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

1. Associated Data Files
2. Array Design
3. Raw Data
4. Processed Data
5. Sample and Data Relationship

• Data Explanation Files

1. Media:20131118_tavrawdata_teamATK_KM.txt.txt
2. Media:20131118_dataexplanation_teamATK_KM.pdf.pdf

[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

• XML: Media:20131118_UniProtXML_tATK_TIGR4_TPV.xml
• Goa: Media:20131118_GOA_tATK_TIGR4_TPV.goa

[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

• XML: Media:20131118_UniProtXML_tATK_TIGR4_TPV.xml
• Goa: Media:20131118_GOA_tATK_TIGR4_TPV.goa

[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

• XML: Media:20131118_UniProtXML_tATK_TIGR4_TPV.xml
• Goa: Media:20131118_GOA_tATK_TIGR4_TPV.goa

[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] 4 hr

• Media:20131205_teamATK_KM_compiledrawdata_4hr_GMAPP.gex

[edit] 12 hr

• Media:TATK_MAPPFinder_results-Criterion1-GO.txt

• Media:TATK_MAPPFinder_results-Criterion0-GO.txt

• Media:20131119_teamATK_KM_compiledrawdata_GMAPP.gex

[edit] 24 hr

• Media:20131119_teamATK_KM_compiledrawdata_24hr_GMAPP.gex

[edit] 48 hr

• Media:20131119_teamATK_KM_compiledrawdata_48hr_GMAPP.gex

[edit] Team ATK

Team Leader: Tauras

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

[edit] Progress Report Links

• tATK Week 12 Status Report
• tATK Week 13 Status Report
• tATK Week 15 Status Report

[edit] Individual Assessment and Reflection

• Kevin's Assessment and Reflection
• Alina's Assessment and Reflection

[edit] Template

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

Data Information

• Kmeilak Week 10, Kmeilak Week 11, Kmeilak Week 12, Kmeilak Week 13
• Taur.vil Week 10, Taur.vil Week 11, Taur.vil Week 12, Taur.vil Week 13, Taur.vil Week 14, Taur.vil Week 15
• Ajvree Week 10, Ajvree Week 11, Ajvree Week 12, Ajvree Week 13, Ajvree Week 14, Ajvree Week 15Template: Team ATK