Apoptosis Reference Genome Targets (Archived): Difference between revisions

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==Families to annotate (BATCH 1) ==
==Families to annotate (BATCH 1) ==
1. '''PTHR10454 - Caspases'''
PTHR10454:SF13:  Caspase 1
- chicken
ENTREZ=395764|UniProtKB=O42284
- human
UniProtKB=P29466 (BHF priority (low); KRUK priority)
- mouse
MGI=96544|UniProtKB=P29452
- rat
RGD=2274|UniProtKB=P43527
PTHR10454:SF28 Caspase 1
- Drosophila
FB=FBgn0010501|UniProtKB=O02002
FB=FBgn0019972|UniProtKB=O01382
FB=FBgn0028381|UniProtKB=Q9VET9 
PTHR10454:SF30: Caspase 3
- rat
RGD=2275|UniProtKB=P55213
- mouse
MGI=MGI=107739|UniProtKB=P70677
- human
UniProtKB=P42574
-chicken
ENTREZ=395476|UniProtKB=O93417 
-zebrafish
ZDB-GENE-070607-1|UniProtKB=Q0PKX2
ZFIN=ZDB-GENE-011210-1|UniProtKB=Q98UI8
'''2. PTHR12768 FAMILY NOT NAMED (includes beclin-1) This has previously been a target, but some groups have not up-to-date annotations.'''
Human
- UniProtKB=A8MW95
- UniProtKB=Q14457
S. Pombe
-GeneDB_Spombe=SPAC20G8.10c|UniProtKB=P87117
s.cerevisiae
SGD=S000006041|UniProtKB=Q02948
rat
RGD=1563293|NCBI=XP_001059251
RGD=620190|UniProtKB=Q91XJ1
mouse
MGI=MGI=2684950|NCBI=XP_129608
MGI=MGI=1891828|UniProtKB=O88597 
C.elegans
WB=WBGene00000247|UniProtKB=Q22592 
Arabidopsis
TAIR=locus=2076715|NCBI=NP_567116 
chicken
ENTREZ=420018|UniProtKB=Q5ZKS6
Drosophila
FB=FBgn0010709|UniProtKB=Q9VCE1
'''3. PTHR15077 FAMILY NOT NAMED(FADD)'''
rat
RGD=628700|UniProtKB=Q8R2E7
mouse
MGI=MGI=109324|UniProtKB=Q61160 
human
ENSEMBL=ENSG00000168040|UniProtKB=Q13158  (BHF priority low)
chicken
ENTREZ=423146|NCBI=XP_421073
ENTREZ=776859|NCBI=XP_001236356 
drosophila
FB=FBgn0038928|UniProtKB=Q9V3B4 
Zebrafish
ENSEMBL=ENSDARG00000068099|ENSEMBL=ENSDARP00000089060
'''4. PTHR22964:SF1 DEATH- ASSOCIATED PROTEIN KINASE '''
Danio rerio 4
Gallus gallus 3
Homo sapiens 3
ENSEMBL=ENSG00000167657|UniProtKB=O43293
ENSEMBL=ENSG00000035664|UniProtKB=Q9UIK4 
ENSEMBL=ENSG00000196730|UniProtKB=P53355 (KRUK target)
Mus musculus 3
Rattus norvegicus 2
'''5. PTHR10315:SF11  E3 UBIQUITIN-PROTEIN LIGASE SIAH2 (SEVEN IN ABSENTIA HOMOLOG 2)'''
Danio rerio 1
Gallus gallus 1
Homo sapiens 1 (KRUK target)
Mus musculus 1
Rattus norvegicus 1
'''6. PTHR10315:SF10 E3 UBIQUITIN-PROTEIN LIGASE SIAH1 (SEVEN IN ABSENTIA HOMOLOG 1) '''
Caenorhabditis elegans 1
Danio rerio 1
Drosophila melanogaster 5
Gallus gallus 1
Homo sapiens 1
Mus musculus 2
Rattus norvegicus 1
'''7.PTHR12582 FAMILY NOT NAMED, includes NETRIN RECEPTORS'''
Caenorhabditis briggsae 1
Caenorhabditis elegans 1
Danio rerio 3
Drosophila melanogaster 1
Gallus gallus 4
Homo sapiens 4 (includes one KRUK priority)
Mus musculus 4
Rattus norvegicus 4
'''8. PTHR24361:SF84 SUBFAMILY NOT NAMED (contains serine/threonine protein kinase PAKs)'''
Caenorhabditis elegans 3
Danio rerio 7
Drosophila melanogaster 3
Gallus gallus 6
Homo sapiens 6
- Q13153 (BHF priority; low)
- Q13177 (BHF priority; low)
- O75914
- O96013
- Q9NQU5
- Q9P286 (BHF priority; low)
Mus musculus 6
Rattus norvegicus 6
Saccharomyces cerevisiae 3
Schizosaccharomyces pombe 2
'''9. (PTHR23257:SF93)'''
- human
UniProtKB=Q13546 (BHF priority (low)
- rat
RGD=1305538|NCBI=XP_345938
RGD=1310158|NCBI=XP_001065998 
- mouse
MGI=MGI=108212|UniProtKB=Q60855
- chicken
ENTREZ=378921|UniProtKB=Q7ZZX8
- zebrafish
ENSEMBL=ENSDARG00000006677|UniProtKB=Q0MSH9


== Annotation targets/progress table (BATCH 1) ==
== Annotation targets/progress table (BATCH 1) ==

Revision as of 13:33, 28 February 2011

Project leaders

UniProtKB GOA team, Emily Dimmer

Justification (Impact and significance)

Apoptosis is the process of programmed cell death (PCD) that may occur in multicellular organisms.

Biochemical events lead to characteristic cell changes (morphology) and death. These changes include rounding-up of the cell, retraction of pseudopodes, plasma membrane blebbing, loss of cell membrane asymmetry and attachment,reduction of cellular volume (pyknosis), nuclear fragmentation (karyorrhexis), chromatin condensation, and chromosomal DNA fragmentation. Apoptosis produces cell fragments called apoptotic bodies that surrounding cells are able to engulf (often associated with phagocytes) and quickly remove before the contents of the cell can spill out onto surrounding cells and cause damage. Apoptosis is not synonymous with programmed cell death (PCD).

In addition to its importance as a biological phenomenon, defective apoptotic processes have been implicated in an extensive variety of diseases. Excessive apoptosis causes atrophy, such as in ischemic damage, whereas an insufficient amount results in uncontrolled cell proliferation, such as cancer. [1],[2]


Notes for curators

Although the presence of active caspases and DNA fragmentation is helpful in identifying possible apoptosis, they should not be employed as an exclusive means to demonstrate this process as apototic cell death can occur without th DNA fragmentation or caspase activity.[1]


Cell death is frequently considered to be ‘caspase-dependent’ when it is suppressed by broad-spectrum caspase inhibitors such as N-benzyloxycarbonyl-Val-Ala-Asp-fluoromethylketone (Z-VAD-fmk). As a word of caution, however, it should be noted that Z-VAD-fmk does not act on all caspases with an equal efficiency, and it also inhibits calpains and cathepsins, especially at high concentrations (>10 μM). Moreover, Z-VAD-fmk has been associated with several off-target effects that would result from the binding to cysteines on proteins other than cysteine proteases[1]

Range of species in which the pathway is found

Apoptosis Experts

Ontology status

Time frame of the project

see also: http://wiki.geneontology.org/index.php/Apoptosis

Background reading

[1] [Classification of cell death: recommendations of the Nomenclature Committee on Cell Death 2009. Kroemer G, Galluzzi L, Vandenabeele P, Abrams J, Alnemri ES, Baehrecke EH, Blagosklonny MV, El-Deiry WS, Golstein P, Green DR, Hengartner M, Knight RA, Kumar S, Lipton SA, Malorni W, Nuñez G, Peter ME, Tschopp J, Yuan J, Piacentini M, Zhivotovsky B, Melino G; Nomenclature Committee on Cell Death 2009.Cell Death Differ. 2009 Jan;16(1):3-11. Epub 2008 Oct 10. http://www.ncbi.nlm.nih.gov/pubmed/18846107]

Highly recommended to read before starting curation; contains definitions of different types of cell death (apoptosis/necrosis/autophagic cell death/cornification, as described by the Nomenclature Committee on Cell Death.

[2] http://en.wikipedia.org/wiki/Apoptosis

Families to annotate (BATCH 1)

Annotation targets/progress table (BATCH 1)