Differences between revisions 42 and 74 (spanning 32 versions)

OICR Cancer Stem Cell Program

Experimental Design and Statistical Analysis

Changjiang Xu, Gary Bader

OICR CSC Projects: Biostatistical Part (PI's name and/or project title listed below)
Biostatistics service

-  ⇤ ← Revision 42 as of 2014-12-12 20:12:43 → 
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+   ← Revision 74 as of 2021-06-21 20:48:17 → ⇥
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  Editor: ChangjiangXu
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-{{attachment:logobiostat.png|OICR_CSC Pathway and Network Analysis Logo Map Logo|align="right"}} <<BR>>
= OICR CSC Statistical Analysis Service =
+= OICR Cancer Stem Cell Program =
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-== OICR Cancer Stem Cell program ==
+== Experimental Design and Statistical Analysis ==
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-Changjiang Xu, Gary Bader
+[[ChangjiangXu |Changjiang Xu]], [[GaryBader | Gary Bader]]
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- * OICR CSC Projects (PI's name and/or project title listed below)
   * [[CancerStemCellProject/ChangjiangXu/LA02 | Laurie Ailles, Crosstalk between CAFs and ovarian cancer cells (LA02_CAF_ovarian_Laurie) ]]
   * [[CancerStemCellProject/ChangjiangXu/PD03 | Peter Dirks, Role of dopamine D4 receptor in glioblastoma stem cells]]
+ * OICR CSC Projects: Biostatistical Part (PI's name and/or project title listed below) 
   * Aaron Schimmer
     * [[CancerStemCellProject/ChangjiangXu/AS02 | AS02 (Some points in the reviewed paper to be addressed): Association between ClpP expression and known AML mutations]]
     * [[CancerStemCellProject/ChangjiangXu/AS03_06 | AS03-06: Gene expression of protein import / the cardiolipin pathway / HTRA2 / MTCH2 in AMLs]]
     * [[CancerStemCellProject/ChangjiangXu/AS04_import_proteins_Danny | AS04_import_proteins_Danny: Gene expression of the mitochondrial import proteins MPPbeta in AML and HSC]]
   * Laurie Ailles
     * [[CancerStemCellProject/ChangjiangXu/LA02 | LA02 (LA02_CAF_ovarian_Laurie): Crosstalk between CAFs and ovarian cancer cells]]
       1. [[CancerStemCellProject/ChangjiangXu/LA02#Differential_Expression_Analysis | Differential expression analysis]]
       1. [[CancerStemCellProject/ChangjiangXu/LA02#TCGA_OV_Data_Analysis | TCGA OV data analysis]]
     * [[CancerStemCellProject/ChangjiangXu/LA03 | LA03 (LA03_part3_CAF_H&N_Keira): Crosstalk between CAFs and epithelial cancer cells in the Head and Neck cancer]]
   * Peter Dirks
     * [[CancerStemCellProject/ChangjiangXu/PD03 | PD03: Role of dopamine D4 receptor in glioblastoma stem cells]]
       1. [[CancerStemCellProject/ChangjiangXu/PD03#PD03-part2:_Normal_Cells | Part2: normal cells]]
       1. [[CancerStemCellProject/ChangjiangXu/PD03#PD03-part3:_TCGA_Glioblastoma_Data_Analysis | Part3: TCGA GBM data analysis]]
       1. [[CancerStemCellProject/ChangjiangXu/PD03#Comparison_of_TCGA_GBM_Affymetrix_and_RNAseq_Data | Comparison of TCGA GBM Affymetrix and RNAseq data]]
   * John Dick
     * HALT02/JAK2
       1. [[CancerStemCellProject/ChangjiangXu/HALT02_SRC | Differential expression analysis of SRC high vs low (negative) sub-populations]]
       1. [[CancerStemCellProject/ChangjiangXu/HALT02_JAK2 | Comparison of the pathways for XG-R/PF-R, XG-NR/PF-NR, and XG-R/PF-NR]]
     * [[CancerStemCellProject/ChangjiangXu/JD12_relapsedAML | JD12_relapsedAML_Liran: Clustering and pathway analysis of patients with relapsed AML]]
     * [[CancerStemCellProject/ChangjiangXu/JD13_Itgb7_Peter | JD13_Itgb7_Peter: ITGb7+ and ITGb7– hematopoietic stem cells]]
     * [[CancerStemCellProject/ChangjiangXu/JD14_Sasan_FL_BM | JD14_Sasan_FL_BM: Differential expression analysis and gene-set enrichment analysis on hematopoietic stem cells derived from bone marrow or fetal liver]]
   * Bret Pearson
     * [[CancerStemCellProject/ChangjiangXu/BP03 | BP03: Spatial Organization of the planarian transcriptome]]
     * [[CancerStemCellProject/ChangjiangXu/BP04 | BP04: Mechanisms driving asymmetric cell fate outcomes in planarian adult stem cell lineages]]
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-   * HALT02/JAK2
     * [[CancerStemCellProject/ChangjiangXu/HALT02_SRC | Differential expression analysis of SRC high vs low (negative) sub-populations]]
     * [[CancerStemCellProject/ChangjiangXu/HALT02_JAK2 | Comparison of the pathways for XG-R/PF-R, XG-NR/PF-NR, and XG-R/PF-NR]]
   * [[CancerStemCellProject/ChangjiangXu/KH01 | Kristin Hope]]
   * [[CancerStemCellProject/ChangjiangXu/BP03 | Bret Pearson, Spatial Organization of the planarian transcriptome]]
   * [[CancerStemCellProject/ChangjiangXu/BP04 | Bret Pearson, Mechanisms driving asymmetric cell fate outcomes in planarian adult stem cell lineages]]
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- * [[CancerStemCellProject/VeroniqueVoisin/BiostatisticProjects | Potential Biostatistics Projects from Bioinformatics Service]]
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- * [[CSCBiostatService | Biostatistics Service]]
   * [[CSCBiostatService/AffymetrixDataAnalysis | Affymetrix microarray data analysis]]
   * [[CSCBiostatService/IlluminaChipDataAnalysis | Illumina’s BeadChip microarray data analysis]]
   * [[CSCBiostatService/RNAseqDataAnalysis | RNA-seq data analysis]]
   * [[CSCBiostatService/flowCytometryDataAnalysis | Flow cytometry data analysis]]

 * Software Tools 
   * limma (see [[CSCBiostatService/limma | a note]])
   * GSEA (see [[CSCBiostatService/GSEA | a summary of GSEA methods and software]])
   * '''VLOOKUP''': After the analysis of a gene expression experiment, often you have a few Excel spreadsheets and want to find out which genes are common between the two spread sheets. With large data sets, this can be a daunting task. Efficient use of Excel function VLOOKUP can help you find commonalities between the two spreadsheets. The VLOOKUP function can also be used to pull information from one spreadsheet on the basis of some reference values from the other spreadsheet & concatenate the set of information with the 2nd spreadsheet. For detailed instructions, please download [[attachment:vlookup_new.xlsx| the vlookup_new.xlsx]] file instead of viewing it in web browser.
   * [[CSCPathwayAnalysisService/Tutorials | More]]
+ * [[CSCBiostatService | Biostatistics service]]
   1. [[CSCBiostatService/AffymetrixDataAnalysis | Affymetrix microarray data analysis]]
   1. [[CSCBiostatService/IlluminaChipDataAnalysis | Illumina’s BeadChip microarray data analysis]]
   1. [[CSCBiostatService/RNAseqDataAnalysis | RNA-seq data analysis]]
   1. [[CSCBiostatService/flowCytometryDataAnalysis | Flow cytometry data analysis]]
   1. [[CSCBiostatService/survivalAnalysis | Survival analysis]]