moving the lamppost

random musings of a molecular biologist turned code jockey in the era of big data and open science.

Lab meeting 2013-08-21

1 Introduction

1.1 Purpose

Introduce core concepts relating to my project such as:

  1. Importance of Dengue and Malaria
  2. Transmission cycle dependant on Mosquitoes
  3. Limited effectiveness (medical/finacial) of treatment of the diseases in rural poor human communities
  4. Vector Control Strategies
  5. How Transgenesis modifies the vector control landscape
  6. Elements of Successful Transgenic Vector Control
  7. Introduction to control of transcription and importance of CRE/CRMs

2 Review of Literature Contributions and Development of Analytical Approach

2.1 Purpose

Review a selection of my contributions to the literature that have informed the approach used in this project throughout my tenure as a member of the lab and explain the methods that I have used based on the lessons learned.

  1. Sieglaff, D. H., Dunn, W. A., Xie, X. S., Megy, K., Marinotti, O., & James, A. A. (2009). Comparative genomics allows the discovery of cis-regulatory elements in mosquitoes. Proceedings of the National Academy of Sciences of the United States of America, 106(9), 3053–8. doi:10.1073/pnas.0813264106

    • Use of comparative genomics to discover putative CREs from orthologous promoter regions in mosquitoes that were able to be correlated with bloodmeal associated transcription control
    • For any specific transcription profile, typically a single motif was found to be significantly enriched in the corresponding promoter regions (modules not obvious)
  2. Bonizzoni, M., Dunn, W. A., Campbell, C. L., Olson, K. E., Dimon, M. T., Marinotti, O., & James, A. A. (2011). RNA-seq analyses of blood-induced changes in gene expression in the mosquito vector species, Aedes aegypti. BMC genomics, 12(1), 82. doi:10.1186/1471-2164-12-82

    • Provided first experience in data handling and analysis of RNA-seq big data

    • Illustrated challenges to using flanking regions as putative promoters in genomes at this level of annotation completion/quality
      • annotation contains missed first exons and other incorrect feature definitions
      • upstream genes sometimes more likely to represent exon of downstream gene
    • Nevertheless using SCOPE, putative CRMs were able to be predicted

  3. Bonizzoni, M., Dunn, W. a., Campbell, C. L., Olson, K. E., Marinotti, O., James, a. a., & Kulathinal, R. (2012). Strain Variation in the Transcriptome of the Dengue Fever Vector, Aedes aegypti. G3: Genes|Genomes|Genetics, 2(1), 103–114. doi:10.1534/g3.111.001107

    • Provided continued lessons on managing and analyzing RNAseq big data
    • Revealed that the transcriptomes of Ae. aegypti mosquitoes from distinct strains vary significantly in complexity and abundance of specific transcripts. This variation is evident in non- blood-fed mosquitoes and is enhanced after a bloodmeal.
    • differential use of paralogous genes
    • Support the need to take precautions when comparing differences in transcript abundance profiles between species that may have last shared a common ancestor as far back as 200 mya.
  4. Bonizzoni, M., Dunn, W. A., Campbell, C. L., Olson, K. E., Marinotti, O., & James, A. A. (2012). Complex Modulation of the Aedes aegypti Transcriptome in Response to Dengue Virus Infection. PloS one, 7(11), e50512. doi:10.1371/journal.pone.0050512

    • Example of how results (CRE-discovery in this case) are sensitive to the gene-sets use for analysis.
  5. Functional Genomics can be thought of as a problem of generating meaningful gene-sets

    • signal-to-noise is major challenge in generating useful gene-sets
  6. This project aims to generate meaningful gene-sets through integration of multiple data-types

    • comparative genomics (N-way 1-to-1 orthologs)
    • comparative transcriptomics (identical RNA-seq experiements on divergent Mosquito species with shared trait: bloodfeeding)
    • phylogenetics (estimated divergence since last common ancestor)
    • existing knowledge about certain bloodmeal related transcriptional control programs (20E interacting TFBS motifs)
  7. The last item presents analysis challenges that I addressed through custom graph-based analysis model (gFunc)


3 Software Development to Support Analytical Approach

3.1 Purpose

Illustrate how lessons learned in previous chapter (as well as new lessons introduced here) are addressed through custom software solutions.

  1. RNA-seq analysis, reproducibility, updating (blacktie)
  2. Integration of multiple disparate Omics scale data types (gFunc)
  3. Documentation of exactly how analyses were carried out (IPython notebooks and automated log keeping built in to blacktie)