User:JonSDSUGrad/Sandbox/PBB Log3

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Contents

[edit] Log file for Protein Box Bot

Log page index: User:JonSDSUGrad/Sandbox/PBB_Log_Index

[edit] Quick Protein List - Date: 18:10, 10 August 2007 (UTC)

User:JonSDSUGrad/Sandbox/TEST2_AKT1 User:JonSDSUGrad/Sandbox/TEST2_APOE User:JonSDSUGrad/Sandbox/TEST2_APP
User:JonSDSUGrad/Sandbox/TEST2_AR User:JonSDSUGrad/Sandbox/TEST2_BCL2 User:JonSDSUGrad/Sandbox/TEST2_BRCA1
User:JonSDSUGrad/Sandbox/TEST2_CASP3 User:JonSDSUGrad/Sandbox/TEST2_CDKN1A User:JonSDSUGrad/Sandbox/TEST2_CDKN2A
User:JonSDSUGrad/Sandbox/TEST2_MMP9

[edit] Condensed Log - Date: 18:10, 10 August 2007 (UTC)

[edit] Updated Protein Pages

APOE APP AR BRCA1 CASP3
CDKN1A CDKN2A MMP9

[edit] Skipped Proteins

AKT1 APOE BCL2 BRCA1

[edit] Vebose Log - Date: 18:10, 10 August 2007 (UTC)

AKT1

  • NO BOT: Encounted 'No Bot Edits' flag for this protein. {August 10, 2007 11:07:31 AM PDT}
  • NO JOB: Location: User:JonSDSUGrad/Sandbox/TEST2_AKT1 {August 10, 2007 11:07:31 AM PDT}
 <!-- BOT: MANUAL_INSPECTION_REQUIRED = NO - change this option to YES to have the protein box bot require an operator inspection before updating occurs.  -->

<!-- BOT: PROTEIN BOX UPDATE = YES - This protein box is automatically updated by protein box bot. Change the update option to NO to have the bot skip updating this protein box -->
{{GNF_Protein_box
 | image = PBB_Protein_AKT1_image.jpg
 | image_source = [[Protein_Data_Bank|PDB]] rendering based on 1h10.
 | PDB = {{PDB2|1h10}}, {{PDB2|1unp}}, {{PDB2|1unq}}, {{PDB2|1unr}}, {{PDB2|2uvm}}
 | Name = v-akt murine thymoma viral oncogene homolog 1
 | HGNCid = 391
 | Symbol = AKT1
 | AltSymbols =; AKT; MGC99656; PKB; PRKBA; RAC; RAC-ALPHA
 | OMIM = 164730
 | ECnumber =  
 | Homologene = 3785
 | MGIid = 87986
 | GeneAtlas_image =  
 <!-- The Following entry is a time stamp of the last bot update.  It is typically hidden data -->
 | DateOfBotUpdate = ~~~~~
 | Function = {{GNF_GO|id=GO:0000060 |text = protein import into nucleus, translocation}} {{GNF_GO|id=GO:0000166 |text = nucleotide binding}} {{GNF_GO|id=GO:0004672 |text = protein kinase activity}} {{GNF_GO|id=GO:0004674 |text = protein serine/threonine kinase activity}} {{GNF_GO|id=GO:0005351 |text = sugar:hydrogen ion symporter activity}} {{GNF_GO|id=GO:0005524 |text = ATP binding}} {{GNF_GO|id=GO:0005634 |text = nucleus}} {{GNF_GO|id=GO:0005737 |text = cytoplasm}} {{GNF_GO|id=GO:0005819 |text = spindle}} {{GNF_GO|id=GO:0005975 |text = carbohydrate metabolic process}} {{GNF_GO|id=GO:0005978 |text = glycogen biosynthetic process}} {{GNF_GO|id=GO:0006006 |text = glucose metabolic process}} {{GNF_GO|id=GO:0006417 |text = regulation of translation}} {{GNF_GO|id=GO:0006468 |text = protein amino acid phosphorylation}} {{GNF_GO|id=GO:0006809 |text = nitric oxide biosynthetic process}} {{GNF_GO|id=GO:0006810 |text = transport}} {{GNF_GO|id=GO:0006915 |text = apoptosis}} {{GNF_GO|id=GO:0006954 |text = inflammatory response}} {{GNF_GO|id=GO:0007165 |text = signal transduction}} {{GNF_GO|id=GO:0007186 |text = G-protein coupled receptor protein signaling pathway}} {{GNF_GO|id=GO:0007281 |text = germ cell development}} {{GNF_GO|id=GO:0008286 |text = insulin receptor signaling pathway}} {{GNF_GO|id=GO:0008637 |text = apoptotic mitochondrial changes}} {{GNF_GO|id=GO:0009408 |text = response to heat}} {{GNF_GO|id=GO:0009725 |text = response to hormone stimulus}} {{GNF_GO|id=GO:0015758 |text = glucose transport}} {{GNF_GO|id=GO:0016567 |text = protein ubiquitination}} {{GNF_GO|id=GO:0016740 |text = transferase activity}} {{GNF_GO|id=GO:0030027 |text = lamellipodium}} {{GNF_GO|id=GO:0030163 |text = protein catabolic process}} {{GNF_GO|id=GO:0042640 |text = anagen}} {{GNF_GO|id=GO:0042802 |text = identical protein binding}} {{GNF_GO|id=GO:0045884 |text = regulation of survival gene product activity}} {{GNF_GO|id=GO:0046777 |text = protein amino acid autophosphorylation}} {{GNF_GO|id=GO:0048009 |text = insulin-like growth factor receptor signaling pathway}} 
 | Orthologs = {{GNF_Ortholog_box
    | Hs_EntrezGene = 207
    | Hs_Ensembl = ENSG00000142208
    | Hs_RefseqProtein = NP_001014431
    | Hs_RefseqmRNA = NM_001014431
    | Hs_GenLoc_db =  
    | Hs_GenLoc_chr = 14
    | Hs_GenLoc_start = 104306734
    | Hs_GenLoc_end = 104333125
    | Hs_Uniprot = P31749
    | Mm_EntrezGene = 11651
    | Mm_Ensembl = ENSMUSG00000001729
    | Mm_RefseqmRNA = NM_009652
    | Mm_RefseqProtein = NP_033782
    | Mm_GenLoc_db =  
    | Mm_GenLoc_chr = 12
    | Mm_GenLoc_start = 113101636
    | Mm_GenLoc_end = 113122084
    | Mm_Uniprot =  
  }}
}}
<!-- BOT: SUMMARY BEGIN UPDATE = YES - This summary is automatically updated by protein box bot.  Change the update option to NO to have the bot skip updating this summary -->

==Summary==
The serine-threonine protein kinase encoded by the AKT1 gene is catalytically inactive in serum-starved primary and immortalized fibroblasts. AKT1 and the related AKT2 are activated by platelet-derived growth factor. The activation is rapid and specific, and it is abrogated by mutations in the pleckstrin homology domain of AKT1. It was shown that the activation occurs through phosphatidylinositol 3-kinase. In the developing nervous system AKT is a critical mediator of growth factor-induced neuronal survival. Survival factors can suppress apoptosis in a transcription-independent manner by activating the serine/threonine kinase AKT1, which then phosphorylates and inactivates components of the apoptotic machinery. Multiple alternatively spliced transcript variants have been found for this gene.
<!-- BOT: SUMMARY END -->

APOE

  • UPDATE PROTEIN BOX: Updating Protein Box, No errors. {August 10, 2007 11:07:39 AM PDT}
  • UPDATE SUMMARY: Updating Summary, No Errors. {August 10, 2007 11:07:39 AM PDT}
  • INSPECTION: Manual Inspection Required for this protein: User:JonSDSUGrad/Sandbox/TEST2_APOE {August 10, 2007 11:07:39 AM PDT}
 <!-- BOT: MANUAL_INSPECTION_REQUIRED = yes - change this option to YES to have the protein box bot require an operator inspection before updating occurs.  -->

<!-- BOT: PROTEIN BOX UPDATE = YES - This protein box is automatically updated by protein box bot. Change the update option to NO to have the bot skip updating this protein box -->
{{GNF_Protein_box
 | image = PBB_Protein_APOE_image.jpg
 | image_source = [[Protein_Data_Bank|PDB]] rendering based on 1b68.
 | PDB = {{PDB2|1b68}}, {{PDB2|1bz4}}, {{PDB2|1ea8}}, {{PDB2|1gs9}}, {{PDB2|1h7i}}, {{PDB2|1le2}}, {{PDB2|1le4}}, {{PDB2|1lpe}}, {{PDB2|1nfn}}, {{PDB2|1nfo}}, {{PDB2|1or2}}, {{PDB2|1or3}}
 | Name = apolipoprotein E
 | HGNCid = 613
 | Symbol = APOE
 | AltSymbols =; AD2; MGC1571; apoprotein
 | OMIM = 107741
 | ECnumber =  
 | Homologene = 30951
 | MGIid = 88057
 | GeneAtlas_image =  
 <!-- The Following entry is a time stamp of the last bot update.  It is typically hidden data -->
 | DateOfBotUpdate = ~~~~~
 | Function = {{GNF_GO|id=GO:0000302 |text = response to reactive oxygen species}} {{GNF_GO|id=GO:0001540 |text = beta-amyloid binding}} {{GNF_GO|id=GO:0005319 |text = lipid transporter activity}} {{GNF_GO|id=GO:0005543 |text = phospholipid binding}} {{GNF_GO|id=GO:0005576 |text = extracellular region}} {{GNF_GO|id=GO:0005737 |text = cytoplasm}} {{GNF_GO|id=GO:0006707 |text = cholesterol catabolic process}} {{GNF_GO|id=GO:0006869 |text = lipid transport}} {{GNF_GO|id=GO:0006874 |text = cellular calcium ion homeostasis}} {{GNF_GO|id=GO:0006917 |text = induction of apoptosis}} {{GNF_GO|id=GO:0007010 |text = cytoskeleton organization and biogenesis}} {{GNF_GO|id=GO:0007271 |text = synaptic transmission, cholinergic}} {{GNF_GO|id=GO:0007611 |text = learning and/or memory}} {{GNF_GO|id=GO:0008015 |text = circulation}} {{GNF_GO|id=GO:0008034 |text = lipoprotein binding}} {{GNF_GO|id=GO:0008201 |text = heparin binding}} {{GNF_GO|id=GO:0016209 |text = antioxidant activity}} {{GNF_GO|id=GO:0030516 |text = regulation of axon extension}} {{GNF_GO|id=GO:0042157 |text = lipoprotein metabolic process}} {{GNF_GO|id=GO:0042311 |text = vasodilation}} {{GNF_GO|id=GO:0042627 |text = chylomicron}} {{GNF_GO|id=GO:0042632 |text = cholesterol homeostasis}} {{GNF_GO|id=GO:0046907 |text = intracellular transport}} {{GNF_GO|id=GO:0048156 |text = tau protein binding}} {{GNF_GO|id=GO:0048168 |text = regulation of neuronal synaptic plasticity}} {{GNF_GO|id=GO:0050749 |text = apolipoprotein E receptor binding}} {{GNF_GO|id=GO:0051262 |text = protein tetramerization}} 
 | Orthologs = {{GNF_Ortholog_box
    | Hs_EntrezGene = 348
    | Hs_Ensembl = ENSG00000130203
    | Hs_RefseqProtein = NP_000032
    | Hs_RefseqmRNA = NM_000041
    | Hs_GenLoc_db =  
    | Hs_GenLoc_chr = 19
    | Hs_GenLoc_start = 50100879
    | Hs_GenLoc_end = 50104489
    | Hs_Uniprot = P02649
    | Mm_EntrezGene = 11816
    | Mm_Ensembl = ENSMUSG00000002985
    | Mm_RefseqmRNA = NM_009696
    | Mm_RefseqProtein = NP_033826
    | Mm_GenLoc_db =  
    | Mm_GenLoc_chr = 7
    | Mm_GenLoc_start = 18854795
    | Mm_GenLoc_end = 18857574
    | Mm_Uniprot =  
  }}
}}

<!-- BOT: SUMMARY BEGIN UPDATE = YES - This summary is automatically updated by protein box bot.  Change the update option to NO to have the bot skip updating this summary -->
==Summary==
Chylomicron remnants and very low density lipoprotein (VLDL) remnants are rapidly removed from the circulation by receptor-mediated endocytosis in the liver. Apolipoprotein E, a main apoprotein of the chylomicron, binds to a specific receptor on liver cells and peripheral cells.  ApoE is essential for the normal catabolism of triglyceride-rich lipoprotein constituents.  The APOE gene is mapped to chromosome 19 in a cluster with APOC1 and APOC2.  Defects in apolipoprotein E result in familial dysbetalipoproteinemia, or type III hyperlipoproteinemia (HLP III), in which increased plasma cholesterol and triglycerides are the consequence of impaired clearance of chylomicron and VLDL remnants.
<!-- BOT: SUMMARY END -->

APP

  • UPDATE PROTEIN BOX: Updating Protein Box, No errors. {August 10, 2007 11:07:42 AM PDT}
  • UPDATE SUMMARY: Updating Summary, No Errors. {August 10, 2007 11:07:42 AM PDT}

AR

  • UPDATE PROTEIN BOX: Updating Protein Box, No errors. {August 10, 2007 11:07:58 AM PDT}
  • UPDATE SUMMARY: Updating Summary, No Errors. {August 10, 2007 11:07:58 AM PDT}

BCL2

  • NO JOB: Aborted upload due to both updates being turned off. No errors. {August 10, 2007 11:08:16 AM PDT}
  • NO JOB: Location: User:JonSDSUGrad/Sandbox/TEST2_BCL2 {August 10, 2007 11:08:16 AM PDT}

BRCA1

  • UPDATE SUMMARY: Updating Summary Only. {August 10, 2007 11:08:23 AM PDT}
  • INSPECTION: Manual Inspection Required for this protein: User:JonSDSUGrad/Sandbox/TEST2_BRCA1 {August 10, 2007 11:08:23 AM PDT}
 <!-- BOT: MANUAL_INSPECTION_REQUIRED = yes - change this option to YES to have the protein box bot require an operator inspection before updating occurs.  -->

<!-- BOT: PROTEIN BOX UPDATE = no - This protein box is automatically updated by protein box bot. Change the update option to NO to have the bot skip updating this protein box -->
{{GNF_Protein_box
 | image =  
 | image_source =  
 | PDB =  
 | Name = breast cancer 1
 | HGNCid = 1100
 | Symbol = BRCA1
 | AltSymbols =; BRCAI; BRCC1; IRIS; PSCP; RNF53
 | OMIM = 113705
 | ECnumber =  
 | Homologene = 5276
 | MGIid = 104537
 | GeneAtlas_image =  
 <!-- The Following entry is a time stamp of the last bot update.  It is typically hidden data -->
 | DateOfBotUpdate = 23:21, 24 July 2007 (UTC)
 | Function = {{GNF_GO|id=GO:0000075 |text = cell cycle checkpoint}} {{GNF_GO|id=GO:0000151 |text = ubiquitin ligase complex}} {{GNF_GO|id=GO:0000793 |text = condensed chromosome}} {{GNF_GO|id=GO:0003674 |text = molecular_function}} {{GNF_GO|id=GO:0003677 |text = DNA binding}} {{GNF_GO|id=GO:0003684 |text = damaged DNA binding}} {{GNF_GO|id=GO:0003713 |text = transcription coactivator activity}} {{GNF_GO|id=GO:0004842 |text = ubiquitin-protein ligase activity}} {{GNF_GO|id=GO:0005515 |text = protein binding}} {{GNF_GO|id=GO:0005575 |text = cellular_component}} {{GNF_GO|id=GO:0005622 |text = intracellular}} {{GNF_GO|id=GO:0005634 |text = nucleus}} {{GNF_GO|id=GO:0005737 |text = cytoplasm}} {{GNF_GO|id=GO:0006260 |text = DNA replication}} {{GNF_GO|id=GO:0006281 |text = DNA repair}} {{GNF_GO|id=GO:0006357 |text = regulation of transcription from RNA polymerase II promoter}} {{GNF_GO|id=GO:0006359 |text = regulation of transcription from RNA polymerase III promoter}} {{GNF_GO|id=GO:0006633 |text = fatty acid biosynthetic process}} {{GNF_GO|id=GO:0006978 |text = DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator}} {{GNF_GO|id=GO:0007049 |text = cell cycle}} {{GNF_GO|id=GO:0007059 |text = chromosome segregation}} {{GNF_GO|id=GO:0007098 |text = centrosome cycle}} {{GNF_GO|id=GO:0008270 |text = zinc ion binding}} {{GNF_GO|id=GO:0008274 |text = gamma-tubulin ring complex}} {{GNF_GO|id=GO:0008630 |text = DNA damage response, signal transduction resulting in induction of apoptosis}} {{GNF_GO|id=GO:0009048 |text = dosage compensation, by inactivation of X chromosome}} {{GNF_GO|id=GO:0015631 |text = tubulin binding}} {{GNF_GO|id=GO:0016481 |text = negative regulation of transcription}} {{GNF_GO|id=GO:0016567 |text = protein ubiquitination}} {{GNF_GO|id=GO:0019899 |text = enzyme binding}} {{GNF_GO|id=GO:0030521 |text = androgen receptor signaling pathway}} {{GNF_GO|id=GO:0031398 |text = positive regulation of protein ubiquitination}} {{GNF_GO|id=GO:0031436 |text = BRCA1-BARD1 complex}} {{GNF_GO|id=GO:0042127 |text = regulation of cell proliferation}} {{GNF_GO|id=GO:0042981 |text = regulation of apoptosis}} {{GNF_GO|id=GO:0045717 |text = negative regulation of fatty acid biosynthetic process}} {{GNF_GO|id=GO:0045739 |text = positive regulation of DNA repair}} {{GNF_GO|id=GO:0045786 |text = negative regulation of progression through cell cycle}} {{GNF_GO|id=GO:0045893 |text = positive regulation of transcription, DNA-dependent}} {{GNF_GO|id=GO:0046600 |text = negative regulation of centriole replication}} {{GNF_GO|id=GO:0046872 |text = metal ion binding}} {{GNF_GO|id=GO:0050681 |text = androgen receptor binding}} 
 | Orthologs = {{GNF_Ortholog_box
    | Hs_EntrezGene = 672
    | Hs_Ensembl = ENSG00000012048
    | Hs_RefseqProtein = NP_009225
    | Hs_RefseqmRNA = NM_007294
    | Hs_GenLoc_db =  
    | Hs_GenLoc_chr = 17
    | Hs_GenLoc_start = 38449840
    | Hs_GenLoc_end = 38530994
    | Hs_Uniprot = P38398
    | Mm_EntrezGene = 12189
    | Mm_Ensembl = ENSMUSG00000017146
    | Mm_RefseqmRNA = NM_009764
    | Mm_RefseqProtein = NP_033894
    | Mm_GenLoc_db =  
    | Mm_GenLoc_chr = 11
    | Mm_GenLoc_start = 101305657
    | Mm_GenLoc_end = 101367902
    | Mm_Uniprot = P48754
  }}
}}
<!-- BOT: SUMMARY BEGIN UPDATE = YES - This summary is automatically updated by protein box bot.  Change the update option to NO to have the bot skip updating this summary -->
==Summary==
This gene encodes a nuclear phosphoprotein that plays a role in maintaining genomic stability and acts as a tumor suppressor. The encoded protein combines with other tumor suppressors, DNA damage sensors, and signal transducers to form a large multi-subunit protein complex known as BASC for BRCA1-associated genome surveillance complex. This gene product associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complex. This protein thus plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. Alternative splicing plays a role in modulating the subcellular localization and physiological function of this gene. Many alternatively spliced transcript variants have been described for this gene but only some have had their full-length natures identified.
<!-- BOT: SUMMARY END -->

CASP3

  • UPDATE PROTEIN BOX: Updating Protein Box, No errors. {August 10, 2007 11:08:30 AM PDT}
  • UPDATE SUMMARY: Updating Summary, No Errors. {August 10, 2007 11:08:30 AM PDT}

CDKN1A

  • UPDATE PROTEIN BOX: Updating Protein Box, No errors. {August 10, 2007 11:08:52 AM PDT}
  • UPDATE SUMMARY: Updating Summary, No Errors. {August 10, 2007 11:08:52 AM PDT}

CDKN2A

  • UPDATE PROTEIN BOX: Updating Protein Box, No errors. {August 10, 2007 11:09:07 AM PDT}
  • UPDATE SUMMARY: Updating Summary, No Errors. {August 10, 2007 11:09:07 AM PDT}

MMP9

  • UPDATE PROTEIN BOX: Updating Protein Box, No errors. {August 10, 2007 11:09:21 AM PDT}
  • UPDATE SUMMARY: Updating Summary, No Errors. {August 10, 2007 11:09:21 AM PDT}

end log.