by adrenergic receptor signaling pathway ; GO:0071880
activation of adenylate cyclase activity by dopamine receptor signaling pathway ; GO:0007191
activation of adenylate cyclase activity by glucose-triggered G-protein signaling pathway ; GO:0010619
activation of adenylate cyclase activity by serotonin receptor signaling pathway
activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway ; GO:0007205
activation of phospholipase D activity by G-protein coupled receptor protein signaling pathway ; GO:0031583
activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger ; GO:0007200
activation of phospholipase C activity by adrenergic receptor signaling pathway ; GO:0071882
activation of phospholipase C activity by dopamine receptor signaling pathway ; GO:0060158
negative regulation of phospholipase C-activating dopamine receptor signaling pathway ; GO:0060162
activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway ; GO:0007206
activation of phospholipase C activity by muscarinic acetylcholine receptor signaling pathway ; GO:0007207
activation of phospholipase C activity by serotonin receptor signaling pathway ; GO:0007208
activation of phospholipase C activity by tachykinin receptor signaling pathway ; GO:0007209
inhibition of phospholipase C activity involved in G-protein coupled receptor signaling ; GO:0030845
Therefore, these GPCR signaling pathway terms need to be changed to 'VIA' syntax with HAS_PART relationships, similar to other pathways. One issue, is that they need to tie in with the second-messenger-mediated signaling terms:
second-messenger-mediated signaling ; GO:0019932
A series of molecular signals in which an ion or small molecule is formed or released into the cytosol, thereby helping relay the signal within the cell.
G-protein signaling, coupled to cyclic nucleotide second messenger ; GO:0007187
G-protein signaling, coupled to cAMP nucleotide second messenger ; GO:0007188
G-protein signaling, coupled to cGMP nucleotide second messenger ; GO:0007199
G-protein signaling, coupled to S1P second messenger (sphingosine kinase activating) ; GO:0001789
rhodopsin mediated G-protein signaling, coupled to IP3 second messenger ; GO:0030265
[[File:Screen_shot_2011-09-14_at_13.53.40.png]]
For an overview of second-messenger signaling, see [http://en.wikipedia.org/wiki/Second_messenger_system Wikipedia] and the diagram below.
[[File:GPCR_overview.jpg]]
'''IN SUMMARY:''' Binding of ligand to a GPCR, activates the Galpha protein by promoting the exchange of GTP for GDP. The active Galpha subunit dissociates from the G protein trimer (alpha-beta-gamma), and signals to a PRIMARY EFFECTOR (E.g. phospholipase C or adenylate cyclase). The PRIMARY EFFECTOR causes production or release of a SECONDARY MESSENGER (E.g cAMP, IP3, Ca++). The second messenger effects a change in a SECONDARY EFFECTOR (E.g. PKC). The route of the signal depends on the type of G protein. The main routes are:
*1. cAMP system
** 1a  Gs protein activates adenylate cyclase to promote formation of cAMP
** 1b. Gi protein inhibits adenylate cyclase to inhibit formation of cAMP
[[File:GPCR_AC1.jpg]]
[[File:GPCR_GiAC.jpg]]
*2. IP3 system: Gq protein activates PLC, to promote formation of IP3 and DAG. IP3 binds to receptors on the ER, which causes release of Ca++ into the cytosol. DAG reimains tethered to the plasma membrane where it recruits PKC. PKC goes on to phosphorylate a range of molecules.
[[File:Pip2_cleavage_to_IP3_and_DAG.jpg]]
===Outstanding GPCR Questions===
Q1. Where does 'second-messenger-mediated signaling' begin? It is under 'intracellular signal tranduction ; GO:0035556' so is limited to events within the (receiving) cell. The intracellular steps are:
* Receptor signals to activate a G protein
* G protein activates a PRIMARY EFFECTOR (PLC/AC)
* PRIMARY EFFECTOR generates a SECOND MESSENGER (cAMP, IP3)
* SECOND MESSENGER signals to a SECONDARY EFFECTOR (PKC)
* SECONDARY EFFECTOR signals to downstream proteins......
Does second-messenger signaling begin once the second messenger has been activated/released? Or does it begin upstream of this?
===Proposed Format For GPCR Terms===
G-protein coupled receptor signaling pathway VIA activation of adenylate cyclase ; GO:0007189
HAS_PART: activation of adenylate cyclase activity ; GO:0007190
BUT... need to work out if activation of AC is part of second-messenger-mediated signaling, or if it's an upstream step.
===GPCRs===
For edits to the GPCR function terms, see the [http://gocwiki.geneontology.org/index.php/RECEPTORS#GPCRs receptor] section of the wiki.
==NF-KappaB==
Pablo needs some [http://en.wikipedia.org/wiki/NF-%CE%BAB NF-KappaB] terms for apoptosis, which has highlighted some problems with the 'I-kappaB kinase/NF-kappaB cascade ; GO:0007249' terms.
[[File:Screen_shot_2011-10-21_at_11.07.54.png]]
A summary of the signaling events:
[[File:NFKB_mechanism_of_action.png]]


# In resting phase, NF-KB dimers are bound to inhibitory IKB proteins, sequestering NF-KB in the cytoplasm.
# IKK is activated by signaling from upstream receptors and intracellular signaling proteins (E.g. TRAFs)
# IKK (IKB kinase complex, consisting of IKKalpha (kinase), IKKbeta (kinase) and IKKgamma (regulatory) subunits) phosphorylates IKB.
# Phosphorylated IKB proteins are targeted for ubiquitination and degradation.
# Degradation of IKB releases the NF-KB dimers, which translocate to the nucleus.
# NF-KB dimers are subject to futher PTMs to regulate them.
# NF-KB dimers bind to promoter/enhancer regions in DNA to enhance/repress transcription.


'''Oustanding Questions:'''
* What does the cascade cover? Most steps in the current cascade (eg 'cytoplasmic sequestering of NF-kappaB ; GO:0007253') prevent the signal from being passed on.
* Would it be better renamed as NF-KappaB signaling, with positive and negative regulation terms?
* If we rename it to NF-KappaB signaling, where does this start? If it starts with a released NF-KappaB, there's not many steps to it.
See PMID 21772278 for an overview, useful figures etc.


==Naming The Cascades==
==Naming The Cascades==
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* There was a concern that ‘cascade’ implied amplification of a signal.
* There was a concern that ‘cascade’ implied amplification of a signal.
* The SWG and experts discussed various options including 'cascade, cassette, module'.
* The SWG and experts discussed various options including 'cascade, cassette, module'.
* It was decided to stick with 'cascade' in GO, and making it clear in the definitions that amplification of a signal was not required.


In November 2013, the 'cascade' wording was removed from intracellular signaling terms that did NOT amplify a signal. 'x signal transduction' exact synonyms were added to all the intracellular signaling terms.


==Cascade Problems Still To Address==
==Cascade Problems Still To Address==
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For those that are just one mediator, it's harder to define a start and stop point. Where, for example, does the PI3K cascade begin and end? For these, it may be easier to rename them to 'PI3K signaling'. If we keep it as an instance of intracellular signal transduction, it can be defined as any signaling event within the cell where PI3K passes the signal on.
For those that are just one mediator, it's harder to define a start and stop point. Where, for example, does the PI3K cascade begin and end? For these, it may be easier to rename them to 'PI3K signaling'. If we keep it as an instance of intracellular signal transduction, it can be defined as any signaling event within the cell where PI3K passes the signal on.
The cascades were discussed at the call on 25th November 2013: [http://gocwiki.geneontology.org/index.php/Signaling_2013-11-25]. On this call it was suggested that:
-PI3K signaling would refer to any intracellular signal transduction that goes VIA PI3K. E.g. events above and below PI3K
-We would create signaling cassettes consisting of at least 2 signaling components, and define a start and stop for these cassettes. E.g. PI3K-AKT-TOR cassette.
Becky emailed this proposal to Prof. Mike Tyers, Andrew Winter and Andrew Chatyr-Aryamontri. We need to make sure this we could still capture a GP that regulates e.g. PKB activity.

Latest revision as of 17:00, 21 April 2014

Return to GOC Main Page

Return to Signaling Main Page [[1]]


Cascade Examples

phosphatidylinositol 3-kinase cascade ; GO:0014065

protein kinase A signaling cascade ; GO:0010737

protein kinase B signaling cascade ; GO:0043491

protein kinase C signaling cascade ; GO:0070528

JAK-STAT signaling cascade ; GO:0007259

TOR signaling cascade ; GO:0031929

hippo signaling cascade ; GO:0035329

PKR signal transduction ; GO:0039585

stress-activated protein kinase signaling cascade ; GO:0031098

cAMP-mediated signaling ; GO:0019933


Connecting Intracellular Cascades To Cell Surface Receptors

  • For the problems of connecting the intracellular signaling cascades with the cell surface receptors above them, see slides 26-32 of the overview from the LA GOC meeting, May 2011.
  • From the GO signaling workshop and the LA 2011 GO meeting, it was agreed that 'VIA' (and HAS_PART relationships) was the most appropriate syntax for these terms.
  • For the current discussions on representing the regulatory nature of signaling pathways, see [2]



EDITS: SEPTEMBER 8th 2011

OBSOLETED:
intracellular signal transduction involved in cell surface receptor linked signaling ; GO:0035557
phosphatidylinositol 3-kinase cascade involved in insulin receptor signaling ; GO:0035558
MAPKKK cascade involved in epidermal growth factor receptor signaling ; GO:0035559 


Created new Replacement Terms:

id: GO:0038028
name: insulin receptor signaling pathway via phosphatidylinositol 3-kinase cascade
namespace: biological_process
def: "The series of molecular signals generated as a consequence of the insulin receptor binding to its physiological ligand, where the signal is passed on via the   phosphatidylinositol 3-kinase cascade." [GOC:bf, GOC:signaling, PMID:19322168, PMID:20696212]
synonym: "insulin receptor signaling pathway via PI3K cascade" EXACT [GOC:bf]
synonym: "insulin receptor signaling via PI3K" EXACT [GOC:bf]
is_a: GO:0008286 ! insulin receptor signaling pathway
relationship: has_part GO:0014065 ! phosphatidylinositol 3-kinase cascade
id: GO:0038029
name: epidermal growth factor receptor signaling pathway via MAPKKK cascade
namespace: biological_process
def: "The series of molecular signals generated as a consequence of an epidermal growth factor receptor binding to one of its physiological ligands, where the signal is  passed on via the MAPKKK cascade." [GOC:bf, GOC:signaling, PMID:21167805]
synonym: "EGFR signaling pathway via MAPKKK cascade" EXACT [GOC:bf]
synonym: "EGFR signaling via MAPKKK cascade" EXACT [GOC:bf]
synonym: "EGFR/MAPK signaling" EXACT [GOC:bf]
synonym: "epidermal growth factor receptor signalling pathway via MAPKKK cascade" EXACT [GOC:bf]
is_a: GO:0007173 ! epidermal growth factor receptor signaling pathway
relationship: has_part GO:0000165 ! MAPKKK cascade
For SF:3023417, created:
non-canonical Wnt receptor signaling pathway via MAPKKK cascade ; GO:0038030
non-canonical Wnt receptor signaling pathway via JNK cascade ; GO:0038031


Related SourceForge Items




Naming The Cascades

For the problems of connecting the intracellular signaling cascades with the cell surface receptors above them, see slide 32 of the overview from the LA GOC meeting, May 2011.

IN SUMMARY:

  • There was a concern that ‘cascade’ implied amplification of a signal.
  • The SWG and experts discussed various options including 'cascade, cassette, module'.

In November 2013, the 'cascade' wording was removed from intracellular signaling terms that did NOT amplify a signal. 'x signal transduction' exact synonyms were added to all the intracellular signaling terms.

Cascade Problems Still To Address

Q: Where does a cascade start and stop?


Intracellular signaling units can be split into those that are a group of proteins:

  • MAPKKK cascade
  • JNK cascade
  • Hippo cascade

and those that are really just one mediator/protein:

  • PI3K
  • PKB (aka AKT) (NB: PI3K and AKT NORMALLY (but not always) signal together so we need to look at how we can connect them.
  • TOR
  • Ca++ signaling
  • Activation/inhibition of adenylate cyclase in GPCR signaling

For those that are just one mediator, it's harder to define a start and stop point. Where, for example, does the PI3K cascade begin and end? For these, it may be easier to rename them to 'PI3K signaling'. If we keep it as an instance of intracellular signal transduction, it can be defined as any signaling event within the cell where PI3K passes the signal on.


The cascades were discussed at the call on 25th November 2013: [3]. On this call it was suggested that:

-PI3K signaling would refer to any intracellular signal transduction that goes VIA PI3K. E.g. events above and below PI3K -We would create signaling cassettes consisting of at least 2 signaling components, and define a start and stop for these cassettes. E.g. PI3K-AKT-TOR cassette.

Becky emailed this proposal to Prof. Mike Tyers, Andrew Winter and Andrew Chatyr-Aryamontri. We need to make sure this we could still capture a GP that regulates e.g. PKB activity.