https://github.com/kkchau/NACEP-Analysis-of-Prostate-Cancer-Cells

https://github.com/kkchau/NACEP-Analysis-of-Prostate-Cancer-Cells

Last synced: 3 months ago
JSON representation

• Host: GitHub
• URL: https://github.com/kkchau/NACEP-Analysis-of-Prostate-Cancer-Cells
• Owner: kkchau
• Created: 2017-10-02T00:28:57.000Z (about 8 years ago)
• Default Branch: master
• Last Pushed: 2018-03-07T06:08:08.000Z (over 7 years ago)
• Last Synced: 2024-08-05T10:08:34.672Z (about 1 year ago)
• Language: R
• Size: 28.9 MB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

• awesome-ai-cancer - kkchau/NACEP-Analysis-of-Prostate-Cancer-Cells - NACEP Analysis of Tumorigenic prostate epithelial cells (Code / Repositories)

README

          
# NACEP Analysis of Tumorigenic prostate epithelial cells

Written as a final project for BENG 183: "Applied Genomic Technologies"

Source data and study: Time-course differential expression of immortal prostate epithelial cells versus tumorigentic prostate epithelial cells  

Accessed via the NCBI Gene Expression Omnibus at:  

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE77460

See "docs/final essay.pdf" for report. 

## Overall Process:

1. Data downloaded from NCBI GEO into files "GSE77460_EMP-gene-count-matrix" and "GSE77460_iPrEC-gene-count-matrix"

2. Gene lengths compiled using script "generateCoordinates.sh" and "discontinuedGeneLengths.py"

    - Employs NCBI E-UTILITIES

3. Conversion from count matrix to tpm matrix with "quantification.R"

4. Filtering performed with "DATA/filter/filterMethods.R"

    - expressionFilter params: expressionFilter(, 0.17, 39)

    - varianceFilter params: varianceFilter(, 2.4, T)

    - Output: "ANALYSIS/dataFilter.txt"

5. NACEP run: "run.sh" calls "run.R" which calls "NACEP.R"

    - Output: Distances.txt, sorted by statistical significance

### INSTALLING NCBI EDIRECT (E-UTILITIES)

    cd ~

    perl -MNet::FTP -e \

      '$ftp = new Net::FTP("ftp.ncbi.nlm.nih.gov", Passive => 1);

       $ftp->login; $ftp->binary;

       $ftp->get("/entrez/entrezdirect/edirect.tar.gz");'

    gunzip -c edirect.tar.gz | tar xf -

    rm edirect.tar.gz

    export PATH=$PATH:$HOME/edirect

    ./edirect/setup.sh

### QUERYING NCBI FOR GENE UID

    esearch -db gene -query " [UID] AND human [ORGN]" | efetch -format docsum | xtract -pattern GenomicInfoType -element ChrAccVer ChrStart ChrStop

## References

1.  Huang, W., Cao, X., & Zhong, S. (2010). Network-based comparison of temporal gene expression patterns. Bioinformatics, 26(23), 2944–2951. http://doi.org/10.1093/bioinformatics/btq561

2.  Berger, P. L., Winn, M. E., Miranti, C. K. (2016). Miz1, a Novel Target of ING4, Can Drive Prostate Luminal Epithelial Cell Differentiation. The Prostate. 77(1), 49-59. http://doi.org/10.1002/pros.23249