Summary: Mouse, Rat, Chicken, Zfish, Worm report orthologs
Annotations: Human, Mouse, Rat, Zfish, Worm have GO annotations. Chicken does not have any GO annotations.
Summary:
Orthologs: Mouse, Rat, Chicken, Zfish, and Worm report orthologs; No orthologs for Fly, Dicty, Dicot, Yeast, Pombe and E. coli.
Annotations: Human, Mouse, Rat, Zfish, Worm have GO annotations. Chicken does not have any GO annotations.
MF: Human, Mouse and Rat all have annotations to the high level term 'binding'. So should chicken, Zfish and worm ISS to this? The term itself may not be very informative to users, just that it binds something.
MF: Human and Rat have 'catalytic activity'. The IEA annotation for worm has 'protein serine/threonine kinase activity', based on the presence of this motif in the worm. For catalytic activities I think I would be comfortable leaving it at the level of the IEA, and in this case it is already based on motif presence.
Not sure that converting such annotations to ISS would give it much more validity. Catalytic activities can be lost in some species even though the relevant motif is present.
MF: Rat has 'molecular transducer activity'; high level term; Maybe other organisms could consider ISSing to this?
MF: Human has specific binding terms--'activin binding', 'SMAD binding'. Rat has 'SMAD binding' too. I don't think I would be comfortable ISSing to such granular terms for the worm, at least.
CC: Human and rat have cc annotations to both 'cell' and 'cell part'. They also have 'cell surface' and 'integral to plasma membrane'. Rat also has 'macromolecular complex', maybe worth looking into for ISSing for similar species.
BP: Human and Worm (and in some cases zfish) have annotated to several high level terms like 'biological regulation', 'developmental process', 'cellular process'. Rat has ISS to several high level terms. Safe enough to transfer via ISS.
Based on this experience I think transfering annotations via ISS of orthologs would be on a case-by-case basis. Database alerts and reports would help a lot here, but this process still
requires curator time.
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Originator: YES
Reference Genome Ortholog Completion set:
Human gene: ACVR1B
Entrez gene ID:
Summary: Mouse, Rat, Chicken, Zfish, Worm report orthologs
Annotations: Human, Mouse, Rat, Zfish, Worm have GO annotations. Chicken does not have any GO annotations.
Human gene: ACVR1B, ACVRLK4, ALK4
Disease association: Pancreatic cancer, somatic
Entrez ID: 91
Worm Gene: daf-1
Summary:
Orthologs: Mouse, Rat, Chicken, Zfish, and Worm report orthologs; No orthologs for Fly, Dicty, Dicot, Yeast, Pombe and E. coli.
Annotations: Human, Mouse, Rat, Zfish, Worm have GO annotations. Chicken does not have any GO annotations.
MF: Human, Mouse and Rat all have annotations to the high level term 'binding'. So should chicken, Zfish and worm ISS to this? The term itself may not be very informative to users, just that it binds something.
MF: Human and Rat have 'catalytic activity'. The IEA annotation for worm has 'protein serine/threonine kinase activity', based on the presence of this motif in the worm. For catalytic activities I think I would be comfortable leaving it at the level of the IEA, and in this case it is already based on motif presence.
Not sure that converting such annotations to ISS would give it much more validity. Catalytic activities can be lost in some species even though the relevant motif is present.
MF: Rat has 'molecular transducer activity'; high level term; Maybe other organisms could consider ISSing to this?
MF: Human has specific binding terms--'activin binding', 'SMAD binding'. Rat has 'SMAD binding' too. I don't think I would be comfortable ISSing to such granular terms for the worm, at least.
CC: Human and rat have cc annotations to both 'cell' and 'cell part'. They also have 'cell surface' and 'integral to plasma membrane'. Rat also has 'macromolecular complex', maybe worth looking into for ISSing for similar species.
BP: Human and Worm (and in some cases zfish) have annotated to several high level terms like 'biological regulation', 'developmental process', 'cellular process'. Rat has ISS to several high level terms. Safe enough to transfer via ISS.
Based on this experience I think transfering annotations via ISS of orthologs would be on a case-by-case basis. Database alerts and reports would help a lot here, but this process still
requires curator time.