CACAO Spring 2014
My Annotations
| Status | Page | Date/Time | GO Term (Aspect) | Reference | Evidence | Notes | Links |
|---|
| unacceptable | 9ENTR:E7BBJ0 | 2014-04-01 13:02:07 CDT | GO:0017053 transcriptional repressor complex (C) | PMID:21183667 | ECO:0000315 mutant phenotype evidence used in manual assertion | PigS predicted to be an ArsR-family transcriptional repressor controlling pigS-pmpABC and blhA-orfY operons. Figure 3 shows mutation assays where transcript of blhA is increased in a pigS knockout mutant in comparison to wild type. Figure 6 shows lowered Pig production in pigS mutants in association with the blhA-orfY overexpression.
| challenge |
| unacceptable | ARATH:HFA4A | 2014-04-01 20:06:51 CDT | GO:0042538 hyperosmotic salinity response (P) | PMID:24676858 | ECO:0000315 mutant phenotype evidence used in manual assertion | Figure 2 has an overexpressor mutant of HSFA4A compared to wild type Arabidopsis thaliana grown in high NaCl media conditions. Overexpressng plants had higher rates of survival, root, and rosette growth in comparison to wild type. Figure 4 shows the growth of a HSFA4A t-DNA knockout mutant grown on high salinity media compared to wild type. The HSFA4A knockout had lower rates of survival and smaller rosette size when compared to wild type. Complementation of the HSFA4A gene had a partial restoration of function seen in larger rosettes and higher survival rates with high concentrations of NaCl.
| challenge |
| updatedbyinstructor | MOUSE:TAF4B | 2014-04-02 11:32:31 CDT | GO:2000648 positive regulation of stem cell proliferation (P) | PMID:23350932 | ECO:0000315 mutant phenotype evidence used in manual assertion | Figure 5 shows transfected mouse embryo cells with TAF4b silenced by siRNAs. Those with silenced TAF4b had lower rates of embryonic cell growth when compared to control.
| challenge |
| updatedbyinstructor | CAPAN:Q08ET5 | 2014-04-03 11:07:23 CDT | GO:0016298 lipase activity (F) | PMID:17929052 | ECO:0000315 mutant phenotype evidence used in manual assertion | | challenge |
| updatedbyinstructor | GEOSE:AXE2 | 2014-04-03 11:30:49 CDT | GO:0046555 acetylxylan esterase activity (F) | PMID:21994937 | ECO:0000314 direct assay evidence used in manual assertion | Figure 3 shows the deacetylation of xylobiose peracetate by Axe2 at pH 7 visualized on a TLC plate.
| challenge |
| updatedbyinstructor | TANCI:H6U1I8 | 2014-04-03 11:48:44 CDT | GO:0016412 serine O-acyltransferase activity (F) | PMID:22385412 | ECO:0000315 mutant phenotype evidence used in manual assertion | GDSL lipase was purified and recombineered into E. coli with a maltose binding protein fusion. The reaction transfers the chrysanthemoyl group from coenzyme A to pyrethrolone. Figure 3 shows mutations in serine of the GDSL domain eliminate acetyltransferase activity and maltose binding protein alone does not have acetyltransferase activity.
| challenge |
| unacceptable | ORYSJ:GL84 | 2014-04-03 12:16:17 CDT | GO:0010017 red or far-red light signaling pathway (P) | PMID:17048141 | ECO:0000315 mutant phenotype evidence used in manual assertion | Figure 4 shows transcript levels of PhyA and PhyB mutants in the dark and with a red light pulse. Those with one phytochrome mutated had an increase in transcript level after the red light pulse and mutants wit both phytocromes mutated had no GER1 response. Figure 2 shows an accumulation of GER1 in red and far red light for wild type and little induction of GER1 in hebiba mutant with impaired light response.
| challenge |
| acceptable | BACSU:LIPC | 2014-04-06 11:34:31 CDT | GO:0016042 lipid catabolic process (P) | PMID:17220230 | ECO:0000314 direct assay evidence used in manual assertion | Figure 6 shows an SDS & zymography assay performed using an empty vector, a vector with YtsK, and bovine serum albumin. Lane 2 is YtsK's SDS and shows the protein's molecular weight. Lane 5 is YtsK's zymography assay and it shows lysis activity at the same kDa as in the SDS indicating YtsK has lypolytic activity. The control's zymogen assay showed no activity.
| challenge |
| unacceptable | CAPCH:O81647 | 2014-04-06 16:02:09 CDT | GO:0009627 systemic acquired resistance (P) | PMID:24642849 | ECO:0000315 mutant phenotype evidence used in manual assertion | Figure 1 shows plants with an empty vector control and silenced CaPAL1 genes infected with Xcv. Plants with silenced CaPAL1 genes had higher levels of leaf lesions, higher Xcv count, and lower induction of PAL-an enzyme induced under stresses including pathogen stress. In figure 4, the salicylic acid levels in these mutants in response to Xcv show the silenced CaPAL1 gene having lower levels of free and total SA compared to control.
| challenge |
| acceptable | CAPAN:F6JSQ7 | 2014-04-06 16:17:36 CDT | GO:0004674 protein serine/threonine kinase activity (F) | PMID:24686111 | ECO:0000314 direct assay evidence used in manual assertion | Figure 5 C): assay showing the detection of anti-phospho-serine antibody with wild type and mutated SGT1 and PIK1 genes. Phosphorylation is observed only with WT PIK1 genes. Phosphorylation occurs on WT SGT1 and on the SGT1 mutated in the 161 serine. Other mutated serines unable to be phosphorylated by PIK1 indicate active residues.
| challenge |
acceptable:2
unacceptable:4
requires_changes:0
flagged:0
Annotations challenged by Grevever
| Status | Author,Group | Page | GO Term (Aspect) | Reference | Evidence | Links | Page history |
|---|
| acceptable | Djgulizia,
Team Texas Aggies | YEAST:VPS74 | GO:0035269 - protein O-linked mannosylation (P) | PMID:18410729 | ECO:0000315 mutant phenotype evidence used in manual assertion | challenge | C: 1
|
| unacceptable | Djgulizia,
Team Texas Aggies | HUMAN:MY18A | GO:0051645 - Golgi localization (P) | PMID:24485452 | ECO:0000315 mutant phenotype evidence used in manual assertion | challenge | C: 1
|
| unacceptable | Djgulizia,
Team Texas Aggies | HUMAN:GOLP3 | GO:0000138 - Golgi trans cisterna (C) | PMID:19837035 | ECO:0000314 direct assay evidence used in manual assertion | challenge | C: 1
|
| updatedbyinstructor | Cmpete,
Team Honey Badgers 14 | HUMAN:GDIR2 | GO:1901164 - negative regulation of trophoblast cell migration (P) | PMID:24554735 | ECO:0000314 direct assay evidence used in manual assertion | challenge | C: 2
fixed by Grevever |
| updatedbyinstructor | Trange,
Team Kitten Me Right Meow | MOUSE:DNAS1 | GO:0004530 - deoxyribonuclease I activity (F) | PMID:15015938 | ECO:0000315 mutant phenotype evidence used in manual assertion | challenge | C: 1
fixed by Grevever |
| updatedbyinstructor | Sgus,
Team C terminals | HUMAN:PLPL3 | GO:0036153 - triglyceride acyl-chain remodeling (P) | PMID:24511104 | ECO:0000314 direct assay evidence used in manual assertion | challenge | C: 2
|
| updatedbyinstructor | Kyoung,
Team Pnut Butter Squares | HUMAN:BRCA1 | GO:0033147 - negative regulation of intracellular estrogen receptor signaling pathway (P) | PMID:17505062 | ECO:0000315 mutant phenotype evidence used in manual assertion | challenge | C: 3
fixed by Grevever |
| updatedbyinstructor | Malexander2,
Team Pancakes At Nite | HUMAN:CIB1 | GO:0005886 - plasma membrane (C) | PMID:20473878 | ECO:0000314 direct assay evidence used in manual assertion | challenge | C: 3
fixed by Grevever |
| unacceptable | Grolfe,
Team Pancakes At Nite | HUMAN:CIB1 | GO:0051592 - response to calcium ion (P) | PMID:20473878 | ECO:0000314 direct assay evidence used in manual assertion | challenge | C: 3
|
4 annotations fixed by Grevever
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