MLL3

This repository hosts the code used in my research on how the loss of MLL3 affects ER-alpha regulation in ER+ breast cancer. Research performed at Vanderbilt University, under Thomas Stricker, MD PhD.

1. GERP analysis

2. DEMETER dependence tool - https://depmap.org/rnai/genedeps?gene=KMT2C

3. RNA-seq

   1. Tophat
      • Version 2.0.13
   2. Cufflinks
      • Version 2.2.1
   3. Cuffnorm
      • Version 2.2.1
   4. Differential Gene Expression Scripts
      1. TCGA
      2. ZR751
   5. WebGestalt
      • WebGestalt 2019 Version
      • Parameters
        • Minimum Number of Genes for a Category = 3
        • Maximum Number of Genes for a Category = 2000
        • Multiple Test Adjustment = BH
        • Functional Database = others
          • Uploaded MSigDB Release 7.0
   6. iRegulon
      • Cytoscape Version 3.7.1

4. ChIP-seq

   1. BWA Alignment
      • Version 0.7.5a-r405
   2. Peak Calling via SPP according to ENCODE best practices
      • SPP version 1.15.5
      • ENCODE 3 Pipeline v1 https://docs.google.com/document/d/1lG_Rd7fnYgRpSIqrIfuVlAz2dW1VaSQThzk836Db99c/edit#
      • IDR version 2.0.3
   3. Enrichment Analysis
      1. GREAT
         • Version 3.0.0
      2. WebGestalt
         • See Info Above
   4. Motif Analysis
      1. MEME-Suite
         • Version 4.11.2
   5. Peak Assignment
      1. Bedtools
         • Version 2.26.0
      2. Assessment of permutation-based assignment

5. Proliferation Assays

   1. GRMetrics
      • Version 1.10.0
      • R Version 3.6.1
      • Bioconducter Version 3.9

6. Accession Numbers

   1. RNA-seq data
   2. ChIP-seq data