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User:ASarahAli

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CACAO Fall 2017

My Annotations

StatusPageDate/TimeGO Term (Aspect)ReferenceEvidenceNotesLinks
acceptableMOUSE:RAC12017-10-01 18:41:30 CDTGO:0035774 positive regulation of insulin secretion involved in cellular response to glucose stimulus (P)PMID:23412604ECO:0000315 mutant phenotype evidence used in manual assertion

Mus, Ras-related C3 botulinum toxin substrate 1 (RAC1)

In Figure 5d and 5e, perfusion analysis was used to show how RAC1 deficiency in mouse cells resulted in the second phase of insulin secretion being greatly decreased. This shows that RAC1 must be involved in the positive regulation of insulin secretion in response to glucose stimulus, which is the second phase of insulin secretion.

challenge
acceptableHUMAN:LIMC12017-10-01 18:45:43 CDTGO:0051496 positive regulation of stress fiber assembly (P)PMID:28228547ECO:0000315 mutant phenotype evidence used in manual assertion

Homo Sapiens; LIM and calponin homology domains-containing protein 1 (LIMCH1)

Figure 6a and 6b show that LIMCH1-depleted cells (LIMCH1.2) in humans showed reduced intensity of total stress fibers, particularly near the center of the cell.

challenge
acceptableHUMAN:LIMC12017-10-10 12:53:20 CDTGO:0001725 stress fiber (C)PMID:28228547ECO:0000314 direct assay evidence used in manual assertion

Homo Sapiens; LIM and calponin homology domains-containing protein 1 (LIMCH1)

Figure 1b shows that LIMCH1 is colocalized with actin stress fibers in human cells, and Figure 1c confirms this. Since “actin stress fiber” doesn’t exist as a GO term, stress fiber is the closest annotation.

challenge
acceptableHUMAN:LIMC12017-10-11 16:41:56 CDTGO:0030336 negative regulation of cell migration (P)PMID:28228547ECO:0000315 mutant phenotype evidence used in manual assertion

Homo Sapiens; LIM and calponin homology domains-containing protein 1 (LIMCH1)

Figure 8D, 8E, and 8F all show how in LIMCH1 depleted cells (LIMCH1.2) in humans, the cells experience quicker and more frequent cell migration, implying that LIMCH1 would otherwise be negatively regulating cell migration.

challenge
acceptableHUMAN:LIMC12017-10-11 16:42:36 CDTGO:0060327 cytoplasmic actin-based contraction involved in cell motility (P)PMID:28228547ECO:0000315 mutant phenotype evidence used in manual assertion

Homo Sapiens; LIM and calponin homology domains-containing protein 1 (LIMCH1)

Figure 8B and 8C both show how, compared to the wild type, a human cell depleted in LIMCH1 decreases in cell contraction. LIMCH1 attenuates actin stress fibers, as seen in Figure 6a and 6b, which can decrease cell motility. The paper concludes that LIMCH1 increases cell motility by decreasing the number of actin stress fibers.

challenge
acceptableCRIGR:G3H4V12017-10-11 16:49:13 CDTGO:0016460 myosin II complex (C)PMID:17981136ECO:0000314 direct assay evidence used in manual assertion

Cricetulus griseus; Septin-2 (SEPT2)

In Figure 1A, immunostaining of myosin-II and SEPT2 in the cells of Chinese hamsters shows that they colocalize.

challenge
acceptableRAT:STX22017-10-29 21:36:03 CDTGO:0000281 mitotic cytokinesis (P)PMID:12737809ECO:0000315 mutant phenotype evidence used in manual assertion

Rattus norvegicus, Syntaxin-2;

Syntaxin-2D can act as a dominant-negative inhibitor of the function of Syntaxin-2. In Figures 2B-2E, it is shown that when the function of Syntaxin-2 is inhibited, mitotic cytokinesis does not fully take place and the result is an increase in binucleated cells.

challenge
acceptableRAT:STX22017-10-29 21:37:55 CDTGO:0061952 midbody abscission (P)PMID:12737809ECO:0000315 mutant phenotype evidence used in manual assertion

Rattus norvegicus, Syntaxin-2;

Syntaxin-2D can act as a dominant-negative inhibitor of the function of Syntaxin-2. In Figure 2C, it is shown that when Syntaxin-2D is present, everything that should take place for cytokinesis is indistinguishable from the control except for midbody abscission, indicating that syntaxin-2 is involved in midbody abscission.

challenge
acceptableRAT:VAMP82017-10-29 21:43:55 CDTGO:0030496 midbody (C)PMID:12737809ECO:0000314 direct assay evidence used in manual assertion

Rattus norvegicus, Vesicle-associated membrane protein 8 (endobrevin);

In Figure 3B, it is shown through immunostaining that endobrevin localizes to the midbody of the normal rat kidney cell.

challenge
acceptableRAT:VAMP32017-10-31 13:41:35 CDTGO:0097708 intracellular vesicle (C)PMID:12737809ECO:0000314 direct assay evidence used in manual assertion

Rattus norvegicus, Vesicle-associated membrane protein 3;

In figure 3A it is shown that cellubrevin is found on intracellular vesicles in late telophase.

challenge
acceptableHUMAN:RFIP32017-10-31 14:40:46 CDTGO:0036449 microtubule minus-end (C)PMID:15601896ECO:0000314 direct assay evidence used in manual assertion

Homo Sapiens, Rab11 family-interacting protein 3 (FIP3)

In figure 3E, fixed HeLa cells show that FIP3 starts accumulating at the minus end of microtubules during telophase.

challenge
acceptableHUMAN:RFIP32017-11-14 13:32:37 CSTGO:0051233 spindle midzone (C)PMID:15601896ECO:0000314 direct assay evidence used in manual assertion

Homo Sapiens, Rab11 family-interacting protein 3 (FIP3)

In Figure 3D, it is shown that FIP3 is associated with the spindle midzone during anaphase.

challenge
acceptableMOUSE:SEPT22017-11-14 22:00:06 CSTGO:0070938 contractile ring (C)PMID:9203580ECO:0000314 direct assay evidence used in manual assertion

Mouse; Neural precursor cell expressed developmentally down-regulated protein 5 (Nedd5)

In Figures 3Aa-3Ac, it is shown that Nedd5 localizes to the plasma membrane in early telophase.

challenge
acceptableMOUSE:SEPT22017-11-14 22:00:06 CSTGO:0030496 midbody (C)PMID:9203580ECO:0000314 direct assay evidence used in manual assertion

Mouse; Neural precursor cell expressed developmentally down-regulated protein 5 (Nedd5)

In Figures 3Ad-3Af, it is shown that Nedd5 localizes to the midbody during late telophase.

challenge
acceptableHUMAN:RHG182017-11-16 14:50:33 CSTGO:0005881 cytoplasmic microtubule (C)PMID:28251925ECO:0000314 direct assay evidence used in manual assertion

Homo sapiens, ARHGAP18 (RhoGTPase activating protein 18)

Figures 1E and 1F show that ARHGAP18 is localized in individual puncta along microtubule filaments.

challenge
acceptableHUMAN:RHG182017-11-16 14:50:34 CSTGO:0001726 ruffle (C)PMID:28251925ECO:0000314 direct assay evidence used in manual assertion

Homo sapiens, ARHGAP18 (RhoGTPase activating protein 18)

Figures 1A show that ARHGAP18 localizes to the peripheral membrane ruffles in endothelial cells.

challenge
acceptableHUMAN:FR1OP2017-11-19 22:23:08 CSTGO:0005814 centriole (C)PMID:23554904ECO:0000314 direct assay evidence used in manual assertion

Human; FGFR1 oncogene partner (FOP)

According to Figure 1A and S1, FOP localizes to centrioles at all cell stages.

challenge
unacceptableHUMAN:FR1OP2017-11-19 22:29:24 CSTGO:0034451 centriolar satellite (C)PMID:23554904ECO:0000314 direct assay evidence used in manual assertion

Human; FGFR1 oncogene partner (FOP)

According to figure 1B and 1C, FOP localizes to centriolar satellites in all cell stages except for G1.

challenge
updatedbyinstructorMOUSE:HDAC62017-11-21 19:15:04 CSTGO:0016575 histone deacetylation (P)PMID:24882211ECO:0000315 mutant phenotype evidence used in manual assertion

Mouse; HDAC6

According to Figure 5C, HDAC6 is involved in core histone deacetylation.

challenge
acceptableMOUSE:HDAC62017-11-21 19:17:00 CSTGO:0004407 histone deacetylase activity (F)PMID:24882211ECO:0000315 mutant phenotype evidence used in manual assertion

Mouse; HDAC6

According to Figure 5C, HDAC6 is involved in core histone deacetylation.

challenge

acceptable:18
unacceptable:1
requires_changes:0
flagged:0

Annotations challenged by ASarahAli

StatusAuthor,GroupPageGO Term (Aspect)ReferenceEvidenceLinksPage history
unacceptableJonathanMarcias,
Team SEAL Team Ricks
MOUSE:HDAC6GO:0000209 - protein polyubiquitination (P)PMID:24882211ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 1
updatedbyinstructorJonathanMarcias,
Team SEAL Team Ricks
MOUSE:HDAC6GO:0031648 - protein destabilization (P)PMID:24882211ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 1

fixed by ASarahAli

1 annotations fixed by ASarahAli

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