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Category:RefGenome Electronic Jamboree 2009-07 SLC11A1/2

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

Orthoset

Ortholog set at PPOD

Participants

Name Group Organism(s)/Genome(s) Notes

Rob Nash

SGD

S. cerevisiae

Stan Laulederkind

RGD

Rat

Petra Fey

dictyBase

D. discoideum

Pascale Gaudet

dictyBase

D. discoideum

Li Ni

MGI

Mouse

Slc11a1=MGI:1345275=UniProtKB:P41251 Slc11a2=MGI:1345279=UniProtKB:P49282

Dmitry Sitnikov

MGI

Mouse

Slc11a1=MGI:1345275=UniProtKB:P41251

Susan Tweedie

flyBase

D. melanogaster

Brenley McIntosh

ecoliwiki

E. coli

ECOLI:mntH (P0A769)

Jodi Hirschman

SGD

S. cerevisiae

Emily Dimmer

GOA

Human

Yasmin Alam-Faruque

GOA

Human

Rachael Huntley

GOA

Human

Varsha Khodiyar

BHF-UCL

Human

Ruth Lovering

BHF-UCL

Human

Debby Siegele

ecoliwiki

E. coli

ECOLI:mntH (P0A769)

Kimberly Van Auken

WormBase

C. elegans

smf-1=WBGene00004876, smf-2=WBGene00004877, smf-3=WBGene00004878

Ranjana Kishore

WormBase

C. elegans

smf-1=WBGene00004876, smf-2=WBGene00004877, smf-3=WBGene00004878

Lakshmi Pillai

AgBase

G. gallus

Tanya Berardini

TAIR

A. thaliana


edit table

Annotations

Aspect ID Term TAIR

AT1G15960.1

TAIR

AT1G47240.1

TAIR

AT1G80830.1

TAIR

AT2G23150.1

TAIR

AT4G18790.1

TAIR

AT5G67330.1

WB

smf‑1

WB

smf‑2

WB

smf‑3

ZFIN

slc11a2

dictyBase

nramp1

FB

Mvl

MGI

Slc11a1

MGI

Slc11a2

SGD

SMF1

SGD

SMF2

SGD

SMF3

SCHPO

PDT1

Biological ProcessGO:0000041transition metal ion transport ISS ISS ISS IMP ISO
Biological ProcessGO:0000060protein import into nucleus, translocation IMP
Biological ProcessGO:0000165MAPKKK cascade ISO
Biological ProcessGO:0001818negative regulation of cytokine production IMP
Biological ProcessGO:0001819positive regulation of cytokine production IMP
Biological ProcessGO:0002309T cell proliferation during immune response IMP
Biological ProcessGO:0002369T cell cytokine production IMP
Biological ProcessGO:0002606positive regulation of dendritic cell antigen processing and presentation IMP
Biological ProcessGO:0002827positive regulation of T-helper 1 type immune response IMP
Biological ProcessGO:0006778porphyrin-containing compound metabolic process IMP
Biological ProcessGO:0006779porphyrin-containing compound biosynthetic process IMP
Biological ProcessGO:0006783heme biosynthetic process IMP
Biological ProcessGO:0006824cobalt ion transport IDA  ISO IGI
Biological ProcessGO:0006825copper ion transport IMP ISO IGI
Biological ProcessGO:0006826iron ion transport IMP  ISO IDA  IMP IGI IMP
Biological ProcessGO:0006828manganese ion transport TAS TAS TAS IMP ISO IMP IMP
Biological ProcessGO:0006875cellular metal ion homeostasis NAS NAS NAS NAS NAS NAS
Biological ProcessGO:0006876cellular cadmium ion homeostasis ISO IGI
Biological ProcessGO:0006877cellular cobalt ion homeostasis IGI
Biological ProcessGO:0006878cellular copper ion homeostasis IGI
Biological ProcessGO:0006879cellular iron ion homeostasis IGI IDA  IMP IMP  ISO IMP
Biological ProcessGO:0006909phagocytosis IEP IMP
Biological ProcessGO:0006919activation of cysteine-type endopeptidase activity involved in apoptotic process ISO
Biological ProcessGO:0006950response to stress IMP
Biological ProcessGO:0006954inflammatory response IMP
Biological ProcessGO:0007035vacuolar acidification IMP
Biological ProcessGO:0007611learning or memory IMP
Biological ProcessGO:0009617response to bacterium IEP IMP IMP  ISO
Biological ProcessGO:0009624response to nematode IEP
Biological ProcessGO:0010038response to metal ion IGI IGI IGI IDA
Biological ProcessGO:0010039response to iron ion IEP IDA
Biological ProcessGO:0010042response to manganese ion IMP IMP IMP ISO
Biological ProcessGO:0010043response to zinc ion IEP
Biological ProcessGO:0010628positive regulation of gene expression IMP
Biological ProcessGO:0010670positive regulation of oxygen and reactive oxygen species metabolic process IGI IGI
Biological ProcessGO:0015674di-, tri-valent inorganic cation transport IGI
Biological ProcessGO:0015675nickel cation transport ISO
Biological ProcessGO:0015676vanadium ion transport ISO
Biological ProcessGO:0015677copper ion import IMP
Biological ProcessGO:0015684ferrous iron transport IDA  ISO
Biological ProcessGO:0015691cadmium ion transport TAS TAS TAS IGI
Biological ProcessGO:0015692lead ion transport TAS TAS TAS ISO
Biological ProcessGO:0015707nitrite transport IDA
Biological ProcessGO:0015992proton transport IDA
Biological ProcessGO:0030001metal ion transport ISS  NAS ISS  NAS TAS TAS ISS  NAS TAS
Biological ProcessGO:0030026cellular manganese ion homeostasis IMP IMP IGI
Biological ProcessGO:0032147activation of protein kinase activity IMP
Biological ProcessGO:0032496response to lipopolysaccharide IDA  IMP  ISO
Biological ProcessGO:0032623interleukin-2 production IMP
Biological ProcessGO:0032632interleukin-3 production IMP
Biological ProcessGO:0032729positive regulation of interferon-gamma production IMP
Biological ProcessGO:0033212iron assimilation IDA
Biological ProcessGO:0034341response to interferon-gamma IDA
Biological ProcessGO:0034599cellular response to oxidative stress IMP ISO
Biological ProcessGO:0034755iron ion transmembrane transport IDA  IMP
Biological ProcessGO:0035162embryonic hemopoiesis IMP
Biological ProcessGO:0035444nickel cation transmembrane transport ISO
Biological ProcessGO:0042060wound healing IMP
Biological ProcessGO:0042116macrophage activation IDA  IMP
Biological ProcessGO:0042541hemoglobin biosynthetic process IMP
Biological ProcessGO:0042742defense response to bacterium IMP IMP IMP
Biological ProcessGO:0042832defense response to protozoan IMP
Biological ProcessGO:0043091L-arginine import IDA
Biological ProcessGO:0045342MHC class II biosynthetic process IMP
Biological ProcessGO:0045730respiratory burst IDA
Biological ProcessGO:0045944positive regulation of transcription from RNA polymerase II promoter IMP
Biological ProcessGO:0046688response to copper ion IDA
Biological ProcessGO:0046718viral entry into host cell IMP
Biological ProcessGO:0048002antigen processing and presentation of peptide antigen IMP
Biological ProcessGO:0048255mRNA stabilization IMP
Biological ProcessGO:0048813dendrite morphogenesis IMP
Biological ProcessGO:0048821erythrocyte development IMP
Biological ProcessGO:0050766positive regulation of phagocytosis IMP
Biological ProcessGO:0050829defense response to Gram-negative bacterium IMP
Biological ProcessGO:0050916sensory perception of sweet taste IMP
Biological ProcessGO:0055070copper ion homeostasis IMP
Biological ProcessGO:0055071manganese ion homeostasis IMP IMP IMP
Biological ProcessGO:0055072iron ion homeostasis IMP IMP IMP IMP
Biological ProcessGO:0055076transition metal ion homeostasis IMP
Biological ProcessGO:0060586multicellular organismal iron ion homeostasis IDA IMP IMP  ISO
Biological ProcessGO:0070482response to oxygen levels IEP
Biological ProcessGO:0070574cadmium ion transmembrane transport ISO ISO
Biological ProcessGO:0070627ferrous iron import IDA  IMP  ISO
Biological ProcessGO:0070838divalent metal ion transport IGI
Biological ProcessGO:0070839divalent metal ion export IDA
Biological ProcessGO:0071421manganese ion transmembrane transport IMP ISO IMP  TAS
Biological ProcessGO:0071577zinc ion transmembrane transport ISO
Cellular ComponentGO:0000329fungal-type vacuole membrane IDA
Cellular ComponentGO:0005634nucleus ISO
Cellular ComponentGO:0005737cytoplasm ISO
Cellular ComponentGO:0005739mitochondrion IDA
Cellular ComponentGO:0005764lysosome IDA ISO
Cellular ComponentGO:0005765lysosomal membrane ISO
Cellular ComponentGO:0005768endosome IDA
Cellular ComponentGO:0005769early endosome IDA  ISO
Cellular ComponentGO:0005770late endosome IDA  IMP ISO
Cellular ComponentGO:0005773vacuole ISO
Cellular ComponentGO:0005774vacuolar membrane IDA IDA
Cellular ComponentGO:0005783endoplasmic reticulum IDA
Cellular ComponentGO:0005802trans-Golgi network IDA ISO
Cellular ComponentGO:0005886plasma membrane IDA  NAS ISO IDA  ISO IDA
Cellular ComponentGO:0005887integral to plasma membrane ISM  NAS IDA
Cellular ComponentGO:0005903brush border IDA
Cellular ComponentGO:0009279cell outer membrane IDA
Cellular ComponentGO:0009986cell surfaceNOT IDA IDA  ISO
Cellular ComponentGO:0010008endosome membrane IDA
Cellular ComponentGO:0012505endomembrane system IDA
Cellular ComponentGO:0012506vesicle membrane IDA
Cellular ComponentGO:0016020membrane IDA IDA
Cellular ComponentGO:0016021integral to membrane ISO ISM ISM ISM
Cellular ComponentGO:0016023cytoplasmic membrane-bounded vesicle IDA
Cellular ComponentGO:0016324apical plasma membrane IDA IDA IDA ISO
Cellular ComponentGO:0030176integral to endoplasmic reticulum membrane IC
Cellular ComponentGO:0030670phagocytic vesicle membrane IDA  IMP  ISO
Cellular ComponentGO:0031410cytoplasmic vesicle ISO
Cellular ComponentGO:0031902late endosome membrane ISO
Cellular ComponentGO:0032010phagolysosome IDA
Cellular ComponentGO:0043229intracellular organelle IDA
Cellular ComponentGO:0044444cytoplasmic part IDA
Cellular ComponentGO:0045177apical part of cell ISO
Cellular ComponentGO:0045178basal part of cell ISO
Cellular ComponentGO:0045335phagocytic vesicle IDA
Cellular ComponentGO:0048471perinuclear region of cytoplasm ISO
Cellular ComponentGO:0055037recycling endosome IDA  ISO
Cellular ComponentGO:0070821tertiary granule membrane ISO
Cellular ComponentGO:0070826paraferritin complex ISO
Molecular FunctionGO:0005215transporter activity ISS
Molecular FunctionGO:0005375copper ion transmembrane transporter activity IMP ISO
Molecular FunctionGO:0005381iron ion transmembrane transporter activity IDA IDA IMP IDA  ISO
Molecular FunctionGO:0005384manganese ion transmembrane transporter activity TAS TAS TAS IMP IMP ISO TAS
Molecular FunctionGO:0005385zinc ion transmembrane transporter activity ISO
Molecular FunctionGO:0005506iron ion binding ISO
Molecular FunctionGO:0005507copper ion binding ISO
Molecular FunctionGO:0008270zinc ion binding ISO
Molecular FunctionGO:0015078hydrogen ion transmembrane transporter activity IDA
Molecular FunctionGO:0015082di-, tri-valent inorganic cation transmembrane transporter activity IDA IDA
Molecular FunctionGO:0015086cadmium ion transmembrane transporter activity ISO
Molecular FunctionGO:0015087cobalt ion transmembrane transporter activity IDA  ISO
Molecular FunctionGO:0015093ferrous iron transmembrane transporter activity IDA  ISO
Molecular FunctionGO:0015094lead ion transmembrane transporter activity ISO
Molecular FunctionGO:0015099nickel cation transmembrane transporter activity ISO
Molecular FunctionGO:0015100vanadium ion transmembrane transporter activity ISO
Molecular FunctionGO:0015103inorganic anion transmembrane transporter activity ISS ISS ISS ISS ISS ISS
Molecular FunctionGO:0015293symporter activity IGI
Molecular FunctionGO:0015295solute:hydrogen symporter activity ISO IDA
Molecular FunctionGO:0016151nickel cation binding ISO
Molecular FunctionGO:0022890inorganic cation transmembrane transporter activity ISO IDA IDA
Molecular FunctionGO:0030145manganese ion binding ISO
Molecular FunctionGO:0042803protein homodimerization activity ISO
Molecular FunctionGO:0046870cadmium ion binding ISO
Molecular FunctionGO:0046915transition metal ion transmembrane transporter activity ISS ISS ISS ISO
Molecular FunctionGO:0050897cobalt ion binding ISO
Molecular FunctionGO:0051139metal ion:hydrogen antiporter activity ISO
Molecular FunctionGO:0046873metal ion transmembrane transporter activity ISS  NAS ISS  NAS TAS TAS ISS  NAS TAS ISS

Molecular Function graph



RefGenome graph at MGI.


Biological Process graph



RefGenome graph at MGI.


Cellular Component graph



RefGenome graph at MGI.


Genes needing annotation

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Notes

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  • When a fusion to a reporter protein, such as GFP or PhoA, is used to determine the localization of a membrane protein, is it appropriate to use the IDA evidence code? Based on a search of the Gene Ontology website, that seems to be what dictyBASE and SGD have done in the past. Is that still the case? Debby (WB also annotates membrane protein::GFP fusions to CC terms using the IDA evidence code. --Kimberly)
  • Does functional expression inform subcellular localization? For example, if a transporter is expressed in Xenopus oocytes and experiments demonstrate functional transporter activity, can a Cellular Component annotation be made? If so, with what evidence code? --Kimberly

For just the mammalian A1 genes see Category:SLC11A1


Minutes

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SLC11A1/2 Jamboree Notes

  • Summary of Action Items (also embedded in context of discussion below)

ACTION ITEM: Debby could send a link to where E. coli group was looking in the documentation regarding IDA vs IMP for subcellular localization of fusion proteins

ACTION ITEM: (from ruth) next jamboree, decide on proteins, try to encourage ontology experts for relevant branches of the ontology to participate

ACTION ITEM: add equivalent metal ion terms to the ontology for different metal ions

ACTION ITEM: there's a link to the binding term documentation on the talk page - please give feedback to work out a range of opinions before the consortium meeting

ACTION ITEM create a wiki page where people can start suggesting/annotating genes for future jamborees to encourage broader participation


  • Items from talk page:

Jim and Brenley - can you use IDA or IMP if you are measuring the localization of a GFP-fusion protein?

Emily - GOA uses IDA if localization is intended to be a measure of the wild-type protein Don't really use IMP for localization annotations. IDA or not at all.

Pascal - Only time to use IMP would be for comparing WT vs mutant protein.

Debby - seems reasonable What is in the evidence code documentation? SGD and dicty both use IDA.

Could improve the documentation.

ACTION ITEM: Debby could send a link to where E. coli group was looking in the documentation.


  • Related component question:

Does a functional assay inform localization?

GOA would annotate to a component term using IDA.

MGI, WormBase, coli would use IC in these cases, as there is no direct localization data.

Isn't the functional assay enough?

Jim: isn't this analogous to a TF localizing to the nucleus? This is the example on the GO evidence code documentation page.

How do these two situations differ? What actually happens in transfection experiments when a reporter and a TF are transfected together?

Could we leave this issue up to the individual curator?

Wasn't the point of IC to illustrate that there was no direct evidence? Isn't IC a safer annotation?

Two experiments: measure transporter activity AND immunolocalization test to show membrane location Would this be better?

Is expression in an oocyte reflective of normal localization? This is a general concern for expressing a protein outside of its normal environment.

Pascal: problem with IC -- there are two kinds: those based on ISS, those based on a direct assay a cc annotation in this case would be more like one based on a direct assay

Ruth: if these people have actually done an immunofluorescence assay, would we be happy with an IDA if you're showing its functional, it's like doing an immunofluoresence assay

Li: we agree that we don't transfer IC from ISS? if there is experimental evidence, we can use IC

the documentation, however, allows IC from ISS or even IEA

Susan: try to find experimental evidence first would favor annotation to species being annotated, though


  • Annotating to transport process terms from transporter activity assays

Emily - found a number of papers measured the capacity of this gene product to transport a number of different cations transported, but only a few of these have evidence for a proper physiological basis iron, manganese, possibly lead or copper, but authors also cite experiments for cadmium, cobalt, nickel, etc. across membranes

some of the cations don't seem to have any obvious usefulness in the human body we were quite unsure of how to annoate these experiments. came across a paper where the research community seemed unsure of which transport functions are relevant could there be a role in detox of metal ions?

it's interesting that it has this activity, it'd be useful to see the full range of activities

GOA has annotated individually for each of the different transport activities and also included some NOT annotations

the question: what biological process annotations? for only a few annotations is there physiological relevance known?

could annotate to ion transport, but do we want to provide transport processes for each of the ions transported e.g. cobalt ion transport. link MF and BP annotations? how far to go? investigators aren't sure themselves, assay all sorts of cations for this protein this is a normal wild-type protein just being assayed for different types of transport

Pascal: in terms of tranpsort, the mf and bp terms are essentially synonymous

Tanya: make the process annotations as well as the MF annotations

Emily: normally it would never come into contact with these ions, e.g. vanadium

vanadium is used in some drugs

E: investigators acknowledge a grey area for what is physiologically relevant

Tanya: down the road, someone might be experimenting with these ions and looking for transport(er) terms

P: the function and the process are essentially synonymous is there a situation where you would not make the transport annotation for the transporter activity?

No.

Debby: another example--one of the recent ref genome targets there were e. coli enzymes that were shown to hydrolyze a whole bunch of sugar substrates, all have a broad range of overlapping activities, but it's not clear what biological process those activities are associated with. debby felt comfortable annotating showing the activity, but was hesitant to say it was involved in the substrate metabolism without additional evidence.

Jodi: typically would not make an annotation to process, for in vitro assay, would just leave the function annotation

debby: should we annotate to the biological transport process?

pascal: also depends upon the genomic context - if you have a single enzyme, it's probably the one involved in the process

susan: annotate according to the intent of the authors - annotate to metal ion transport, but not each individual transport term.

ruth: affinities could inform the annotations - what are relevant levels of solutes? agree with susan, if the authors were quite hesitant, unless curators feel confident authors are dealing with physiological levels of ions, then make the annotation.

debby: there's a difference between going with what the authors intend vs going past what the authors intend

tanya: but then why do they present the data? we're annotating to the experiments.

pascal: authors don't really know the significance

emily: it does seem the affinity for transport doesn't necessarily correlate with in vivo activity

pascal: an annotation to lead transporter activity, why not to lead transport?

ruth: several papers and reviews have been published, numerous groups are not willing to say that these proteins are involved in a given metal ion transport process

tanya: the structure of the ontology is such that metal ion transport will be found if annotations are made to the more specific child term

what ions are physiologically relevant?

why would the terms be in the ontology if they weren't biologically informative?

pascal: humans have evolved ways to deal with all kinds of toxic chemicals

debby: reading the introduction of the paper that emily put the pubmed id up for--this protein is a widely expressed ferrous iron transport that plays a vital role in iron homeostasis, general agreement for role in iron transport biochemically common to check other ions to characterize the transporter, but how specific are the transporter activites? would feel very confident annotating to metal ion transport and maybe based on other papers annotate to more specific biological process terms. wouldn't feel comfortable annotating to more specific terms from this paper, unless there was some other evidence that is was involved in that biological process. mf annotations would help people get to these gps.

discussion of transport terms

ruth: think about the intent of the authors. in this case, the authors don't intend to prove that cadmium is transported by this protein. because there are so many different metal ion transporters, you can't be sure which ones actually tranport in vivo

tanya: the potential is what can be annotated

ruth: the authors do not intend to show that this is the enzyme that actually does this process. could do this experiment with a variety of different transporters, but that isn't the experiment they did.

pascal: how would you be convinced, in human, to annotate to iron transport?

ruth: if there was a mutation in humans that affected iron levels, that would be very good evidence.

pascal: but these are very large gene families

ruth: but the authors don't intend to prove that this particular transporter is involved in this process


  • Homeostasis term annotations

emily: when to annotate to homeostasis terms? this protein transports ions and knock-outs are associated with anemia? do people co-annotate to iron homeostasis? homeostasis is the regulation of the process of ion transport? can't get homeostasis if the transporter is knocked out how much information is needed for an IMP annotation to iron homeostasis?

would anyone have a problem with iron homeostasis?

No, sounds reasonable.

should iron transport be related to iron homeostasis? should transport be a part_of homeostasis?

would you have a term, vanadium homeostasis?

how do people feel about a formal part_of link between transport and homeostasis?

if you're moving ion levels around, aren't you also affecting the homeostatic process? is this a leap too far? maybe just put a comment in for the transport term

would probably want to annotate to homeostasis if you were convinced that ion actually had a role in your organism maybe that's a reason for putting this into the comments for the term

petra: would now annotate to homeostasis terms for the dicty protein

jim: iron homeostasis seems to be a very central role for the transporters would you make a homeostasis annotation for a calcium transporter?

ruth: return of levels of calcium to resting state could be annotated to homeostasis

pascal: was anyone involved in the reorganization of the transport branches of the ontologies?

tanya: there was a transport group...who was in it?

pascal: have transport annotation guidelines? some very basic things we're talking about, but we don't all seem to be annotating the same way

ACTION ITEM: (from ruth) next jamboree, decide on proteins, try to encourage recent ontology experts to participate


  • Ontology development for metal ion terms

emily: creating different annotations for different metal ions because there's a lack of terms to describe different metal ions equivalent terms for iron and manganese don't exist

ACTION ITEM: add equivalent metal ion terms to the ontology for different metal ions


  • Binding term documentation
  • ruth: binding terms

had a binding term annotation conference call ruth has written out the minutes and proposed guidelines please take a look

from the meeting, we were not going to do any ICs for binding?

the concepts discussed in the binding meeting--if a protein has iron transport activity, you don't have to annotate to iron binding if there's a direct experiment to test for iron binding, then add the annotation otherwise, just annotate to the transport activity

debby: thought the conclusion was that you didn't need to do it, but that it was okay to do it

ruth: it'd be really great to finish off this documentation. if this is still not clear, then the binding discussion group needs to sort this out.

it'd be good to resolve this and get the proposal agreed upon at the September consortium meeting.

ACTION ITEM: there's a link to the binding term documentation on the talk page - please give feedback to work out a range of opinions before the consortium meeting


  • Suggestions for jamboree genes to encourage broader participation

emily: a really good idea from Li regarding selection of targets

have a table of a number of potential targets, each group could indicate the number of papers to help get maximal participation in the calls

mgi/goa are often overwhelmed by the number of papers, other groups have very little literature

ACTION ITEM:pascal: start making the page now and people can start suggesting/annotating the genes

References

See Help:References for how to manage references in GONUTS.
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