Trial_GO_OA_analysis.xlsx
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DiscussedPaperOverlap OA and GOGOOAIn vitro assay/ heterologous expressionCommentActionFollow-Up Work
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YESWBPaper00050743elli-1, part_of cytoplasm, IDA, pgl-1, part_of P granule, IDAwould put cytoplasm and P-body. would not curate in OA pgl-1 as it is a known parker for P-granules‘Within the rachis, ELLI- 1 foci partially overlap with the P-body component CGH-1, suggesting these foci are associated with RNA.’
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YESWBPaper00001929GO, but no OA (this is a transfection and fractionation experiment)ace-1: extracellular region (updated to extracellular space), (membrane - removed)YESp9961 Transfection with this shortened cDNA led to the production of an active enzyme secreted into the culture medium. Five days postinfection approximately half of the AChE activity was found in the medium and half in the cell pellet.Removed annotation to membrane; updated extracellular region to extracellular space. Will check remaining annotations to 'extracellular region' to determine if they can be moved to the more granular child term of 'extracellular space': pnc-1, cpg-1, madd-4, let-756, asm-1, asm-2.Fixed: pnc-1, cpg-1, madd-4
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YESWBPaper00002776aex-3: cellReporter fusion used promoter and up to codon 49.
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YESWBPaper00002884Curated in OA- April 14th 2017glp-1 : plasma membrane part_of(germ line)glp-1 : plasma membrane part_of(germ line)Flagged as false positive in curation status. Updated on april 14th 2017Add germ line stem cell to AO with synonym 'proliferating germ cell' or 'mitotically proliferating germ cell' or something along those lines.
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YESWBPaper00003556NO OA (that is correct)Removed annotation to 'cell', as it was incorrect (just a promoter fusion). Will check any remaining annotations to 'cell' as these are not likely correct or helpful. ace-1, ace-2, aex-3, aps-2, cab-1, cdd-2, cdk-4, cyn-3, dpy-18, egl-15, egl-20, emo-1, mec-18, meg-3, nsy-1. (Note also all of the IOLs that are IEAs.)
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YESWBPaper00006050NO OA, was flagged negative by SVM and not detected with other flagging methods.In vitro assay, transfection of CHO cells with npr-1. We normally annotate to in vivo localization (or c. elegans extracts). YESCellular fractionation as part of ligand-receptor studies.
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YESWBPaper00004932NO OA (that is correct)ace-2: celln/aRemoved this annotation from Protein2GO, as this is a promoter::GFP fusion and doesn't address subcellular localization.
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YESWBPaper00006481MATCH

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YESWBPaper00013416Partial matchcytoplasm, nucleuscytoplasm, nucleus, axon, neuronal cell bodyThe translational fusion also showed strong constitutive expression in the cell bodies and axons of the bilateral motor interneurons AVB, but we do not know the significance of this expression. The LIN-46:GFP fusion protein localized to both cytoplasm and nucleus, but mostly in the non-nucleolar part of the nucleus. Should nucleus in both annotations be changed to nucleoplasm?
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YESWBPaper00024364Partial matchatx-2 - cytoplasm; him-3 -chromosome (UniProt)atx-2 - cytoplasmhim-3 annotated for condensed nuclear chromosome in GO, http://www.wormbase.org/species/c_elegans/gene/WBGene00001862#13--10. In OA him-3 has condensed nuclear chromosome for Expr1163 and condensed chromosome for Expr12535. Shall we change them all to condensed nuclear chromosome?
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WBPaper00024437Partial match, but updated GO CC annotations as part of Noctua curationcondensed chromosome kinetochore: kbp-1, -2, -3, -4, -5, knl-3, mis-12condensed nuclear chromosome, chromosome, kinetochore for the same list of genes. Question about ndc-80 - OA says 'Data and methods not shown in this paper.'
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OKWBPaper00024672NO GO CC

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OKWBPaper00026846Partial matchdcap-2: P granule, P body. dcs-1: cytoplasm, nuclear envelope
GO also has cgh-1 and ncbp-2 annotations
dcap-2: P granule, ADDED P body. dcs-1: cytoplasm. GO also has cgh-1 and ncbp-2 annotationsADDED P body
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OKWBPaper00027655Do not match
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WBPaper00030808yop-1cortical endoplasmic reticulumcortical endoplasmic reticulum, nuclear envelopeYOP-1 localizes to the peripheral ER as well as the nuclear envelope.Kimberly is taking a look and give feedback. GO lacks nuclear envelope and ret-1 annotation. Nuclear envelope annotation is unclear for yop-1: fig S1A title is: 'YOP-1 localizes to the peripheral ER as well as the nuclear envelope.' but in other parts of the paper they say it's largley excluded.
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WBPaper00030819NO GO CC
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WBPaper00030824NO GO CC
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WBPaper00031585NO GO CC
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WBPaper00031840NO GO CC
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WBPaper00032076MATCH for syg-1Kimberly will take a look: igcm-1 not in GO
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WBPaper00032092NO GO CC
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Kimberly will look at it, see action column
WBPaper00032183Partial matchlegocc : sax-7, part_of plasma membrane, IDA
legocc : sax-7, part_of sarcomere, IDA
sarcomereSAX-7 is localized to sarcomeres and membrane boundaries; both signals are absent in sax-7(eq1) animals.Kimberly: will take a look at the papaer and change if need be. Daniela's comment: I did align the OA annotations with GO. One question is: use neuronal cell body instead of cell body? Daniela: Check the 'cell body' annotations in OA and add extensions or change to neuronal cell body. Daniela checked on June 9th 2017. All the annotations but one (referring to spermatids) were changed to neuronal cell body.
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YESWBPaper00032338MATCHlego has additional genes
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YESWBPaper00032404MATCHlegocc : sod-1, part_of cytosol, IDA
legocc : sod-1, part_of mitochondrion, IDA
cytosol, mitochondrial intermembrane spacechanged mitochondrial intermembrane space into mitochondrion, not enough evidence in the paper to determine it.
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WBPaper00032467NO GO CC
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WBPaper00034709different genes curated for the 2 pipelines
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Kimberly take a look at action itemsWBPaper00035180DO NOT MATCHlegocc : wts-1, part_of apical plasma membrane, IDA, UniProt_GOA
legocc : wts-1, part_of membrane, IDA, UniProt_GOA
cell periphery ( GO:0071944 ) from the paper: 'The subcellular
localization of Ce-WTS-1 appears to be close to the membrane
or membrane-associated, i.e., in gut apical membrane, vulval cell
membrane, spermathecal cell membrane and seam cell membrane,
by comparing Ce-WTS-1 expression patterns with NHX-2::GFP
expression in gut [31], AJM-1::GFP expression in vulval, spermathecal
and seam cells [32]. However, the ‘DAS’ transmembrane domain
prediction program predicted no transmembrane domain in
CE-WTS-1 (data not shown). In addition, neither fly Warts or
human LATS1 contains transmembrane domains [33]. Therefore,
Ce-WTS-1 is likely accumulated intracellularly near the cell membrane
and may interact with membrane or membrane associated
proteins.'
Leave OA as is- Kimberly will follow up with GO
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Kimberly take a look at action itemsWBPaper00035181Daniela added cytoplasm and nucleus and evidence in OAlegocc : mak-2, part_of cytoplasm, IDA
legocc : mak-2, part_of nucleus, IDA
legocc : mak-2, part_of synapse, IDA
mak-2: synapse, neuronal cell body mCherry::MAK-2 was consistently present in cell bodies and synapses but rarely seen in axon commissures. MAK-2 was broadly localized at motor neuron synapses and significantly colocalized with synaptobrevin/SNB-1 but not with RPM-1. Kimberly: 'Add neuronal cell body' in GO
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Kimberly take a look at action itemsWBPaper00035181Partly matching, OA also has neuronal cell body and axonlegocc : cebp-1, part_of cytoplasm, IDA
legocc : cebp-1, part_of nucleus, IDA
legocc : cebp-1, part_of synapse, IDA
general nervous system matching: cytoplasm, nucleus, synapse. Additional specific annotation for TRN: neuronal cell body, axon, synapseIn OA there are 2 different annotations wrt the extensions: 1 is referring to the nervous system in general and that matches the GO annotation. the other one is more specific to touch receptor neurons. See this sentence: 'mCherry::CEBP-1 was detected at synapses, in addition to the cytoplasm and nucleus of the soma. In touch neurons, CEBP-1 was present in the soma, in the synaptic area, and at discrete regions along axons.'Kimberly: Add neuronal cell body, axon
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WBPaper00035189Partly matching, OA also describes cytoplasmic expression in intestinal cellslegocc : tcer-1, part_of nucleus, IDAnucleus, cytoplasm (intestinal_cell)TCER-1::GFP was visible at all stages of embryonic and larval development. In adults, we observed strong nuclear localization of TCER-1::GFP in intestinal cells, many head and body neurons, muscle and hypodermal cells. In some intestinal cells, weak expression was also observed in the cytoplasm.
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WBPaper00035200NO GO CC
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WBPaper00035231DO NOT MATCH/ Changed OA, NOW MATCHINGlegocc : cil-1, part_of axon, IDA
legocc : cil-1, part_of cytoplasm, IDA, UniProt_GOA
legocc : cil-1, part_of dendrite, IDA
legocc : cil-1, part_of neuronal cell body, IDA
legocc : cil-1, part_of non-motile cilium, IDA
legocc : cil-1, part_of nucleus, IDA
missing cilium, the rest was the same-addedmissing cilium, the rest was the same-added
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To be discussedWBPaper00035288NO OA CC. Daniela added 2 annotations in OA (Sept 1st 2017), one for each isoform. Isoform specificity is encoded in the construct used to monitor expression.pnc-1: extracellular regionnoneIsoform-specific localization - not captured correctly in Protein2GO; specifically expressed in muscle to evaluate localizationUpdated pnc-1a isoform to extracellular space; created pnc-1b for cytoplasm and nucleus; did not add annotation extension for the muscle localization
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WBPaper00035404MATCH
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WBPaper00035442DO NOT MATCH/ Changed OA, NOW MATCHINGlegocc : calf-1, part_of endoplasmic reticulum membrane, IDAcalf-1, part_of endoplasmic reticulumCHANGED INTO endoplasmic reticulum membrane
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WBPaper00035442DO NOT MATCH/ Changed OA, NOW MATCHINGlegocc : unc-2, part_of presynaptic active zone membrane, IDApresynaptic active zoneCHANGED INTO presynaptic active zone membrane
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WBPaper00035442MATCHlegocc : unc-36, part_of endoplasmic reticulum membrane, IDA. legocc : unc-36, part_of plasma membrane, IDAendoplasmic reticulum membrane, plasma membrane
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WBPaper00035469NO GO CC
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WBPaper00035573DO NOT MATCH, lin-23nucleuscytosolThe LIN-23 protein is present both in all blast cells of embryos and in the wild-type germline. LIN-23 is present in the germline from the tip of the distal arm to the maturing oocytes. Its abundance seems relatively similar between the distal and proximal zones; however, its localization is concentrated within cytosol and is relatively excluded from nuclei. The distal region of the gonad is a syncytial tube with the germline nuclei packed around the outside with a hollow core. We find that LIN-23 is concentrated throughout the core and in the cytosolic spaces between the nuclei and is either absent from, or present at a much reduced level, in the nuclei themselves. Within developing oocytes in the proximal region of the gonad, it is also more abundant in the cytoplasm than nuclei. An interesting observation was the differential localization of LIN-23 in the cells of the early embryo. It is generally distributed throughout the cytosol, but its localization is dynamic being differentially excluded from the nucleus for much of the cell cycle, but a fraction of it accumulates to the nuclear compartment late in the cycle shortly before cell division. In the embryos shown, the nuclear compartment accumulation of LIN-23 is seen in a late AB blastomere but is absent in a slightly younger AB blastomere. Similarly, it can be seen in both the ABa and ABp blastomeres but absent from the nuclei of the EMS and P2 blastomeres. Because the ABa and ABp blastomeres divide slightly earlier than EMS and P2, they are inevitably later in the cell cycle. However, this pattern is not lineage dependent.It seems that the nuclear localizaton is at defined time frames, i.e. shortly before cell division. I would leave cytoplasm and add another annotation with cell cycle extension for nucleus. Cytoplasmic localization for lin-23 has been described in other papers and annotated in GO (2 IEA instances and 2 IDA instances). Daniela added a line in OA for 'nucleus' in AB, ABa, ABp, and G2/M transition of mitotic cell cycle ( GO:0000086 ) extensions.
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WBPaper00035574NO GO CC
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WBPaper00035920NO GO CC
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WBPaper00035924MATCHadditional genes curated for GOCC
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WBPaper00035928NO GO CC
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WBPaper00035928NO GO CC
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WBPaper00035930NO GO CC
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WBPaper00036137NO GO CC
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WBPaper00036215NO GO CC
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WBPaper00036231MATCHadditional genes in OA
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WBPaper00036408NO GO CC
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WBPaper00037660MATCH
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YESWBPaper00037872MGI annotationlipid particle, cytoplasm lipid particleCould not find cytoplasmic localization. We observed no co-localization of TMEM-135::GFP and Mito- Tracker Red (mitochondrial) (Fig. 4D) in the worm, whereas TMEM-135::GFP and Nile Red displayed very strong co- localization (Fig. 4E). Together, the mouse and worm data provide strong evidence that the TMEM135 protein is associated with fat droplets, supporting our hypothesis that TMEM135 plays a role in fat metabolism.From paper: p4 The sub-cellular localization of this protein appeared to correspond to dot-like cytoplasmic structures of 0.2 to 1 micron in L1 worms. p6 Figure 3. Panels D, E and F reveal that TMEM135 localizes to rounded sub-cellular
organelles of 0.2–0.5 microns in L1 larvae, which are particularly abundant in the intestine. p4 We next tested to determine whether, in C. elegans expressing TMEM-135::GFP, stained organelles would correspond to mitochondria or fat droplets. We used the lipophilic dyes, Nile Red and Mitotracker Red, to assess the co-localization of TMEM-135 with fat droplets or mitochondria, respectively. We observed no co-localization of TMEM-135::GFP and MitoTracker Red (mitochondrial) (Fig. 4D) in the worm, whereas TMEM-135::GFP and Nile Red displayed very strong colocalization (Fig. 4E). Together, the mouse and worm data provide strong evidence that the TMEM135 protein is associated with fat droplets, supporting our hypothesis that TMEM135 plays a role in fat metabolism.
This looks, in part, to be an ontology-related issue. The GO term 'lipid particle' is not related to 'cytoplasm' in the CC ontology; its ancestor is 'intracellular'. In this case, though, I think the annotation to cytoplasm is redundant, but without it, there's no link to 'cytoplasm' in the annotation. One possible solution would be to create a new GO term, 'cytoplasmic lipid droplet' that is_a 'lipid droplet' and is part_of 'cytoplasm' and 'part_of' intracellular.
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YESWBPaper00037877neuron projection,striated muscle dense body,
striated muscle dense bodySimilar to SLO-1 (Wang et al., 2001), BKIP-1 was enriched in the nerve ring and in body-wall muscle dense bodies (Fig. 4 B).I did not curate to neuron projection according to this sentence. I could not find neuron projection expr at a superficial look. If you think there is strong evidence, I will be happy to add it.This is a case of mapping 'nerve ring' localization to a GO CC term. In the WB AO, 'nerve ring' is defined as: the most extensive region of neuropil in the animal, consists of a large toroidal bundle of processes. Localizaton to the ventral or dorsal nerve cords would be an analogous situation.
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WBPaper00037878cytoplasm, phagocytic vesiclecytoplasm, phagocitic vesicle, phagocytic vesicle membranefrom the paper: 'In addition to phagosomal surfaces, SNX-1::GFP and LST-4::GFP were also observed on the highly dynamic membrane tubules extended from phagosomes'. On the GO widget of lst-4 in WormBase there is an IEA for phagocytic vescicle memebranes.snx-1 and snx-6 curated for go, not for Exprgenerally, in expression pattern we curate only genes for which expression was not described before or if the reporter used was different than what used before (or different method, e.g. antibody). We could import in bulk such annotations in OA to have the systems completely synced
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WBPaper00037900MATCH
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WBPaper00037904nucleuschromosome, cytoplasm, nucleusin late anaphase co-localization with the chromosomes was clearly detectable , chromatin association became apparent in late anaphase… chromosome association of MCM-4 is tightly controlled,..cytoplasmic at the onset of anaphase; (if we do curate LEGO style, shall we put in these types of localization (ie. Independent of site of action)
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WBPaper00037906MATCHin GO has extensions from UNIPROT_GOA
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to discuss: astral microtubuleWBPaper00037907DO NOT MATCHcell cortex, cytoplasm, spindlecell cortex, cytoplasm, spindle, astral microtubuleWe found filamentous signals of GFP::DYRB-1 that were similar to the pattern of astral microtubules (Fig. 2 A and D). FIGURE 2D: (D) The pattern of astral microtubules revealed using a GFP::tubulin strain.. These results indicate that cytoplasmic DYRB-1 moves along the astral microtubules in a dynein motor activity-dependent manner. If you think the evidence is not as strong will remove astral microtubule. Can Keep astral microtubules- discussed 08-25
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WBPaper00037927MATCH
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WBPaper00037956MATCH
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WBPaper00037973CANNOT FIND lon-3 nor synonyms in the paper lon-3, part_of annuli extracellular matrix, IDA
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WBPaper00038379NO OAdaf-16 - cytoplasm, nucleus (UniProt)WB doesn't typically annotate all reports of DAF-16 in the cytoplasm and the nucleus, but technically it's not wrong. However, in the LEGO world, DAF-16 cytoplasm annotations would not reflect where the activity occurs.
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WBPaper00040146MATCH
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WBPaper00040163MATCH
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WBPaper00040168MATCH
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WBPaper00040230NO GO CC
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WBPaper00040280MATCH
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WBPaper00040335MATCHmadd-4: extracellular space IDAadded extracellular spaceNeeds update to extracellular space- doneUpdated GO to 'extracellular space'; updated OA to 'extracellular space'
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WBPaper00040347NO GO CC
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WBPaper00040348NO GO CC
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WBPaper00040358NO GO CC
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WBPaper00040420NO GO CC
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WBPaper00040428MATCH
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WBPaper00040459NO GO CC
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WBPaper00040470Do not matchdma-1, part_of plasma membrane, IDA
plasma membrane, GOlgi apparatus, endoplasmic reticulumBright DMA-1::GFP localization can be seen in intracellular membrane structures that are likely to be golgi/ER. The plasma membrane is also clearly visible, indicating that DMA-1::GFP is a cell-surface protein.
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WBPaper00040470plasma membraneGolgi, ER, plasma membraneFigure S5. A thin slice image of the PVD cell body expressing DMA-1::GFP. Bright GFP localization can be seen in intracellular membrane structures that are likely to be golgi/ER. The plasma membrane is also clearly visible, indicating that DMA-1::GFP is a cell-surface protein.
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WBPaper00040473Partial Matchnucleus, let-526, part_of BAF-type complex, ISSnucleusadditional gene in OA
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WBPaper00040492NO GO CC
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WBPaper00040536NO GO CC
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WBPaper00040555MATCH
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WBPaper00040559NO GO CC
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WBPaper00040563Partial Matchlegocc : rab-6.2, colocalizes_with Golgi apparatus, IMP, UniProt_GOA
legocc : rab-6.2, part_of intracellular, IMP, part_of(WBls:0005175) part_of(WBls:0005451) part_of(WBls:0005751) part_of(WBls:0006804) , UniProt_GOA, and additional genes for GO
Golgi apparatus, dendrite, neuronal cell body
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WBPaper00040568NO GO CC
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WBPaper00040572MATCH
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WBPaper00040582MATCH
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WBPaper00040626MATCH
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WBPaper00040627MATCH
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WBPaper00040634NO GO CC
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WBPaper00040645MATCHadditional genes for GOadditional genes for ExprOA
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WBPaper00040649MATCHadditional genes for GO
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WBPaper00040681MATCH
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WBPaper00040689Partial Matchddl-1ddl-1 AND hsf-1Question about AEs. HSF-1 functioning as a sensor in the cytoplasm, but TF in the nucleus?Added hsf-1 to Protein2GO.
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WBPaper00040692NO GO CC
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WBPaper00040694Partial Match ric-7, part_of synapse, IDAsynapse, axon, neuronal cell body
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WBPaper00040730NO GO CC
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WBPaper00040749NO GO CC
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WBPaper00040969NO GO CC
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YESWBPaper00041001do not matchnucleusnucleus, cytoplasmFull-length (isoform-a) SUP-37::GFP and SUP- 37::mcherry fusion proteins localize predominantly to nuclei during late stages of embryogenesis. Expression of these constructs was, however, relatively dim and quite variable as compared with the sup-37 transcriptional reporters. Expression of the SUP-37 translational reporters was also occasionally detected in both the cytoplasm and nuclei of early-stage embryos at time points preceding morphogenesis. OK to keep cytoplasm- 08-25-2017
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WBPaper00041005Partial Match, the one not matching is an ISSeif-3.K, part_of eukaryotic translation initiation factor 3 complex, ISS
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WBPaper00041020MATCHGO has additional genes
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