GONUTS has been updated to MW1.31 Most things seem to be working but be sure to report problems.
Cacao
| Contributes to | GO:0009927 | histidine phosphotransfer kinase activity | 17237174:17237174 | ECO:0000275 IDA: Inferred from Direct Assay | Molecular Function | In a microarray experiment, B-glucuronidase activity was used to determine relative expression levels of uidA+ transcription fusion proteins (Fig 2). Smc00888 is a regulatory factor involved in c-di-GMP signaling that encodes a histidine kinase. During stationary phase, SMc00888 locus expression decreased three-fold in the cbrA::Tn5 mutant compared to WT. The cbrA gene putatively encodes for histidine kinase and was found to be a regulator of the ci-di-GMP signaling pathway. | complete | |
| This annotation made on page: RHIME:Q92RW9 By: CXie (group Team Red B 2019) on 2019-03-31 16:42:15 CDT. | ||||||||
You must be logged in to challenge this annotation.
| Entry Type | Challenging User,Group | Time/Date | Challenge Reason | Points/Assessment | ||||||||||||||||||||||
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| Challenge | PMariano, Team Blue B 2019 | 2019-04-15 09:29:57 CDT | If your annotation is categorized as a biological process, I think you can just leave the qualifier blank. In addition, there appears to be positive regulation of histidine kinase that is supported by beta-glucuronidase transcription fusion evidence. | 2 | ||||||||||||||||||||||
| Challenge | KAtanasoff, Team Blue A 2019 | 2019-04-01 10:23:50 CDT | Beta-glucuronidase activity is not measured using an expression microarray assay (as your ECO term specifies), since it's not directly measuring the actual transcription levels of a particular gene. Rather, it looks like in the paper, the experimenters generated a cbrA deletion mutant, which was then used to show (in figure 2) that the CbrA protein affects expression of different regulatory proteins. So I think your GO term as well as your ECO term is inappropriate for this particular annotation. | None, yet. | ||||||||||||||||||||||
| Public Assessment | Ivanerill | 2019-04-22 09:36:01 CDT | As mentioned before, Fig. 2 does not demonstrate "protein histidine kinase activity", just transcriptional regulation of a gene with such activity. Notes should clearly map to the experimental support for the specific GO term being asserted. | Requires Changes ✔ Protein ✔ Publication ✔ Qualifier ✗ Go term ✔ Evidence ✔ With/From ✗ Notes ✔ Unique/Original | ||||||||||||||||||||||
| Public Assessment | DanielRenfro | 2019-04-21 17:16:19 CDT | This annotation has been flagged because it has been edited since last assessment
| Flagged | ||||||||||||||||||||||
| Public Assessment | Ivanerill | 2019-04-18 11:00:51 CDT | Remove "The cbrA gene putatively encodes for histidine kinase." from the notes. The evidence does not support that "histidine kinase activity" is regulated, just the expression of the gene that encodes it. Check http://geneontology.org/docs/go-annotations/ for use of qualifiers. | Requires Changes ✔ Protein ✔ Publication ✗ Qualifier ✗ Go term ✔ Evidence ✔ With/From ✗ Notes ✔ Unique/Original | ||||||||||||||||||||||
| Public Assessment | DanielRenfro | 2019-04-17 10:37:49 CDT | This annotation has been flagged because it has been edited since last assessment
| Flagged | ||||||||||||||||||||||
| Public Assessment | DanielRenfro | 2019-04-15 09:29:57 CDT | This annotation has been flagged because it has been challenged since last assessment | Flagged | ||||||||||||||||||||||
| Public Assessment | Ivanerill | 2019-04-08 17:06:33 CDT | See http://geneontology.org/docs/go-annotations/ for usage of the "contributes to" qualifier. Use cross-product of evidence with "manual assertion" for your ECO. The type of regulation is demonstrated quite clearly in the Figure. You should annotate to that more specific term. This (Fig.2) is not a microarray analysis result. Read the paper carefully. Your notes also have more conclusions than what the figure warrants. | Requires Changes ✔ Protein ✔ Publication ✗ Qualifier ✗ Go term ✗ Evidence ✔ With/From ✗ Notes | ||||||||||||||||||||||
| Public Assessment | DanielRenfro | 2019-04-03 09:54:36 CDT | This annotation has been flagged because it has been edited since last assessment
| Flagged |
