Category:RefGenome Electronic Jamboree 2009-07 ETFDH

From GONUTS

See the talk page for discussion. See also Help:Annotation Jamborees

Orthoset

Participants

Name	Group	Organism(s)/Genome(s)	Notes
Kimberly Van Auken	WormBase	C. elegans	worm ortholog: WBGene00002855 = let-721
Stan Laulederkind	RGD	Rat
Debby Siegele	ecoliwiki	E. coli	ECOLI:fixC, ECOLI:yidS, ECOLI:ygcN
Li NI	MGI	Mouse	MGI:106100
Jodi Hirschman	SGD	S. cerevisiae	CIR2
Susan Tweedie	flyBase	D. melanogaster
Tanya Berardini	TAIR	A. thaliana
Ruth Lovering	BHF-UCL	Human
edit table

GENE

Aspect	ID	Term	ECOLI fixC	ECOLI ygcN	ECOLI yidS	FB CG12140	HUMAN ETFD	MGI Etfdh	PIG ETFD	RAT ETFD	SCHPO ETFD	SGD CIR2	TAIR AT2G43400.1	WB let‑721
Biological Process	GO:0002119	nematode larval development												IMP
Biological Process	GO:0006119	oxidative phosphorylation				ISS
Biological Process	GO:0006635	fatty acid beta-oxidation					IMP
Biological Process	GO:0006979	response to oxidative stress					ISS	IDA	ISS	ISS
Biological Process	GO:0008150	biological process		ND	ND			ND		ND		ND
Biological Process	GO:0009437	carnitine metabolic process	IEP
Biological Process	GO:0009646	response to absence of light											IEP
Biological Process	GO:0009792	embryonic development ending in birth or egg hatching												IMP
Biological Process	GO:0010171	body morphogenesis												IMP
Biological Process	GO:0022900	electron transport chain					IDA		IDA
Biological Process	GO:0033539	fatty acid beta-oxidation using acyl-CoA dehydrogenase					IMP
Biological Process	GO:0040010	positive regulation of growth rate												IMP
Cellular Component	GO:0005740	mitochondrial envelope											ISS
Cellular Component	GO:0005743	mitochondrial inner membrane				ISS		IDA						ISS
Cellular Component	GO:0005783	endoplasmic reticulum									IDA
Cellular Component	GO:0005811	lipid particle				IDA
Cellular Component	GO:0016020	membrane							IDA
Cellular Component	GO:0017133	mitochondrial electron transfer flavoprotein complex						TAS
Cellular Component	GO:0031305	integral to mitochondrial inner membrane					IDA
Cellular Component	GO:0031966	mitochondrial membrane					IDA			IDA
Cellular Component	GO:0044429	mitochondrial part							IDA
Molecular Function	GO:0003674	molecular function						ND				ND
Molecular Function	GO:0003824	catalytic activity											ISS
Molecular Function	GO:0004174	electron-transferring-flavoprotein dehydrogenase activity	ISA	ISA	ISA	ISS	IDA		IDA					ISS
Molecular Function	GO:0009055	electron carrier activity					IDA		IDA	IDA			ISS
Molecular Function	GO:0016491	oxidoreductase activity					IDA		IDA
Molecular Function	GO:0043783	oxidoreductase activity, oxidizing metal ions with flavin as acceptor					ISS		IDA
Molecular Function	GO:0048038	quinone binding					IDA
Molecular Function	GO:0048039	ubiquinone binding					IDA		IDA
Molecular Function	GO:0050660	FAD binding	ISA	ISA	ISA		ISS		IDA
Molecular Function	GO:0051536	iron-sulfur cluster binding	ISA	ISA	ISA				IDA	IDA
Molecular Function	GO:0051539	4 iron, 4 sulfur cluster binding	ISA				IDA		IDA
Cellular Component	GO:0005739	mitochondrion						IDA				IDA	IDA

Minutes

Attendees: Rob, Jodi, Suzi, Jim, Debby, Brenley, Yasmin, Mike, Kimberly, Emily, Rachael, Susan, Ruth, Varsha, Kara, Stan, Li, Pascale, Petra (who else?)

Term definition question for human annotation: Because this is a dehydrogenase it would be appropriate to annotate to the process 'GO:0033539 fatty acid beta-oxidation using acyl-CoA dehydrogenase', however, it was felt the definition is too narrow.

Def: A fatty acid beta-oxidation pathway in which the initial step, which converts an acyl-CoA to a trans-2-enoyl-CoA, is catalyzed by acyl-CoA dehydrogenase; the electrons removed by oxidation pass through the respiratory chain to oxygen and leave H2O as the product.

Objection to the wording "the initial step", makes it more sound like a 'one enzyme function term'. The Dehydrogenase has several steps to it, definition should be broader. Everyone agreed.

Ruth: create SF item about narrowing the def for GO:0033539.

In general, there's a lack of annotations for ETFDH. Most common annotation is component mitochondrion that can be moved across.

Discussion about annotating experiments from other organisms. Experiments for pig were annotated. There are also annotations from Hamster. These annotations could be propagated at least to all mammals.

Pig annotations were added to GONUTS table. Hamster annotations will also be added to GONUTS. Agreement that experiments from other organisms should be annotated when annotations in the 12 ref genome organisms are scarce.

Annotations can be propagated fom GONUTS to GOA to AmiGO release. Other organisms can also be used in PAINT tool.

Question about which reference to use, not clear in documentation. For pig annotations PPOD reference has been used. If there is no other paper, create/use your own reference.

Action Item: Improve ISS evidence code documentation.

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