Category:RefGenome Electronic Jamboree 2009-07 ETFDH

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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	TAIR AT2G43400.1	WB let‑721	FB CG12140	ECOLI fixC	ECOLI yidS	ECOLI ygcN	HUMAN ETFD	MGI Etfdh	RAT ETFD	SGD CIR2	SCHPO ETFD	PIG ETFD
Biological Process	GO:0002119	nematode larval development		IMP
Biological Process	GO:0006116	NADH oxidation											ISS
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
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	ISO				IDA
Biological Process	GO:0022904	respiratory electron transport chain							TAS
Biological Process	GO:0033539	fatty acid beta-oxidation using acyl-CoA dehydrogenase							IMP	ISO
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	ISS					IDA
Cellular Component	GO:0005759	mitochondrial matrix							TAS
Cellular Component	GO:0005783	endoplasmic reticulum											IDA
Cellular Component	GO:0005811	lipid particle			IDA
Cellular Component	GO:0005875	microtubule associated complex			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	ISO
Cellular Component	GO:0031966	mitochondrial membrane							IDA	ISO	IDA
Cellular Component	GO:0044429	mitochondrial part												IDA
Molecular Function	GO:0003674	molecular function										ND
Molecular Function	GO:0003824	catalytic activity	ISS
Molecular Function	GO:0004174	electron-transferring-flavoprotein dehydrogenase activity		ISS	ISS	ISA	ISA	ISA	IDA	ISO				IDA
Molecular Function	GO:0009055	electron carrier activity	ISS						IDA	ISO	IDA			IDA
Molecular Function	GO:0016491	oxidoreductase activity							IDA	ISO				IDA
Molecular Function	GO:0043783	oxidoreductase activity, oxidizing metal ions with flavin as acceptor							ISS					IDA
Molecular Function	GO:0048038	quinone binding							IDA	ISO
Molecular Function	GO:0048039	ubiquinone binding							IDA	ISO				IDA
Molecular Function	GO:0050660	FAD binding				ISA	ISA	ISA	ISS					IDA
Molecular Function	GO:0051536	iron-sulfur cluster binding				ISA	ISA	ISA		ISO	IDA			IDA
Molecular Function	GO:0051539	4 iron, 4 sulfur cluster binding				ISA			IDA	ISO				IDA
Cellular Component	GO:0005739	mitochondrion	IDA							IDA		IDA IPI	ISS

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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