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User:TheBockster

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CACAO Spring 2017

My Annotations

StatusPageDate/TimeGO Term (Aspect)ReferenceEvidenceNotesLinks
acceptableSALTY:ACSA2017-02-14 14:24:40 CSTGO:0003987 acetate-CoA ligase activity (F)PMID:27974467ECO:0000314 direct assay evidence used in manual assertion

Organism: Salmonella enterica (Salmonella typhimurium).

Protein Name: Acetyl-coenzyme A synthetase (Acs). The control of Figure 1C shows that when molecules such as cAMP inhibit Acetyl-coenzyme A Synthetase, Acetate-CoA ligase activity is downregulated. Thus, SeAcs is involved with Acetate-CoA ligase activity.

challenge
unacceptableSALTY:LYSAC2017-02-14 14:32:55 CSTGO:0051591 response to cAMP (P)PMID:27974467ECO:0000314 direct assay evidence used in manual assertion

Organism: Salmonella enterica (Salmonella typhimurium).

Paper's Protein Name: Protein acetyltransferase OR Lysine acetyltransferase (Pat). UniProt's Protein Name: Protein lysine acetyltransferase. "As shown in Fig. 2C, SePat increases the acetylation level of SeAcs Lys609 in vitro (lane 4), and cAMP promotes Pat-dependent acetylation substantially (lane 7). The addition of cAMP to the acetylation assay system further decreases SeAcs activity, suggesting SeAcs acetylation promoted by cAMP also contributes to the inhibitory effect of cAMP on SeAcs."

challenge
unacceptableSALTY:NPD2017-02-14 14:23:37 CSTGO:0051591 response to cAMP (P)PMID:27974467ECO:0000314 direct assay evidence used in manual assertion

Organism: Salmonella enterica (Salmonella typhimurium).

Paper's Protein Name: NAD+-dependent deacetylase (CobB). UniProt's Protein Name: NAD-dependent protein deacylase. "The result in Fig. 2D confirmed that SeCobB was able to remove the acetyl group on Lys609 of SeAcs (lane 4), and rescued SeAcs activity. However, decrease in the acetylation level as well as the recovery of SeAcs activity by CobB treatment was inhibited remarkably in the presence of cAMP (lane 7)."

challenge
acceptableSALTY:PRPE2017-02-14 14:28:35 CSTGO:0050218 propionate-CoA ligase activity (F)PMID:27974467ECO:0000314 direct assay evidence used in manual assertion

Organism: Salmonella enterica (Salmonella typhimurium).

Paper's Protein Name: Propionyl-CoA synthetase (PrpE). UniProt's Protein Name: Propionate--CoA ligase. The control of Figure 6 shows that propionyl-CoA synthetase is involved with the activity of Propionate-CoA ligase.

challenge
acceptableSALTY:LCFA2017-02-14 14:31:35 CSTGO:0004467 long-chain fatty acid-CoA ligase activity (F)PMID:27974467ECO:0000314 direct assay evidence used in manual assertion

Organism: Salmonella enterica (Salmonella typhimurium).

Paper's Protein Name: Long-chain acyl-CoA synthetase (FadD). UniProt's Protein Name: Long-chain-fatty-acid--CoA ligase. The control of Figure 6 shows that long-chain acyl-CoA synthetase is involved with the activity of Acyl-CoA ligase.

challenge
unacceptableSALTY:ACSA2017-03-17 01:40:31 CDTGO:0051591 response to cAMP (P)PMID:27974467ECO:0000314 direct assay evidence used in manual assertion

Organism: Salmonella enterica (Salmonella typhimurium).

Protein Name: Acetyl-coenzyme A synthetase (Acs). "The potential inhibitory effect of cAMP on Acs was tested using a subsaturated concentration for each of the substrates. cAMP substantially inhibited SeAcs activity only in an enzymatic reaction system with a low concentration of ATP (Fig. 1C), suggesting cAMP inhibits SeAcs via an ATP-competitive mechanism."

challenge
unacceptableMOUSE:DND12017-03-17 02:00:56 CDTGO:0043066 negative regulation of apoptotic process (P)PMID:28297718ECO:0000314 direct assay evidence used in manual assertion

Paper's Protein Name: RNA-binding protein DND1.

UniProt's Protein Name: Dead end protein homolog 1. Organism: Mus musculus (Mouse). Notes: This paper deals with the destabilization of specific mRNA segments by the protein Dnd1. One example of this involves apoptosis. When Dnd1 is mutated and loses function, there is “an upregulation of DND1 PAR-CLIP targets... including positive regulators of apoptosis.” More importantly, Extended figure 6g shows that after GSCs are transduced with DND1’s shRNA targets, cell death occurs within 4 days. The paper also states that “Annexin V-positive cells represent early apoptotic cells and are gated as P8 population (green)” in Extended Figure 6i. As can be seen in the figure, there are clearly more “early apoptotic cells” when the cells in question are transduced with DND1’s shRNA targets. It appears that the process for transduction was done with shRNA targets originating from mice, as is listed in Supplementary Table 9.

challenge
unacceptableMOUSE:DND12017-03-17 04:44:43 CDTGO:0023056 positive regulation of signaling (P)PMID:28297718ECO:0000314 direct assay evidence used in manual assertion

Paper's Protein Name: RNA-binding protein DND1.

UniProt's Protein Name: Dead end protein homolog 1. Organism: Mus musculus (Mouse). Notes: “Pathway analysis of the top 300 DND1 targets showed enrichment for genes associated with signalling pathways regulating pluripotent stem cells and cancer development (for example, TGFβ, WNT and PI3K–AKT signalling) (Extended Data Fig. 4, Supplementary Table 3)."

challenge
acceptableHUMAN:TADBP2017-03-25 00:21:27 CDTGO:0061158 3'-UTR-mediated mRNA destabilization (P)PMID:28335005ECO:0000314 direct assay evidence used in manual assertion

Organism: Homo sapiens.

Paper’s Protein Name: Transactive response DNA-binding protein 43 (TDP-43). UniProt’s Protein Name: TAR DNA-binding protein 43. Notes: This is seen in Figure 2B. The paper states that “to study whether TDP-43 promoted tau mRNA instability through the 3΄-UTR of the mRNA, we fused tau 3΄-UTR to the C-terminal of green fluorescence protein (GFP) to make pEGFP/tau 3΄-UTR plasmid. This plasmid allowed us to study the regulation of tau mRNA through its 3΄-UTR by measuring the expression of GFP.” As can be seen in Figure 2B, expression of GFP decreased with an increased dosage of the protein.

challenge
acceptableHUMAN:ANGT2017-03-25 01:23:47 CDTGO:0000187 activation of MAPK activity (P)PMID:28283184ECO:0000315 mutant phenotype evidence used in manual assertion

Organism: Homo sapiens.

Protein Name: Angiotensin II (Ang II). Notes: Figure 4A is used. As the paper states, the researchers "found an increase in phosphorylation of p38 MAPK when SMCs were treated with Ang II." The chart indeed shows that MAPK levels nearly multiply by three when cells are treated with Ang II. Thus, the increase in MMP-8 levels discussed in the paper is likely due to an activation of MAPK activity. Ang II shares a UniProt page with Ang-(1-7), even though the two are different entities.

challenge
acceptableHUMAN:ANGT2017-03-25 01:41:13 CDTGO:0043407 negative regulation of MAP kinase activity (P)PMID:28283184ECO:0000315 mutant phenotype evidence used in manual assertion

Organism: Homo sapiens.

Protein Name: Angiotensin-(1-7) (Ang-(1-7)). Notes: Figure 4A is used. As the paper states, “the activation of p38 MAPK induced by Ang II was counter-regulated by Ang-(1-7). The MAS receptor antagonist A779 blocked the inhibitory effect of Ang-(1-7) on Ang II-induced p38 MAPK activation.” To be clear, Ang-(1-7) needs the MAS receptor to inhibit the effects Ang II, which explains the effect of the A779 receptor antagonist. The chart indeed shows that MAPK levels decrease by a factor of *NEARLY* two when cells are treated with Ang II and Ang-(1-7) as opposed to just Ang II. Thus, the decrease in MMP-8 levels discussed in the paper (when cells are treated with both proteins as opposed to just Ang II) is likely due to a decrease in MAPK activity. Ang-(1-7) shares a UniProt page with Ang II, even though the two are different entities.

challenge
acceptableHUMAN:S10AB2017-03-25 13:14:06 CDTGO:0014911 positive regulation of smooth muscle cell migration (P)PMID:21139050ECO:0000315 mutant phenotype evidence used in manual assertion

Organism: Homo sapiens.

Protein Name: Protein S100-A11. Notes: Figure 4C is used. The paper states that “after the knockdown of t S100A11 expression, the cell migration induced by HIMF was significantly blocked (C).” Indeed, the corresponding chart does show that the relative area of the cells has significantly decreased upon mutation of S100A11.

challenge
acceptableHUMAN:S10AB2017-03-25 13:34:55 CDTGO:0005886 plasma membrane (C)PMID:21139050ECO:0000314 direct assay evidence used in manual assertion

Organism: Homo sapiens.

Protein Name: Protein S100-A11. Notes: Figure 2 is used. As the notes say, “S100A11 is a cytosol protein, spotted and diffusely distributed in the resting cells (A). With continuing HIMF stimulation, S100A11 aggregated and translocated to the plasma membrane and the nucleus (B, C, and D).” Thus, S100A11 localizes with the plasma membrane.

challenge
acceptableHUMAN:S10AB2017-03-25 13:44:52 CDTGO:0005634 nucleus (C)PMID:21139050ECO:0000314 direct assay evidence used in manual assertion

Organism: Homo sapiens.

Protein Name: Protein S100-A11. Notes: Figure 2 is used. As the notes say, “S100A11 is a cytosol protein, spotted and diffusely distributed in the resting cells (A). With continuing HIMF stimulation, S100A11 aggregated and translocated to the plasma membrane and the nucleus (B, C, and D).” Thus, S100A11 colocalizes with the nucleus.

challenge
unacceptableHUMAN:S10AB2017-03-25 20:09:57 CDTGO:0048660 regulation of smooth muscle cell proliferation (P)PMID:21139050ECO:0000315 mutant phenotype evidence used in manual assertion

Organism: Homo sapiens.

Protein Name: Protein S100-A11. Notes: Figure 4D is used. According to the paper, “cell proliferation was evaluated by a direct cell counting assay using a hemocytometer... As shown in D, S100A11 knockdown did not affect the cell proliferation by HIMF.” The corresponding chart does indeed show that cell proliferation does not change much in comparison to other groups when treated with S100A11.

challenge
unacceptableHUMAN:FUBP22017-03-25 20:04:47 CDTGO:0008284 positive regulation of cell proliferation (P)PMID:28275056ECO:0000315 mutant phenotype evidence used in manual assertion

Organism: Homo sapiens.

Paper’s Protein Name: K homology splicing regulatory protein (KSRP). UniProt’s Protein Name: Far upstream element-binding protein 2 OR ALTERNATIVELY KH type-splicing regulatory protein. Notes: Figures 2C-D are primarily used, but Figures 2A-B help to understand the resuls. This is because Figures 2A-B show that “Transfection of H2122 and H157 with two different KSRP specific siRNAs resulted in a significant reduction of KSRP expression.” Thus, when Figures 2C-D show that the “knockdown conditions” created by these siRNAs lead to decreased cellular proliferation over time, it is clear that KSRP is linked to cellular proliferation. No UniProt term appears to be specific to the non-small cell lung cancer cell line.

challenge
unacceptableHUMAN:FUBP22017-03-25 20:04:48 CDTGO:0030335 positive regulation of cell migration (P)PMID:28275056ECO:0000315 mutant phenotype evidence used in manual assertion

Organism: Homo sapiens

Paper’s Protein Name: K homology splicing regulatory protein (KSRP). UniProt’s Protein Name: Far upstream element-binding protein 2 OR ALTERNATIVELY KH type-splicing regulatory protein. Notes: Figure 3E is used. According to the paper, “the stable knockdown of KSRP resulted in reduced cell migration, when compared to H2122 clones stably expressing control shRNAs.” In other words, decreased levels of KSRP are linked to decreased levels of cellular migration. No UniProt term appears to be specific to the non-small cell lung cancer cell line.

challenge
acceptableHUMAN:FUBP22017-03-25 20:20:35 CDTGO:0061158 3'-UTR-mediated mRNA destabilization (P)PMID:28275056ECO:0000315 mutant phenotype evidence used in manual assertion

Paper’s Protein Name: K homology splicing regulatory protein (KSRP).

UniProt’s Protein Name: Far upstream element-binding protein 2 OR ALTERNATIVELY KH type-splicing regulatory protein. Organism: Homo sapiens. Notes: Figure 6E is used. Figure 4 had already demonstrated that KSRP downregulates the Spry4 protein, and Figure 5D had already demonstrated that KSRP binds to the 3’-UTR mRNA of the Spry4 gene. In the paper, it is claimed that “if the effects of KSRP on Spry4 3’UTR were specific; then upon KSRP knockdown, the KSRP-mediated mRNA repression should be relaxed, as detected by an increase in luciferase activities. Indeed, knockdown of KSRP increased the luciferase activities of Luc-Spry4 UTR, but not the luciferase activities of Luc-Spry4 UTR-F1.” The chart in Figure 6E does indeed show that luciferase activities approximately double when KSRP is mutated. Thus, KSRP destabilizes the mRNA of Spry4 by binding to the 3’-UTR region.

challenge
acceptableHUMAN:DND12017-03-25 22:54:19 CDTGO:0061158 3'-UTR-mediated mRNA destabilization (P)PMID:28297718ECO:0000314 direct assay evidence used in manual assertion

Organism: Homo sapiens.

UniProt’s Name: Dead end protein homolog 1. Paper’s Name: RNA-binding protein DND1. Notes: Extended Figure 2g is primarily used, though other figures help to understand the findings. For instance, the paper had previously indicated that DND1 is responsible for mRNA destabilization, and showed in Figure 1E that with an increase in number of DND1 binding sites lead to a greater decrease in median transcript abundance. More importantly, the paper states that “only binding sites located in the 3′ UTR contributed to the DND1-mediated target mRNA reduction.” Extended Figure 2g indeed shows that mRNA targets (of DND1) with binding sites in the 3’-UTR region also have a greater decrease in median transcript abundance. As this data primarily makes use of “FH–DND1-expressing HEK293 cells,” this is a human protein, not a mouse protein.

challenge
unacceptableHUMAN:RBM242017-03-26 01:25:42 CDTGO:0061158 3'-UTR-mediated mRNA destabilization (P)PMID:24375645ECO:0000314 direct assay evidence used in manual assertion

Organism: Homo sapiens.

Protein Name: RNA-Binding Protein RBM24. Notes: Figures 5G-H and 6D-E are used. First, the former two figures prove that RBM24 destabilizes the mRNA of p63. The paper states that “the half-life of ΔNp63 mRNA was deceased from 3.7 hours in the control cells to 2.7 hours in cells with RBM24 expression, and the half-life of TAp63 mRNA was deceased from 9.3 hours in the control cells to 7.2 hours in cells with RBM24 expression.” As can be seen in the line graphs, the p63 transcripts destabilize more quickly in the presence of RBM24. Thus, RBM24 is linked to mRNA destabilization. It is also linked to 3’UTR-mediated mRNA destabilization in particular, as proven by Figures 6D-E. As the paper states, “we found that RBM24 had no effect on TAp63α expression from an expression vector that only contains TAp63α coding sequence (Fig. 6D). By contrast, TAp63α expression was significantly inhibited by RBM24 when the TAp63α expression vector contains a full-length p63 3′UTR (Fig. 6E).” In Figure 6D, it can be seen that the relative level of TAp63α barely changed when RBM24 was transfected into the cells. However, in Figure 6E, the level decreased significantly, due to the presence of a 3’UTR region. Thus, the inhibition of p63 occurs by the destabilization of its transcripts, specifically the 3’UTR region of mRNA. This links RBM24 to 3’UTR-mediated mRNA destabilization.

challenge
updatedbyinstructorYEAST:SUB12017-04-04 13:23:17 CDTGO:0051053 negative regulation of DNA metabolic process (P)PMID:28369605ECO:0000315 mutant phenotype evidence used in manual assertion

Paper’s Protein Name: Co-transcriptional activator Sub1.

UniProt’s Protein Name: RNA polymerase II transcriptional coactivator SUB1. Organism: Saccharomyces cerevisiae (“all strains derived from YPH45”). Notes: Figure 1B is used. According to the paper “When highly transcribed, the rate of recombination for the pTET-lys2-GTOP was elevated by ∼7-fold in top1Δ sub1Δ strain compared to top1Δ (Figure 1B).” The chart indeed shows exactly this, although it doesn’t use the delta symbols on its labels. If recombination is elevated in Sub1’s absence, this implies that Sub1 negatively regulates DNA recombination.

challenge
updatedbyinstructorHUMAN:TCP42017-04-04 14:50:47 CDTGO:0051053 negative regulation of DNA metabolic process (P)PMID:28369605ECO:0000314 direct assay evidence used in manual assertion

Paper’s Protein Name: “Human homolog of Sub1, variously referred to as hSub1, p15 or PC4.” PC4 is primarily used.

Uniprot’s Protein Name: Activated RNA polymerase II transcriptional coactivator p15. Organism: Homo sapiens. Notes: Figures 2B-E are all applicable, but I will primarily use 2B. The paper states that “the ectopic expression of Sub1 or PC4 reduced the rate of recombination for the pTET-lys2-GTOP construct by 9.6- and 10.3-fold, respectively, thereby resulting in the rates of recombination that are significantly lower than in top1Δ single deletion strains (Figure 2B).” Thus, PC4 seems to be linked to down-regulation of DNA recombination. The procedures of this experiment involve transforming yeast strains with a “PC4 expression vector,” so the evidence code should be IDA.

challenge
unacceptableYEAST:TOP12017-04-08 15:53:41 CDTGO:0045910 negative regulation of DNA recombination (P)PMID:28369605ECO:0000315 mutant phenotype evidence used in manual assertion

Paper’s Protein Name: Top1.

UniProt.’s Protein Name: DNA topoisomerase 1. Organism: Saccharomyces cerevisiae (“all strains derived from YPH45”). Notes: This paper actually implies that Top1’s effects on genome stability and DNA recombination had already been proven beforehand. Nevertheless, this paper provides evidence for the correlation as well, specifically in Figures 1A-B. In Figure 1A, wild type yeast has a DNA recombination rate of about 20*10^-8 for GTOP. However, Figure 1B shows that when the Top1 protein is mutated and knocked out, this rate is over 100*10^-8. It is important to note that these two charts are scaled very differently. Because recombination is elevated in Top1’s absence, it is implied that Top1 negatively regulates DNA recombination.

challenge
updatedbyinstructorHUMAN:ARID22017-04-08 22:02:31 CDTGO:1905168 positive regulation of double-strand break repair via homologous recombination (P)PMID:28381560ECO:0000315 mutant phenotype evidence used in manual assertion

Baf200 (Arid2) PBAF-defining subunit/AT-rich interactive domain-containing protein 2. Homo sapiens.

FIGURE 4. Baf200 and Baf180 expression is important for homologous recombination.

challenge
unacceptableHUMAN:XPA2017-04-20 11:53:27 CDTGO:0005730 nucleolus (C)PMID:28416769ECO:0000314 direct assay evidence used in manual assertion

UniProt’s Protein Name: DNA repair protein complementing XP-A cells.

Paper’s Protein Name: XPA. Organism: Homo sapiens. Notes: Figure 1C is used. According to the paper, the researchers “observed a distinct enrichment of XPA, a critical NER protein [1] in the nucleolus of pre-extracted U2OS and MRC5 cells, starting at 1 hour after UV irradiation.” This can indeed be seen in the cell visualization for Figure 1C. As this only occur after one hour of UV irradiation, the relationship between this protein and the nucleolus is quite clearly transient, and the Colocalizes with qualifier is necessary. U2OS and MRC5 cells are human cells, so the protein is human as well.

challenge
acceptableHUMAN:DNJC22017-04-20 12:15:17 CDTGO:0005730 nucleolus (C)PMID:28416769ECO:0000314 direct assay evidence used in manual assertion

Paper’s Protein Name: H2A-ubiquitin binding protein ZRF1.

UniProt’s Protein Name: DnaJ homolog subfamily C member 2 or alternatively Zuotin-related factor 1. Organism: Homo sapiens. Notes: Figure 5A is used. While “investigating the nuclear distribution of ZRF1 after pre-extraction of U2OS cells, [the researchers] detected ZRF1 in the nucleolus as seen by simultaneous Nucleophosmin (NPM) staining.” This can indeed be seen in the cell visualization for Figure 5A. This protein was present even prior to UV irradiation, so the relationship between the protein and nucleolus is not transient, and the Colocalizes With qualifier is not necessary. U2OS cells are human cells, so the protein is human as well.

challenge
unacceptableHUMAN:KI672017-04-22 19:05:40 CDTGO:0005634 nucleus (C)PMID:28334682ECO:0000314 direct assay evidence used in manual assertion

Organism: Homo sapiens.

Protein Name: Proliferation marker protein Ki-67. Notes: Figure 1D is used. Normal human mammary epithelial cells (HMEC) are stained with Hoechst 33342 to make the nuclei appear blue. They are also immunostained so that Ki67 will appear green. As can be seen in the bottom row, the Ki67 protein is present in the nucleus for HMEC cells whether they are treated with Phytochemicals or not. Thus, Ki67 is linked to the nucleus, in a non-transient manner.

challenge
unacceptableHUMAN:CDN1A2017-04-22 19:08:40 CDTGO:0005634 nucleus (C)PMID:28334682ECO:0000314 direct assay evidence used in manual assertion

Organism: Homo sapiens.

Paper’s Protein Name: “p21, a cell cycle inhibitor.” UniProt Protein Name: Cyclin-dependent kinase inhibitor 1 OR p21. Notes: Figure 1D is used. Normal human mammary epithelial cells (HMEC) and MCF-7 human cancer cells are stained with Hoechst 33342 to make the nuclei appear blue. They are also immunostained so that p21 will appear green. As can be seen in the micrographs, p21 only is present in the cancer cells, and only when they are treated with Phytochemicals. Thus, a link is established between p21 and the nucleus, but it is a transient relationship.

challenge
unacceptableHUMAN:ACTB2017-04-22 20:35:49 CDTGO:0005634 nucleus (C)PMID:28334682ECO:0000314 direct assay evidence used in manual assertion

Organism: Homo sapiens.

Paper’s Protein Name: β-actin. UniProt Protein Name: Actin, cytoplasmic 1 or Beta-actin. Notes: Figure 3F is used. MCF-7 cells (which are human) have their nuclei stained blue and are also immunostained so that β-actin will appear green. As can be seen in the micrographs, there is significant overlap between these colors. Thus a non-transient link is established between β-actin and the nucleus.

challenge
unacceptableHUMAN:COF12017-04-22 21:13:39 CDTGO:0005634 nucleus (C)PMID:28334682ECO:0000314 direct assay evidence used in manual assertion

Organism: Homo sapiens.

Protein Name: Cofilin. Notes: Figure 3G is used. MCF-7 cells (which are human) have their nuclei stained blue and are also immunostained so that cofilin will appear red. As can be seen in the micrographs, cofilin does not have overlap with the nuclei until the cells are exposed to sulforaphane. Thus, a link is established between cofilin and the nucleus, but it is a transient relationship.

challenge
unacceptableHUMAN:LMNA2017-04-22 23:46:42 CDTGO:0005634 nucleus (C)PMID:28334682ECO:0000314 direct assay evidence used in manual assertion

Organism: Homo sapiens.

Paper’s Protein Name: Lamin A/C. UniProt’s Protein Name: Prelamin-A/C. (According to UniProt, this is cleaved into the chain Lamin A/C. Regardless, the official location of Lamin A/C on UniProt is this page.) Notes: Figure 4B is used. MCF-7 cells (which are human) have their nuclei stained blue and are also immunostained so that Lamin A/C will appear green. As can be seen in the micrographs, there is significant overlap of these colors. While Lamin A/C appears to be more vividly colored when the cells are exposed to sulforaphane, it nevertheless can be seen even in the control. Therefore, a non-transient link is established between Lamin A/C and the nucleus.

challenge
unacceptableHUMAN:LMNB12017-04-23 00:00:12 CDTGO:0005634 nucleus (C)PMID:28334682ECO:0000314 direct assay evidence used in manual assertion

Organism: Homo sapiens.

Protein Name: Lamin B1. Notes: Figure 4G is used. MCF-7 cells (which are human) have their nuclei stained blue and are also immunostained so that Lamin B1 will appear green. As can be seen in the micrograph control groups, there is significant overlap of these colors. There thus appears to be a non-transient link between Lamin B1 and the nucleus.

challenge
acceptableHUMAN:RRN32017-04-23 17:34:38 CDTGO:0005730 nucleolus (C)PMID:28334682ECO:0000314 direct assay evidence used in manual assertion

Organism: Homo sapiens.

Protein Name: RNA polymerase I-specific transcription initiation factor RRN3/TIF-IA. Notes: Figure 6B is used. MCF-7 cells (which are human) have their nucleoli stained red and are also immunostained so that RRN3 will appear green. As can be seen in the micrograph control groups, there is significant overlap of these colors. There thus appears to be a non-transient link between RRN3 and the nucleolus.

challenge
unacceptableHUMAN:RRN32017-04-23 00:23:54 CDTGO:0005634 nucleus (C)PMID:28334682ECO:0000314 direct assay evidence used in manual assertion

Organism: Homo sapiens.

Protein Name: RNA polymerase I-specific transcription initiation factor RRN3/TIF-IA. Notes: Figure 6B is used. MCF-7 cells (which are human) have their nuclei stained blue and are also immunostained so that RRN3 will appear green. As can be seen in the micrograph control groups, there is significant overlap of these colors. There thus appears to be a non-transient link between RRN3 and the nucleus.

challenge

acceptable:13
unacceptable:18
requires_changes:0
flagged:0

Annotations challenged by TheBockster

StatusAuthor,GroupPageGO Term (Aspect)ReferenceEvidenceLinksPage history
updatedbyinstructorSStone15,
Team Lily Whale
MOUSE:RABP2GO:0005634 - nucleus (C)PMID:27609837ECO:0000314 direct assay evidence used in manual assertionchallengeC: 1
updatedbyinstructorLoganMcCurry,
Team Gene String
SCHPO:YPT3GO:0035838 - growing cell tip (C)PMID:27082518ECO:0000314 direct assay evidence used in manual assertionchallengeC: 3

fixed by TheBockster
updatedbyinstructorCherylrood,
Team Voldemort
NOSS1:Q8YP05GO:0016163 - nitrogenase activity (F)PMID:27102494ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 2

fixed by SarahCouv
acceptableCSears,
Team Girl, you trypsin
HUMAN:PTPRJGO:0005899 - insulin receptor complex (C)PMID:26063811ECO:0000314 direct assay evidence used in manual assertionchallengeC: 3
acceptableCSears,
Team Girl, you trypsin
RAT:SNX5GO:0005903 - brush border (C)PMID:25825816ECO:0000314 direct assay evidence used in manual assertionchallengeC: 2
acceptableCSears,
Team Girl, you trypsin
MOUSE:CAV1GO:0038016 - insulin receptor internalization (P)PMID:27110488ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 1
acceptableCSears,
Team Girl, you trypsin
HUMAN:SNX5GO:0048471 - perinuclear region of cytoplasm (C)PMID:25825816ECO:0000314 direct assay evidence used in manual assertionchallengeC: 1
updatedbyinstructorSeannash,
Team Voldemort
PORGN:A0A0E2LMN8GO:0044011 - single-species biofilm formation on inanimate substrate (P)PMID:17020544ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 3
unacceptableZiba0916,
Team Girl, you trypsin
GIBZE:I1RWM5GO:0009405 - obsolete pathogenesis (Fusarium graminearum, GIL1 (FGSG_08701) Fig. 5C)PMID:28212314IMP: Inferred from Mutant Phenotype challengeC: 2
updatedbyinstructorLoganMcCurry,
Team Gene String
SCHPO:SEC2GO:0090619 - meiotic spindle pole (C)PMID:27630562ECO:0000314 direct assay evidence used in manual assertionchallengeC: 7
unacceptableCSears,
Team Girl, you trypsin
HUMAN:PTPROGO:1990264 - peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity (P)PMID:26063811ECO:0000314 direct assay evidence used in manual assertionchallengeC: 3
unacceptableCSears,
Team Girl, you trypsin
HUMAN:PTPRHGO:1990264 - peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity (P)PMID:26063811ECO:0000314 direct assay evidence used in manual assertionchallengeC: 2
unacceptableCSears,
Team Girl, you trypsin
HUMAN:PTPRBGO:1990264 - peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity (P)PMID:26063811ECO:0000314 direct assay evidence used in manual assertionchallengeC: 2
updatedbyinstructorMCGU2014,
Team Lily Whale
ORYSI:A0A165TZX1GO:0005634 - nucleus (C)PMID:24534105ECO:0000314 direct assay evidence used in manual assertionchallengeC: 1

fixed by TheBockster
updatedbyinstructorMCGU2014,
Team Lily Whale
ORYSI:A0A165TZX1GO:0005737 - cytoplasm (C)PMID:24534105ECO:0000314 direct assay evidence used in manual assertionchallengeC: 1

fixed by TheBockster
unacceptableZiba0916,
Team Girl, you trypsin
ORYSJ:Q8LRC7GO:0000145 - exocyst (C)PMID:28163713ECO:0000314 direct assay evidence used in manual assertionchallengeC: 2
updatedbyinstructorAmelianichols,
Team Six
SALTY:INVGGO:0030257 - type III protein secretion system complex (C)PMID:10944190ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 1
updatedbyinstructorMCGU2014,
Team Lily Whale
YEAST:TRM1GO:0004809 - tRNA (guanine-N2-)-methyltransferase activity (F)PMID:2426253ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 6

fixed by TheBockster
updatedbyinstructorSStone15,
Team Lily Whale
HPV16:VE4GO:0030430 - host cell cytoplasm (C)PMID:15767402ECO:0000314 direct assay evidence used in manual assertionchallengeC: 4

fixed by TheBockster
updatedbyinstructorSarahswartz,
Team Lysis to Kill
LIBAP:C6XHE2GO:0051920 - peroxiredoxin activity (F)PMID:27987036ECO:0000314 direct assay evidence used in manual assertionchallengeC: 2

fixed by TheBockster
unacceptableICourvertier,
Team Splice splice baby
ARATH:SMU1GO:0008380 - RNA splicing (P)Q8W117:Q8W117ECO:0000314 direct assay evidence used in manual assertionchallengeC: 2
unacceptableAWynn,
Team All about that base
HUMAN:SOSB1GO:0071168 - protein localization to chromatin (P)PMID:26261212ECO:0000314 direct assay evidence used in manual assertionchallengeC: 2
updatedbyinstructorAlexstangel,
Team Moldevort
MYCTU:PPE18GO:0051701 - biological process involved in interaction with host (P)PMID:23300718ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 2

fixed by CSears
unacceptableMHAoufi,
Team Integreats
FOAMV:GAGGO:0039715 - nuclear viral factory (C)PMID:22393357ECO:0000314 direct assay evidence used in manual assertionchallengeC: 1
unacceptableMHAoufi,
Team Integreats
FOAMV:GAGGO:0044444 - obsolete cytoplasmic part (C)PMID:21255441ECO:0000314 direct assay evidence used in manual assertionchallengeC: 1
unacceptableMHAoufi,
Team Integreats
FOAMV:GAGGO:0033655 - host cell cytoplasm part (C)PMID:21255441ECO:0000314 direct assay evidence used in manual assertionchallengeC: 1
updatedbyinstructorMHAoufi,
Team Integreats
SFVCP:GAGGO:0042025 - host cell nucleus (C)PMID:21255441ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 1
unacceptableJoshuakrank,
Team Moldevort
STAA8:QUEFGO:0043708 - cell adhesion involved in biofilm formation (P)PMID:27144398ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 4
unacceptableSarahCouv,
Team Lily Whale
MOUSE:P63GO:0005634 - nucleus (C)PMID:22035303ECO:0000314 direct assay evidence used in manual assertionchallengeC: 5

6 annotations fixed by TheBockster

What do the icons mean in the status column?

assessment icons.jpg