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User:CSears

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CACAO Spring 2017

My Annotations

StatusPageDate/TimeGO Term (Aspect)ReferenceEvidenceNotesLinks
acceptableMOUSE:PTPRJ2017-01-29 21:30:55 CSTGO:0046627 negative regulation of insulin receptor signaling pathway (P)PMID:26063811ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 4A: Mice with Ptprj expression knocked down show increased tyrosine phosphorylation of the insulin receptor in the presence of insulin. In addition, figure 4B shows that mice with Ptprj expression knocked down show increased activation via phosphorylation of Akt, a downstream effector of insulin signaling.

challenge
acceptableMOUSE:PTPRJ2017-01-29 21:30:55 CSTGO:1990264 peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity (P)PMID:26063811ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 4A: Mice with Ptprj expression knocked down show increased tyrosine phosphorylation of the insulin receptor (a member of the receptor protein tyrosine kinase superfamily) in the presence of insulin. In addition, figure 4B shows that mice with Ptprj expression knocked down show increased phosphorylation of Akt, a downstream effector of insulin signaling.

challenge
acceptableMOUSE:PTPRJ2017-01-29 21:30:56 CSTGO:0042593 glucose homeostasis (P)PMID:26063811ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 5A: Mice with Ptprj expression knocked down show decreased effect of injected glucose on blood glucose levels.

challenge
acceptableHUMAN:PTPRJ2017-02-14 13:45:43 CSTGO:0005899 insulin receptor complex (C)PMID:26063811ECO:0000314 direct assay evidence used in manual assertion

Figure 3C: Ptprj is shown by immunostaining to colocalize with the IR at the cell surface in HEK293T cells.

challenge
unacceptableMOUSE:PTPRJ2017-02-14 13:47:49 CSTGO:0035335 peptidyl-tyrosine dephosphorylation (P)PMID:26063811ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 4A: Mice with Ptprj expression knocked down show increased tyrosine phosphorylation of the insulin receptor in the presence of insulin.

challenge
unacceptableHUMAN:PTPRB2017-02-14 13:50:19 CSTGO:1990264 peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity (P)PMID:26063811ECO:0000314 direct assay evidence used in manual assertion

Figure 2B and 2C: Ptprb dephosphorylates tyrosine 1146 in the activation loop of the insulin receptor (a member of the receptor protein tyrosine kinase superfamily) in HEK293T (human embryonic kidney) cells

challenge
unacceptableHUMAN:PTPRH2017-02-14 13:51:53 CSTGO:1990264 peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity (P)PMID:26063811ECO:0000314 direct assay evidence used in manual assertion

Figure 2B and 2C: Ptprh dephosphorylates tyrosine 1146 in the activation loop of the insulin receptor (a member of the receptor protein tyrosine kinase superfamily) in HEK293T (human embryonic kidney) cells

challenge
unacceptableHUMAN:PTPRO2017-02-14 13:53:28 CSTGO:1990264 peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity (P)PMID:26063811ECO:0000314 direct assay evidence used in manual assertion

Figure 2B and 2C: Ptpro dephosphorylates tyrosine 1146 in the activation loop of the insulin receptor (a member of the receptor protein tyrosine kinase superfamily) in HEK293T (human embryonic kidney) cells

challenge
acceptableRAT:SNX52017-02-15 11:40:56 CSTGO:0005903 brush border (C)PMID:25825816ECO:0000314 direct assay evidence used in manual assertion

Figure 1B: SNX5 colocalizes at the brush border of renal proximal tubule cells in rat kidney.

challenge
unacceptableHUMAN:SNX52017-02-15 11:44:36 CSTGO:0005899 insulin receptor complex (C)PMID:25825816ECO:0000314 direct assay evidence used in manual assertion

Figure 1C: In human renal proximal tubule cells, SNX5 colocalized with the IR at the basal state and increasingly after administration of insulin.

challenge
acceptableHUMAN:SNX52017-02-15 11:44:37 CSTGO:0048471 perinuclear region of cytoplasm (C)PMID:25825816ECO:0000314 direct assay evidence used in manual assertion

Figure 1C: In human renal proximal tubule cells, SNX5 colocalized with the insulin receptor in the perinuclear area

challenge
acceptableHUMAN:INSR2017-02-14 14:31:35 CSTGO:0002092 positive regulation of receptor internalization (P)PMID:25401701ECO:0000314 direct assay evidence used in manual assertion

Figure 1B, 1C: Cells coexpressing human insulin receptor and beta-2-adrenergic receptor show increased internalization of beta-2-adrenergic receptor as compared to cells expressing only beta-2-adrenergic receptor

challenge
acceptableMOUSE:CAV12017-02-21 09:37:14 CSTGO:0038016 insulin receptor internalization (P)PMID:27110488ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 5D-F: Overexpression of mutant mouse CAV-1 results in increased domain density of the insulin receptor, increased size of insulin receptor domains, and increased numbers of insulin receptors present on the plasma membrane, indicating a decrease in insulin receptor internalization with the nonfunctional protein.

challenge
acceptableHUMAN:SNX52017-02-28 14:52:17 CSTGO:0046628 positive regulation of insulin receptor signaling pathway (P)PMID:25825816ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 3A: Ratio of phosphorylated to dephosphorylated IRS1, an adaptor protein which initiates downstream insulin signaling activity, was decreased in basal-state human renal proximal tubule cells with SNX5 expression knocked down. Figure 3D: After addition of insulin, phosphorylated PKB, a downstream effector of insulin signaling, was increased to a lesser extent in human renal proximal tubule cells with SNX5 expression knocked down as compared to mock control.

challenge
acceptableHUMAN:SNX52017-02-28 14:52:17 CSTGO:0045893 positive regulation of transcription, DNA-templated (P)PMID:25825816ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 2D, 2E: insulin receptor mRNA expression is decreased in human renal proximal tubule cells with SNX5 expression knocked down.

challenge
acceptableHUMAN:DRD12017-02-28 15:01:39 CSTGO:0005903 brush border (C)PMID:25825816ECO:0000314 direct assay evidence used in manual assertion

Figure 4A: Dopamine D1 receptor colocalizes at the brush border of human renal proximal tubule cells.

challenge
acceptableHUMAN:DRD12017-02-28 15:01:39 CSTGO:0005899 insulin receptor complex (C)PMID:25825816ECO:0000314 direct assay evidence used in manual assertion

Figure 4C: Dopamine D1 receptor colocalizes with the IR in the perinuclear area in human renal proximal tubule cells at the basal state and increasingly after administration of insulin.

challenge
acceptableRAT:DRD12017-02-28 14:59:27 CSTGO:0005903 brush border (C)PMID:25825816ECO:0000314 direct assay evidence used in manual assertion

Figure 4B: Dopamine D1 receptor colocalizes at the brush border of renal proximal tubule cells in rat kidney.

challenge
unacceptableRAT:DRD12017-02-28 14:59:27 CSTGO:0005899 insulin receptor complex (C)PMID:25825816ECO:0000314 direct assay evidence used in manual assertion

Figure 4B: Dopamine D1 receptor colocalized with the IR at the brush border of renal proximal tubule cells in rat kidney.

challenge
unacceptableMOUSE:PTPRO2017-04-04 13:51:03 CDTGO:0035335 peptidyl-tyrosine dephosphorylation (P)PMID:26063811ECO:0000314 direct assay evidence used in manual assertion

Figure 1B: mouse Ptpro dephosphorylates tyrosine-phosphorylated IR in vitro

challenge
acceptableMOUSE:PTPRO2017-04-04 13:51:04 CDTGO:1990264 peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity (P)PMID:26063811ECO:0000314 direct assay evidence used in manual assertion

Figure 2B and 2C: mouse Ptpro dephosphorylates tyrosine 1146 in the activation loop of the insulin receptor (a member of the receptor protein tyrosine kinase superfamily) in HEK293T (human embryonic kidney) cells

challenge
unacceptableMOUSE:PTPRH2017-04-04 13:51:10 CDTGO:0035335 peptidyl-tyrosine dephosphorylation (P)PMID:26063811ECO:0000314 direct assay evidence used in manual assertion

Figure 1B: mouse Ptprh dephosphorylates tyrosine-phosphorylated IR in vitro

challenge
acceptableMOUSE:PTPRH2017-04-04 13:51:10 CDTGO:1990264 peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity (P)PMID:26063811ECO:0000314 direct assay evidence used in manual assertion

Figure 2B and 2C: mouse Ptprh dephosphorylates tyrosine 1146 in the activation loop of the insulin receptor (a member of the receptor protein tyrosine kinase superfamily) in HEK293T (human embryonic kidney) cells

challenge
unacceptableMOUSE:PTPRB2017-04-04 13:51:15 CDTGO:0035335 peptidyl-tyrosine dephosphorylation (P)PMID:26063811ECO:0000314 direct assay evidence used in manual assertion

Figure 1B: mouse Ptprb dephosphorylates tyrosine-phosphorylated IR in vitro

challenge
acceptableMOUSE:PTPRB2017-04-04 13:51:16 CDTGO:1990264 peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity (P)PMID:26063811ECO:0000314 direct assay evidence used in manual assertion

Figure 2B and 2C: mouse Ptprb dephosphorylates tyrosine 1146 in the activation loop of the insulin receptor (a member of the receptor protein tyrosine kinase superfamily) in HEK293T (human embryonic kidney) cells

challenge
acceptableSALTY:Q8ZQ032017-04-04 13:58:03 CDTGO:0043707 cell adhesion involved in single-species biofilm formation in or on host organism (P)PMID:23451197ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 5: Salmonella enterica Typhimurium expressing mutant ycfR showed decreased cell adhesion on spinach leaves and grape tomatoes after chlorine treatment as compared to the wild type

challenge

acceptable:17
unacceptable:9
requires_changes:0
flagged:0

CACAO Spring 2016

Fall 2016 Grade

20 total annotation credits.

Inning Credits Notes

1

  • Acceptable: 2
  • Fixed Through Challenges: 0
  • NTRs/OTRs: 0
  • Other: 0
  • Total: 2

2 Attempted

2

  • Acceptable: 2
  • Fixed Through Challenges: 2
  • NTRs/OTRs: 0
  • Other: 0
  • Total: 4

5 Attempted

3

  • Acceptable: 0
  • Fixed Through Challenges: 1
  • NTRs/OTRs: 0
  • Other: 0
  • Total: 1

0 Attempted

4

  • Acceptable: 4
  • Fixed Through Challenges: 0
  • NTRs/OTRs: 0
  • Other: 0
  • Total: 4

4 Attempted

5

  • Acceptable: 2
  • Fixed Through Challenges: 3
  • NTRs/OTRs: 4
  • Other: 0
  • Total: 9

16 Attempted

My Annotations

StatusPageDate/TimeGO Term (Aspect)ReferenceEvidenceNotesLinks
acceptableHUMAN:MARH12016-09-17 19:11:48 CDTGO:0000209 protein polyubiquitination (P)PMID:27577745ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 8C shows that wild-type MARCH1 polyubiquitinates INSR beta, while MARCH1 that is E3-ligase activity-defective does not. Figure 8D demonstrates that, in cells, knockdown of MARCH1 results in a decrease in INSR beta ubiquitination.

challenge
updatedbyinstructorHUMAN:FOXO12016-09-17 19:37:03 CDTGO:0045944 positive regulation of transcription from RNA polymerase II promoter (P)PMID:27577745ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 6C and D show that shRNA-mediated knockdown of FOXO1 decrease expression of MARCH1. Figure 6G shows that, while insulin is absent, FOXO1 binds to the MARCH1 promoter, and while insulin is present, FOXO1 binding is inhibited.

challenge
acceptableHUMAN:NF2L22016-10-01 22:28:23 CDTGO:0010628 positive regulation of gene expression (P)PMID:27155659ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 3b: knockdown of Nrf2 prevents tBHQ-induced expression of the IR (insulin receptor) gene

challenge
unacceptableHUMAN:TXLNA2016-10-01 22:40:39 CDTGO:1905476 negative regulation of protein localization to membrane (P)PMID:27155659ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 5c: cells with elevated expression of alpha-taxilin show decreased binding of insulin to receptors on cell membrane, indicating decreased insulin receptors in the membrane.

challenge
acceptableHUMAN:SIR62016-10-01 23:20:21 CDTGO:1901485 positive regulation of transcription factor catabolic process (P)PMID:27457971ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 4B-F: FOXO1 is trafficked from nucleus to cytoplasm in cells expressing Sirt6, followed by degradation in the proteasome. When proteasome activity is inhibited, FOXO1 continues to be trafficked from nucleus to cytoplasm. In cells expressing inactive Sirt6, FOXO1 remains in the nucleus. Sirt6 expression increases ubiquitination and subsequent degradation of FOXO1.

challenge
updatedbyinstructorHUMAN:SIR62016-10-01 23:20:22 CDTGO:0006476 protein deacetylation (P)PMID:27457971ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 3D

challenge
unacceptableHUMAN:SIR62016-10-01 23:23:52 CDTGO:0000209 protein polyubiquitination (P)PMID:27457971ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 4F: expression of Sirt6 increases FOXO1 ubiquitination as compared to mutant Sirt6

challenge
acceptableRAT:F1M7B82016-10-25 19:21:16 CDTGO:1905528 positive regulation of Golgi lumen acidification (P)PMID:23447592ECO:0000315 mutant phenotype evidence used in manual assertion

A fluorometric assay was used to determine Golgi lumen pH in Ube3a-knockdown rat cells as compared to control. Figure 5B shows the calibration curve used to convert YFP:CFP intensity ratio to pH; Figure D shows the fluorescence intensity and figure 5E shows the pH as calculated using the calibration curve.

challenge
acceptableSTREE:H2BJK02016-10-28 23:58:32 CDTGO:0044651 adhesion of symbiont to host epithelial cell (P)PMID:23115034ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 4

challenge
acceptableCHILA:DEFB12016-10-29 00:36:33 CDTGO:0051873 killing by host of symbiont cells (P)PMID:14996845ECO:0000314 direct assay evidence used in manual assertion

Figure 6 - bacteria and C. albicans incubated with cBD-1 show decreased survival with increased concentrations of cBD-1.

challenge
acceptableMOUSE:SIR62016-10-29 00:57:48 CDTGO:0006476 protein deacetylation (P)PMID:27457971ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 3B: In islets with Sirt6 knocked down, acetylation of FOXO1 is increased.

challenge
acceptableHUMAN:SPIR12016-11-08 19:49:08 CSTGO:0031307 integral component of mitochondrial outer membrane (C)PMID:26305500ECO:0000314 direct assay evidence used in manual assertion

Figure 2A - Spire1C is localized at the periphery of the mitochondria. Figure 2D - fluorescence assay demonstrated that the N-terminus of Spire1C is exposed to the cytoplasm while the C-terminus is not

challenge
acceptableHUMAN:SPIR12016-11-08 19:54:14 CSTGO:0090141 positive regulation of mitochondrial fission (P)PMID:26305500ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 4

challenge
unacceptableHUMAN:SPIR12016-11-08 20:06:10 CSTGO:0090141 positive regulation of mitochondrial fission (P)PMID:26305500ECO:0000316 genetic interaction evidence used in manual assertion

Figure 6C and 6D - cells with overexpression of either Spire1C or INF2 or both display short mitochondria, while cells with knocked down expression of INF2 or mutant Spire1C display tubular mitochondria

challenge
unacceptableHUMAN:INF22016-11-08 20:07:53 CSTGO:0090141 positive regulation of mitochondrial fission (P)PMID:26305500ECO:0000316 genetic interaction evidence used in manual assertion

Figure 6C: Cells overexpressing active INF2 and Spire1C show shortened mitochondria as compared to control, while cells overexpressing INF2 and Spire1C that lacks the KIND domain show elongated, tubular mitochondria. Figure 6D: Cells overexpressing Spire1C treated with INF2 siRNA show elongated mitochondria as compared to cells treated with scrambled siRNA.

challenge
unacceptableHUMAN:SPIR12016-11-08 20:31:40 CSTGO:0032233 positive regulation of actin filament bundle assembly (P)PMID:26305500ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 3 - cells with overexpression of Spire1C show increased actin assembly on mitochondria as compared to control, while cells with overexpression of mutant Spire1C do not show increased actin assembly on mitochondria as compared to control

challenge
unacceptableHUMAN:SPIR12016-11-08 20:37:00 CSTGO:0051639 actin filament network formation (P)PMID:26305500ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 3 - cells with overexpression of Spire1C show increased actin assembly on mitochondria as compared to control, while cells with overexpression of mutant Spire1C do not show increased actin assembly on mitochondria as compared to control

challenge
updatedbyinstructorMOUSE:D3YTL82016-11-15 19:55:51 CSTGO:0031307 integral component of mitochondrial outer membrane (C)PMID:26305500ECO:0000314 direct assay evidence used in manual assertion

Figure 2A - Spire1C is localized at the periphery of the mitochondria. Figure 2D - fluorescence assay demonstrated that the N-terminus of Spire1C is exposed to the cytoplasm while the C-terminus is not

challenge
updatedbyinstructorMOUSE:D3YTL82016-11-15 20:00:39 CSTGO:0007015 actin filament organization (P)PMID:26305500ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 3 - cells with overexpression of Spire1C show increased actin assembly on mitochondria as compared to control, while cells with overexpression of mutant Spire1C do not show increased actin assembly on mitochondria as compared to control

challenge
updatedbyinstructorMOUSE:D3YTL82016-11-15 20:44:30 CSTGO:0030041 actin filament polymerization (P)PMID:26305500ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 3 - cells with overexpression of Spire1C show increased actin assembly on mitochondria as compared to control, while cells with overexpression of mutant Spire1C do not show increased actin assembly on mitochondria as compared to control

challenge
updatedbyinstructorMOUSE:D3YTL82016-11-20 16:52:37 CSTGO:0090141 positive regulation of mitochondrial fission (P)PMID:26305500ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 4

challenge
updatedbyinstructorMOUSE:D3YTL82016-11-20 17:55:19 CSTGO:0031307 integral component of mitochondrial outer membrane (C)PMID:26305500ECO:0000314 direct assay evidence used in manual assertion

Figure 2A - Spire1C is localized at the periphery of the mitochondria. Figure 2D - fluorescence assay demonstrated that the N-terminus of Spire1C is exposed to the cytoplasm while the C-terminus is not

challenge

acceptable:9
unacceptable:6
requires_changes:0
flagged:0

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