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User:Michael.torano

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BM: This student has 3 additional annotations that are CORRECT as far as grading for CACAO, but I marked incorrect because they used alternate IDs & were technically duplicates- they won't be accepted in the GAF... but I think that means he has >20 annotations correct, not including the flagged one.


My Annotations

StatusPageDate/TimeGO Term (Aspect)ReferenceEvidenceNotesLinks
unacceptable?2012-09-18 20:25:20 CDTGO:0006916 anti-apoptosis (Figure 5 showed, through silencing of STAT-3 and Rel-A by the Apo BrdU TUNEL assay, which resulted in apoptosis, the anti-apoptosis in Daoy and D283 cells. )PMID:22984561IMP: Inferred from Mutant Phenotype
challenge
acceptableEBVB9:EAR2012-09-18 20:33:57 CDTGO:0033668 negative regulation by symbiont of host apoptotic process (P)PMID:18084238ECO:0000314 direct assay evidence used in manual assertion

Figure 4 shows significantly lower %apoptosis in cells with the BHRF-1 regulator.

challenge
acceptableHUMAN:UPAR2012-09-18 20:55:37 CDTGO:0045742 positive regulation of epidermal growth factor receptor signaling pathway (P)PMID:22984561ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 4A shows that silencing uPAR and MMP-9 inhibits phosphorylation in the EGFR pathway.

challenge
acceptableHUMAN:MMP92012-09-18 21:02:57 CDTGO:0045742 positive regulation of epidermal growth factor receptor signaling pathway (P)PMID:22984561ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 4A shows that silencing uPAR and MMP-9 significantly inhibits the phosphorylation of the EGFR pathway.

challenge
unacceptableHUMAN:UPAR2012-09-21 20:06:34 CDTGO:0006916 anti-apoptosis (P)PMID:22984561ECO:0000314 direct assay evidence used in manual assertion

Figure 1C and 1D show, through the Apo BrdU Assay and the Annexin-V assay, that inhibition of uPAR and MMP-9 induce apoptosis in Daoy and D283 cells.

challenge
acceptableMOUSE:BID2012-09-21 20:22:48 CDTGO:0001836 release of cytochrome c from mitochondria (P)PMID:18084238ECO:0000314 direct assay evidence used in manual assertion

Figures 6a and 6b shows by comparison of % cytochrome release in multiple proteins, that tBID is capable of release of cytochrome c from mitochondria in a mouse liver.

challenge
acceptableEBVB9:EAR2012-09-23 17:40:30 CDTGO:0090201 negative regulation of release of cytochrome c from mitochondria (P)PMID:18084238ECO:0000314 direct assay evidence used in manual assertion

Figure 6C shows the measurements of release of cytochrome C. When BHRF-1 and KSHV BCL-2 were introduced, cytochrome c release was reduced.

challenge
acceptableHUMAN:UPAR2012-10-02 19:33:11 CDTGO:0043388 positive regulation of DNA binding (P)PMID:22984561ECO:0000314 direct assay evidence used in manual assertion

Figure 4C shows (through EMSA) that downregulation of uPAR and MMP-9 significantly inhibits binding activity of nuclear extract to STAT3 DNA probe.

challenge
requireschangesHUMAN:UPAR2012-10-02 20:02:15 CDTGO:0001934 positive regulation of protein phosphorylation (P)PMID:22984561ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 4B shows, through pUM transfection, that silencing uPAR and MMP-9 significantly lowers the amount of phosphorylated STAT protein in the nucleus.

challenge
requireschangesHUMAN:MMP92012-10-02 20:00:19 CDTGO:0001934 positive regulation of protein phosphorylation (P)PMID:22984561ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 4B shows, through pUM transfection, that silencing uPAR and MMP-9 significantly lowers the amount of phosphorylated STAT protein in the nucleus.

challenge
acceptableHUMAN:MMP92012-10-02 19:43:52 CDTGO:0043388 positive regulation of DNA binding (P)PMID:22984561ECO:0000314 direct assay evidence used in manual assertion

Figure 4C shows (through EMSA) that downregulation of uPAR and MMP-9 significantly inhibits binding activity of nuclear extract to STAT3 DNA probe.

challenge
unacceptableHUMAN:UPAR2012-10-02 19:58:25 CDTGO:0008633 obsolete activation of pro-apoptotic gene products (P)PMID:22984561ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 2

challenge
unacceptableHUMAN:MMP92012-10-02 20:00:19 CDTGO:0008633 activation of pro-apoptotic gene products (P)PMID:22984561ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 2

challenge
acceptableHUMAN:UPAR2012-10-16 19:31:49 CDTGO:0001934 positive regulation of protein phosphorylation (P)PMID:22984561ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 4B shows, through pUM transfection, that silencing uPAR and MMP-9 significantly lowers the amount of phosphorylated STAT protein in the nucleus.

challenge
acceptableHUMAN:MMP92012-10-16 19:32:56 CDTGO:0001934 positive regulation of protein phosphorylation (P)PMID:22984561ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 4B shows, through pUM transfection, that silencing uPAR and MMP-9 significantly lowers the amount of phosphorylated STAT protein in the nucleus.

challenge
unacceptableHUMAN:UPAR2012-11-11 23:12:55 CSTGO:0008637 apoptotic mitochondrial changes (P)PMID:22984561ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 2B shows, through the transfection of Daoy and D283 cells, that downregulation of uPAR and MMP-9 reduces mitochondrial cytochrome C and Bak levels.

challenge
acceptableHUMAN:UPAR2012-11-12 09:54:58 CSTGO:0043066 negative regulation of apoptotic process (P)PMID:22984561ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 1C and 1D show, through the Apo BrdU Assay and the Annexin-V assay, that inhibition of uPAR and MMP-9 induce apoptosis in Daoy and D283 cells.

challenge
acceptableHUMAN:MMP92012-11-12 09:56:22 CSTGO:0043066 negative regulation of apoptotic process (P)PMID:22984561ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 1C and 1D show, through the Apo BrdU Assay and the Annexin-V assay, that inhibition of uPAR and MMP-9 induce apoptosis in Daoy and D283 cells.

challenge
acceptable?2012-11-12 11:52:15 CSTGO:0043066 negative regulation of apoptotic process (Figure 5 showed, through silencing of STAT-3 and Rel-A by the Apo BrdU TUNEL assay, which resulted in apoptosis, the anti-apoptosis in Daoy and D283 cells.)PMID:22984561IMP: Inferred from Mutant Phenotype
challenge
requireschanges?2012-11-12 11:55:45 CSTGO:0051092 positive regulation of NF-kappaB transcription factor activity (Figure 5B showed that knockdown of STAT 3 decreased levels of phosphorylated NF-kappaB, indicating a positive regulation of NF-kappaB activity.)PMID:22984561IMP: Inferred from Mutant Phenotype
challenge
acceptableHUMAN:UPAR2012-11-13 19:52:06 CSTGO:2001243 negative regulation of intrinsic apoptotic signaling pathway (P)PMID:22984561ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 2 shows that downregulation of uPAR and MMP9 increases levels of gene products that induce apoptosis, showing that normal function negatively regulates apoptotic signaling pathways.

challenge
acceptableHUMAN:MMP92012-11-13 19:53:07 CSTGO:2001243 negative regulation of intrinsic apoptotic signaling pathway (P)PMID:22984561ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 2 shows that downregulation of uPAR and MMP9 increases levels of gene products that induce apoptosis, showing that normal function negatively regulates apoptotic signaling pathways.

challenge
acceptableHUMAN:UPAR2012-11-15 09:02:05 CSTGO:0090200 positive regulation of release of cytochrome c from mitochondria (P)PMID:22984561ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 2 shows that downregulation of uPAR and MMP9 in medulloblastoma cells decreases the amount of cytosolic cytochrome c, indicating a reduction in release of cytochrome c from mitochondria.

challenge
acceptableHUMAN:MMP92012-11-15 09:26:37 CSTGO:0090200 positive regulation of release of cytochrome c from mitochondria (P)PMID:22984561ECO:0000315 mutant phenotype evidence used in manual assertion

Fig. 2 shows that downregulation of uPAR and MMP9 in Medulloblastoma cells causes a decrease in the amount of cytosolic cytochrome c, indicating a positive regulation of release of cytochrome c from mitochondria.

challenge
unacceptableHUMAN:UPAR2012-11-18 14:15:28 CSTGO:0043154 negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (P)PMID:22984561ECO:0000315 mutant phenotype evidence used in manual assertion

Fig. 3 showed that down regulation of uPAR and MMP9 in Daoy and D283 cells activates caspase activity. Synonym for negative regulation of caspase activity is negative regulation of cysteine-type endopeptidase activity involved in apoptotic process.

challenge
acceptableHUMAN:UPAR2012-11-18 14:33:45 CSTGO:2001268 negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (P)PMID:22984561ECO:0000315 mutant phenotype evidence used in manual assertion

Fig. 3 showed that down regulation of uPAR and MMP9 in Daoy and D283 cells activates caspase activity.

challenge
acceptableHUMAN:MMP92012-11-18 14:35:38 CSTGO:2001268 negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (P)PMID:22984561ECO:0000315 mutant phenotype evidence used in manual assertion

Fig. 3 showed that down regulation of uPAR and MMP9 in Daoy and D283 cells activates caspase activity.

challenge

acceptable:18
unacceptable:6
requires_changes:3
flagged:0