Apoptosis Reference Genome Targets (Archived): Difference between revisions
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ZFIN=ZDB-GENE-011210-1|UniProtKB=Q98UI8 | ZFIN=ZDB-GENE-011210-1|UniProtKB=Q98UI8 | ||
2. PTHR12768 (beclin-1) This has previously been a target, but | 2. PTHR12768 FAMILY NOT NAMED (includes beclin-1) This has previously been a target, but some groups have not up-to-date annotations. | ||
Human | Human | ||
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FB=FBgn0010709|UniProtKB=Q9VCE1 | FB=FBgn0010709|UniProtKB=Q9VCE1 | ||
3. PTHR15077 (FADD) | 3. PTHR15077 FAMILY NOT NAMED(FADD) | ||
rat | rat | ||
RGD=628700|UniProtKB=Q8R2E7 | RGD=628700|UniProtKB=Q8R2E7 | ||
mouse | mouse | ||
MGI=MGI=109324|UniProtKB=Q61160 | MGI=MGI=109324|UniProtKB=Q61160 | ||
human | human | ||
ENSEMBL=ENSG00000168040|UniProtKB=Q13158 (BHF priority low) | ENSEMBL=ENSG00000168040|UniProtKB=Q13158 (BHF priority low) | ||
chicken | chicken | ||
ENTREZ=423146|NCBI=XP_421073 | ENTREZ=423146|NCBI=XP_421073 | ||
ENTREZ=776859|NCBI=XP_001236356 | ENTREZ=776859|NCBI=XP_001236356 | ||
drosophila | drosophila | ||
FB=FBgn0038928|UniProtKB=Q9V3B4 | FB=FBgn0038928|UniProtKB=Q9V3B4 | ||
Zebrafish | Zebrafish | ||
ENSEMBL=ENSDARG00000068099|ENSEMBL=ENSDARP00000089060 | ENSEMBL=ENSDARG00000068099|ENSEMBL=ENSDARP00000089060 | ||
4. | 4. DEATH- ASSOCIATED PROTEIN KINASE (PTHR22964:SF1) | ||
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.FAMILY NOT NAMED (PTHR12582), 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 | |||
- human | |||
UniProtKB=Q13546 (BHF priority (low) | UniProtKB=Q13546 (BHF priority (low) | ||
- rat | - rat | ||
RGD=1305538|NCBI=XP_345938 | RGD=1305538|NCBI=XP_345938 | ||
RGD=1310158|NCBI=XP_001065998 | RGD=1310158|NCBI=XP_001065998 | ||
- mouse | - mouse | ||
MGI=MGI=108212|UniProtKB=Q60855 | MGI=MGI=108212|UniProtKB=Q60855 | ||
- chicken | - chicken | ||
ENTREZ=378921|UniProtKB=Q7ZZX8 | ENTREZ=378921|UniProtKB=Q7ZZX8 | ||
- zebrafish | - zebrafish | ||
ENSEMBL=ENSDARG00000006677|UniProtKB=Q0MSH9 | ENSEMBL=ENSDARG00000006677|UniProtKB=Q0MSH9 | ||
Revision as of 08:13, 24 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
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)
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. DEATH- ASSOCIATED PROTEIN KINASE (PTHR22964:SF1) 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.FAMILY NOT NAMED (PTHR12582), 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