PAINT - Apoptosis (Archived): Difference between revisions

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Revision as of 00:56, 11 February 2014

This page captures PANTHER families with annotations to 'execution phase of apoptosis' GO:0097194). The definition is "A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. The execution phase ends when the cell has died." Thus, all signaling events *upstream from* the effector caspases (those include CASP3, CASP6, CASP7) should *not* be annotated to this term. Initiator caspases (e.g., CASP2, CASP8, CASP9, and CASP10) should also not be annotated to this term. See and for general background.

'Please sign up for a family, and comment after you submit them to the SVN repository.'

Family PTHR ID Curator Execution phase of apoptosis annotation justified?
cell death activator cide PTHR12306 Moni -- committed No - negative regulation of execution phase of apoptosis
DNA fragmentation subunit Beta PTHR13067 Moni -- committed Yes - apoptotic DNA fragmentation
map-kinase activating death domain protein (madd)/denn/aex-3(c.elegans) PTHR13008 Moni
caspase PTHR10454 Paul Yes
calpain PTHR10183 Rama
mitogen-activated kinase kinase kinase PTHR24361 Huaiyu -- committed No. PAKs are target of caspases, but not necessarily in the execution phase of apoptosis.
sorting nexin PTHR10555 Rama
40s ribosomal protein s3a PTHR11830 Pascale - committed No - positive regulation of extrinsic apoptotic signaling pathway. Family also contains CYLD, a ubiquitin dehydrolase, that I annotated in Protein2GO on Dec 19 - still need to annotate "GO:0061578 Lys63-specific deubiquitinase activity" in PAINT
akt-related serine/threonine-protein kinase PTHR24352 DHL
bcl-2 related PTHR11256 Huaiyu -- committed No. Bcl2 related proteins are involved in the cytochrome c release from mitochondria, which leads to the activation of caspase cascade, so they are not in the execution phase of apoptosis.
bcl2/adenovirus e1b 19-kda protein-interacting protein PTHR12112 Moni -- need to resolve family name conflict.
disulfide oxidoreductase PTHR22912 Paul No - caspase-independent apoptosis
ephrin PTHR11304 Li It's a "not" annotation to 'execution phase of apoptosis' GO:0097194. PMID:11870224 shows EphA3-expressing cell show morphological changes such as membrane blebbing. In contrast to apoptotic blebbs, which are static and often detach from the cell surface, ephrin-A5 triggers highly dynamic, spherical membrane protrusions that do not lead to cell fragmentation. "not" apoptosis process instead?
ets PTHR11849 Rama
f-box and wd40 domain protein PTHR22844 Rama
family not named PTHR18834 Li No - SRA overexpression enhanced apoptosis in mammary epithelia
family not named PTHR24025 Karen - not well enough annotated to do PAINT No - Dsg2 is a target of caspase 3, not playing a role in the execution phase itself
group ii pyridoxal-5-phosphate decarboxylase PTHR11999 Rama
microtubule-associated protein PTHR13843 DHL
nadh dehydrogenase-related PTHR22915 Rama
protein arginine n-methyltransferase PTHR11006 Pascale -- committed No (the paper shows that "Transfection of PRMT2 into 293 cells increased their susceptibility to TNF-induced cell death"; is this really sufficient evidence for an annotation?)
protein disulfide isomerase PTHR18929 Paul No - regulation of apoptosis
rbm25 protein PTHR18806 Pascale - committed No - regulation of alternative mRNA splicing, via spliceosome. Note that it regulates BCL-x spilcing.
telomeric repeat binding protein PTHR21717 Li No, regulation term is better choice or just apoptosis process
tumor protein d52 PTHR19307 Karen
type i interferon PTHR11691 Pascale - commited No, should be regulation of apoptosis (human IFNB1)
u3 small nucleolar rna-associated protein 11 PTHR12838 Karen - committed No - experiment supports "positive regulation of apoptotic process" at best; however, fairly old non-specific experiment and this family is now known to be the Utp11 component of the small subunit processome, and that disruption of ribosomal biogenesis and nucleolar structure leads to activation of cell cycle arrest and/or apoptosis; not clear that role of Utp11 in apoptosis is specific
ubiquilin PTHR10677 DHL

To do next: Families annotated to children of 'execution phase of apoptosis'

Family PTHR ID Curator Execution phase of aopoptosis annotation justified?
glucagon PTHR11418 Pascale -- commited No - negative regulation of apoptosis
30s/40s ribosomal protein s3 PTHR11760 Pascale -- commited No - regulation of apoptosis
rho-type gtpase activating protein PTHR12659 Moni
family not named (BNIP3) PTHR15186 Pascale -- committed No - In fact, apoptosis is wrong here. BNIP3 mediate caspase-independent programmed cell death
cop9 signalosome complex subunit 7/dendritic cell protein ga17 PTHR15350
myosin light chain kinase-related PTHR22964
paraneoplastic antigen PTHR23095
translation factor PTHR23115
family not named PTHR24271 Li -- committed yes
family not named PTHR24272 Moni
family not named (PTGIS) PTHR24295 - now PTHR24306 Pascale -- committed No, regulation of apoptosis
family not named PTHR24377 Pascale -- committed No, regulation of apoptosis // Zinc finger - huge family 2000 proteins
family not named PTHR32047 Li no, PMID:11466612 shows activities of caspase-3 like proteases enhanced twofold in Bcl10 transfected 293T cells, further experiments show Bcl10 may involved in apoptosis signaling by alter its binding partners...