Difference between revisions of "Streptococcus pneumoniae"

Latest revision as of 18:50, 13 December 2013

[edit] Group Deliverables

tATK Final Group Deliverables

Team Journal Club Presentation

GenMAPP Gene Database: Media:Streptococcus_pneumoniae_TIGR4_20131125.gdb --known good
ReadMe file (PDF): ReadMe_Streptococcus_pneumoniae_TIGR4_20131125.pdf
Gene Database Schema: Streptococcus_schema_20131210.pdf
Gene Database Testing Report (print from wiki to .pdf file): PDF Gene Testing Report; Gene Testing Report Wiki Page
Processed and analyzed DNA microarray dataset (.xls): 20131125_teamATK_KM_CompiledRawData.xls
GenMAPP Expression Dataset file (.gex): 20131212_teamATK_KM_compiledrawdata_GMAPP.gex
Filtered MAPPFinder Results (.xls): 20131210_tATK_filteredresults.xls
Sample MAPP file of a relevant biological pathway for your species (.mapp): 20131211_tATK_sugar_transmembrane_transporter_activity.mapp

tATK jpeg MAPP

Group Report (.doc or .pdf):

PowerPoint presentation (.ppt, given on Thursday, December 12): tATK presentation

[edit] Papers

[edit] Genome Paper

Title: Genome of the Bacterium Streptococcus pneumoniae Strain R6

By Hoskins et al. (2001)

Web link

PDF

Reference: Hoskins, J., Alborn, W.E. Jr., Arnold, J., Blaszczak, L.C., Burgett, S., Bradley, S., DeHoff, S.T., Estrem, L.F., Fu, D.J., Fuller, W., Geringer, C., Gilmour, R., Glass, J.S., Khoja1, H., Kraft, A.R., Lagace, R.E., LeBlanc, D.J., Lee, L.N., Lefkowitz, E.J., Lu, J., Matsushima, P., McAhren, S.M., McHenney, M., McLeaster, K., Mundy, C.W., Nicas, T.I., Norris, F.H., O'Gara1, M.J., Peery, R.B., Robertson, G.T., Rockey, P., Sun, P.M., Winkler, M.E., Yang, Y., Young-Bellido, M., Zhao, G., Zook, C.A., Baltz, R.H., Jaskunas, S.R., Rosteck Jr., P.R., Skatrud, P.L., and Glass, J.I. (2001) Genome of the bacterium Streptococcus pneumoniae strain R6. Journal of Bacteriology 183(19): 5709-5717. doi: 10.1128/JB.183.19.5709-5717.2001

[edit] Microarray Paper

Sanchez et. al. 2011

Streptococcus pneumoniae in Biofilms Are Unable to Cause Invasive Disease Due to Altered Virulence Determinant Production

Web Link: Biofilm paper

PDF: Media:Biofilms_paper.pdf

Data at: GEO link and Array Express link

Experiments Performed: Examined genes related to biofilm formation of Streptococcus pneumoniae

Replicates: 3 biological replicates, 3+ technical replicates

Reference: Sanchez, C.J., Kumar, N., Lizcano, A., Shivshankar, P., Dunning Hotopp, J.C., Jorgensen, J.H., Tettelin, H., and Orihuela, C.J. (2011) Streptococcus pneumoniae in Biofilms Are Unable to Cause Invasive Disease Due to Altered Virulence Determinant Production. PLoS ONE 6(12): e28738. doi:10.1371/journal.pone.0028738

Found by Kevin

[edit] Downloaded Files

Uniprot XML File:
R6: XML
TIGR4: XML
G54: XML

GOA:
TIGR4: GOA
R6: GOA
G54: GOA

GO-OBO File: GO-OBO zip

Raw Data

Data Explanation Files

[edit] Import-Export Cycle One

tATK Export One: TIGR4 Testing Report

tATK Export One: R6 Testing Report

tATK Export One: G54 Testing Report

Files

G54: Media:20131113 G45export tATK TPV.gdb

R6: Media:20131113 R6export tATK TPV.gdb

TIGR4: Media:20131107_GenMAPPExport_tATK_TIGR4_TPV.gdb

Cycle procedure terminated due to inconsistent/unclear file versions and updated files available.

Taur.vil (talk) 21:36, 18 November 2013 (PST)

[edit] Import-Export Cycle 2

tATK E2: TIGR4 Testing Report

[edit] Files Used

Compressed obo-xml file

TIGR4

[edit] Files Exported

TIGR4

Export: Media:20131118_E2_tATK_TIGR4.gdb

[edit] Import-Export Cycle 3

tATK E3: TIGR4 Testing Report

[edit] Files Used

Compressed obo-xml file

TIGR4

[edit] Files Exported

TIGR4

Media:20131120_E3_tATK_TIGR4.gdb

[edit] Import-Export Cycle 4

tATK E4: TIGR4 Testing Report

[edit] Files Used

Compressed obo-xml file

gmbuilder: dist_Experimental20131121 (created in class 21Nov2013)

TIGR4

[edit] Files Exported

TIGR4

Media:20131125_E4_tATK_TIGR4.gdb

[edit] Compiled Raw Data

Media:20131119_teamATK_KM_compiledrawdata.xls

Media:20131203_tATK_genenotfounderrors.xls

[edit] MAPPFinder Data

[edit] Team ATK

Team Leader: Tauras

Coder: Tauras
Quality Assurance: Alina
GenMAPP User: Kevin Meilak

[edit] Progress Report Links

[edit] Individual Assessment and Reflection

[edit] Template

Alina's User Page

Kevin's User Page

Tauras's User Page

Biological Databases Class Page

Gene Database Project

Gene Database Project Report Guidelines

Streptococcus pneumoniae

Import Export Cycle 1: tATK Export One: TIGR4 Testing Report

Import Export Cycle 2: tATK E2: TIGR4 Testing Report

Import Export Cycle 3: tATK E3: TIGR4 Testing Report

Import Export Cycle 4: tATK E4: TIGR4 Testing Report

Project Roles:

Coder

@@ Line 1: / Line 1: @@
+==Group Deliverables==
+[[tATK Final Group Deliverables]]
+[[Media:TeamATK.pdf|Team Journal Club Presentation]]
+* GenMAPP Gene Database: [[Media:Streptococcus_pneumoniae_TIGR4_20131125.gdb]] --known good
+* ReadMe file (PDF): [[Media:ReadMe_Streptococcus_pneumoniae_TIGR4_20131125.pdf|ReadMe_Streptococcus_pneumoniae_TIGR4_20131125.pdf]]
+*Gene Database Schema: [[Media:Streptococcus_schema_20131210.pdf|Streptococcus_schema_20131210.pdf]]
+* Gene Database Testing Report (print from wiki to ''.pdf'' file): [[Media:Streptococcus pneumoniae TIGR4 20131125 GeneTestingReport.pdf|PDF Gene Testing Report]]; [[Streptococcus_pneumoniae_TIGR4_20131125_GeneTestingReport|Gene Testing Report Wiki Page]]
+* Processed and analyzed DNA microarray dataset (''.xls''): [[Media:20131125_teamATK_KM_CompiledRawData.xls|20131125_teamATK_KM_CompiledRawData.xls]]
+* GenMAPP Expression Dataset file (''.gex''): [[Media:20131212_teamATK_KM_compiledrawdata_GMAPP.gex|20131212_teamATK_KM_compiledrawdata_GMAPP.gex]]
+* Filtered MAPPFinder Results (''.xls''): [[Media:20131210_tATK_filteredresults.xls|20131210_tATK_filteredresults.xls]]
+* Sample MAPP file of a relevant biological pathway for your species (''.mapp''): [[Media:20131211_tATK_sugar_transmembrane_transporter_activity.mapp|20131211_tATK_sugar_transmembrane_transporter_activity.mapp]]
+[[Media:MAPP.JPG|tATK jpeg MAPP]]
+* [[Gene Database Project Report Guidelines#Group Report | Group Report]] (''.doc'' or ''.pdf''):
+* PowerPoint presentation (''.ppt'', given on Thursday, December 12): [[Media:TeamATK_finalpresentation.pdf|tATK presentation]]
 ==Papers==
 ===Genome Paper===
@@ Line 6: / Line 24: @@
 :[[Media: R6_Reference_Genome_Paper.pdf|PDF]]
-:Reference: Hoskins, J, Alborn, WE, Arnold, J, Blaszczak, LC, Burgett, S, DeHoff, BS, et al. (2001). Genome of the bacterium Streptococcus pneumoniae strain R6. Journal of Bacteriology, 183(19): 5709-5717.
+:Reference: Hoskins, J., Alborn, W.E. Jr., Arnold, J., Blaszczak, L.C., Burgett, S., Bradley, S., DeHoff, S.T., Estrem, L.F., Fu, D.J.,  Fuller, W., Geringer, C., Gilmour, R., Glass, J.S., Khoja1, H., Kraft, A.R., Lagace, R.E., LeBlanc, D.J., Lee, L.N., Lefkowitz, E.J., Lu, J., Matsushima, P., McAhren, S.M., McHenney, M., McLeaster, K., Mundy, C.W., Nicas, T.I., Norris, F.H., O'Gara1, M.J., Peery, R.B., Robertson, G.T., Rockey, P., Sun, P.M., Winkler, M.E., Yang, Y., Young-Bellido, M., Zhao, G., Zook, C.A., Baltz, R.H., Jaskunas, S.R., Rosteck Jr., P.R., Skatrud, P.L., and Glass, J.I. (2001) Genome of the bacterium Streptococcus pneumoniae strain R6. Journal of Bacteriology 183(19): 5709-5717. doi: 10.1128/JB.183.19.5709-5717.2001
 <!-- ===1: Identification of Genes That Contribute to the Pathogenesis of Invasive Pneumococcal Disease by In Vivo Transcriptomic Analysis===
@@ Line 30: / Line 48: @@
-:Reference: Yadav, MK, Kwon, SK, Cho, CG, Park, SW, Chae, SW, & Song, JJ (2012). Gene expression profile of early in vitro biofilms of Streptococcus pneumoniae. Microbiology and Immunology, 56: 621–629.
+:Reference: Yadav, MK, Kwon, SK, Cho, CG, Park, SW, Chae, SW, & Song, JJ (2012). Gene expression profile of early in vitro biofilms of Streptococcus pneumoniae. Microbiology and Immunology, 56: 621–629. doi: 10.1111/j.1348-0421.2012.00483.x
 :Found by [[User:Ajvree|Alina]]
@@ Line 74: / Line 92: @@
 Sanchez et. al. 2011
 :Streptococcus pneumoniae in Biofilms Are Unable to Cause Invasive Disease Due to Altered Virulence Determinant Production
-:Web Link: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0028738 Biofilm paper]
+:Web Link: [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26976/?query=Streptococcus+pneumoniae Biofilm paper]
 :PDF: [[Media:Biofilms_paper.pdf]]
-:Data at: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26976 GEO link]
+:Data at: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26976 GEO link] and [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26976/?query=streptococcus+pneumoniae Array Express link]
 :Experiments Performed: Examined genes related to biofilm formation of Streptococcus pneumoniae
 :Replicates: 3 biological replicates, 3+ technical replicates
-:Reference: Sanchez CJ, Kumar N, Lizcano A, Shivshankar P, Dunning Hotopp JC, et al. (2011) Streptococcus pneumoniae in Biofilms Are Unable to Cause Invasive Disease Due to Altered Virulence Determinant Production. PLoS ONE 6(12): e28738. doi:10.1371/journal.pone.0028738
+:Reference: Sanchez, C.J., Kumar, N., Lizcano, A., Shivshankar, P., Dunning Hotopp, J.C., Jorgensen, J.H., Tettelin, H., and Orihuela, C.J. (2011) Streptococcus pneumoniae in Biofilms Are Unable to Cause Invasive Disease Due to Altered Virulence Determinant Production. PLoS ONE 6(12): e28738. doi:10.1371/journal.pone.0028738
 :Found by [[User:Kmeilak|Kevin]]
-==Team==
+==Downloaded Files==
-'''Team Leader: [[User:Ajvree|Alina]]'''
+Uniprot XML File:<br>
+R6: [[Media:20131105_UniProtXML_tATK_R6_AJV.xml|XML]]<br>
+TIGR4: [[Media:20131107_UniProtXML_tATK_TIGR4_AJV.xml|XML]]<br>
+G54: [[Media:20131107_UniProtXML_tATK_G54_AJV.xml|XML]]<br>
+GOA:<br>
+TIGR4: [[Media:20131107_UniProtXML_tATK_TIG4_AJV.goa|GOA]]<br>
+R6: [[Media:20131107_UniProtXML_tATK_R6_AJV.goa|GOA]]<br>
+G54: [[Media:20131107_UniProtXML_tATK_G54_AJV.goa|GOA]]<br>
+GO-OBO File: [[Media:20131107_GO-OBO_tATK_KM.gz|GO-OBO zip]]
+*Raw Data
+#[[Media:20131106_ArrayExpressADF_tATK_KM.adf.txt|Associated Data Files]]
+#[[Media:20131106_ArrayExpressarraydesign_tATK_KM.txt|Array Design]]
+#[[Media:20131106_ArrayExpressrawdata_tATK_KM.zip|Raw Data]]
+#[[Media:20131106_ArrayExpressprocesseddata_tATK_KM.zip|Processed Data]]
+#[[Media:20131106_ArrayExpresssdrf_tATK_KM.txt|Sample and Data Relationship]]
+*Data Explanation Files
+#[[Media:20131118_tavrawdata_teamATK_KM.txt.txt]]
+#[[Media:20131118_dataexplanation_teamATK_KM.pdf.pdf]]
+==Import-Export Cycle One==
+:[[tATK Export One: TIGR4 Testing Report]]
+:[[tATK Export One: R6 Testing Report]]
+:[[tATK Export One: G54 Testing Report]]
+Files
+:G54: [[Media:20131113 G45export tATK TPV.gdb]]
+:R6: [[Media:20131113 R6export tATK TPV.gdb]]
+:TIGR4: [[Media:20131107_GenMAPPExport_tATK_TIGR4_TPV.gdb]]
+Cycle procedure terminated due to inconsistent/unclear file versions and updated files available.
+:[[User:Taur.vil|Taur.vil]] ([[User talk:Taur.vil|talk]]) 21:36, 18 November 2013 (PST)
+==Import-Export Cycle 2==
+:[[tATK E2: TIGR4 Testing Report]]
+===Files Used===
+[[Media:20131118_OBOXML_tATK_TPV.gz|Compressed obo-xml file]]
+TIGR4
+*XML: [[Media:20131118_UniProtXML_tATK_TIGR4_TPV.xml]]
+*Goa: [[Media:20131118_GOA_tATK_TIGR4_TPV.goa]]
+===Files Exported===
+TIGR4
+*Export: [[Media:20131118_E2_tATK_TIGR4.gdb]]
+==Import-Export Cycle 3==
+:[[tATK E3: TIGR4 Testing Report]]
+===Files Used===
+[[Media:20131120_OBOXML_tATK_TPV.gz|Compressed obo-xml file]]
+TIGR4
+*XML: [[Media:20131118_UniProtXML_tATK_TIGR4_TPV.xml]]
+*Goa: [[Media:20131118_GOA_tATK_TIGR4_TPV.goa]]
+===Files Exported===
+TIGR4
+* [[Media:20131120_E3_tATK_TIGR4.gdb]]
+==Import-Export Cycle 4==
+:[[tATK E4: TIGR4 Testing Report]]
+===Files Used===
+[[Media:20131120_OBOXML_tATK_TPV.gz|Compressed obo-xml file]]
+:gmbuilder: dist_Experimental20131121 (created in class 21Nov2013)
+TIGR4
+*XML: [[Media:20131118_UniProtXML_tATK_TIGR4_TPV.xml]]
+*Goa: [[Media:20131118_GOA_tATK_TIGR4_TPV.goa]]
+===Files Exported===
+TIGR4
+* [[Media:20131125_E4_tATK_TIGR4.gdb]]
+==Compiled Raw Data==
+*[[Media:20131119_teamATK_KM_compiledrawdata.xls]]
+*[[Media:20131203_tATK_genenotfounderrors.xls]]
+===MAPPFinder Data===
+====4 hr====
+*[[Media:20131205_teamATK_KM_compiledrawdata_4hr_GMAPP.gex]]
+====12 hr====
+*[[Media:TATK_MAPPFinder_results-Criterion1-GO.txt]]
+*[[Media:TATK_MAPPFinder_results-Criterion0-GO.txt]]
+*[[Media:20131119_teamATK_KM_compiledrawdata_GMAPP.gex]]
+====24 hr====
+*[[Media:20131119_teamATK_KM_compiledrawdata_24hr_GMAPP.gex]]
+====48 hr====
+*[[Media:20131119_teamATK_KM_compiledrawdata_48hr_GMAPP.gex]]
+==Team ATK==
+'''Team Leader: [[User:Taur.vil|Tauras]]'''
 *Coder: [[User:Taur.vil|Tauras]]
@@ Line 90: / Line 220: @@
 *GenMAPP User: [[User:Kmeilak|Kevin Meilak]]
+==Progress Report Links==
+*[[tATK Week 12 Status Report]]
+*[[tATK Week 13 Status Report]]
+*[[tATK Week 15 Status Report]]
+==Individual Assessment and Reflection==
+*[[Kevin's Assessment and Reflection]]
+*[[Alina's Assessment and Reflection]]
+==Template==
+{{Team ATK}}
-[[Main_Page]]
+[[Template: Team ATK]]
 [[Category: Streptococcus pneumoniae]]
-[[Category: Group Project]]
+[[Category: Group Projects]]
+[[Category: Team ATK]]

Difference between revisions of "Streptococcus pneumoniae"

Latest revision as of 18:50, 13 December 2013

Contents

[edit] Group Deliverables

[edit] Papers

[edit] Genome Paper

[edit] Microarray Paper

[edit] Downloaded Files

[edit] Import-Export Cycle One

[edit] Import-Export Cycle 2

[edit] Files Used

[edit] Files Exported

[edit] Import-Export Cycle 3

[edit] Files Used

[edit] Files Exported

[edit] Import-Export Cycle 4

[edit] Files Used

[edit] Files Exported

[edit] Compiled Raw Data

[edit] MAPPFinder Data

[edit] 4 hr

[edit] 12 hr

[edit] 24 hr

[edit] 48 hr

[edit] Team ATK

[edit] Progress Report Links

[edit] Individual Assessment and Reflection

[edit] Template

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