05 June 2014

DAVID, Bioconductor, and semantic similarity

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GO semantic similarity

  • Aphaenophone
  • AE inquired about status of Aphaenogaster genome
    • need to collect colony from Molly Bog and extract gDNA for PacBio!
  • deferred next meeting until August due to busy field schedules
  • Identified three ant species working with NG and Field Guide to the Ants of New England
  • Tapinoma sessile collected from top of Stowe Pinnacle VT
  • Prenolepsis imparis collected by NG from Shelburne VT
  • Aphaenogaster picea collected from East Woods, Burlington VT. confirmed what I knew…
  • Centennial ms
  • Started DNA extraction for 20 Aphaenogaster from East Woods for ddRADseq round 3


From my work over past few days, have discovered two major issues with using DAVID through the RDAVIDWebService R/Bioconductor package.

  1. RDAVIDWebService incorrectly gives value of 1.000 for many, but not all, gene clusters.
  2. Database was last updated in 2009

Regarding (1), I emailed the developer and he quickly responded that he would look into it. It’s straight-forward to manually calculate the correct Enrichment score, but a bit odd that this problem occurs nonetheless. Also, I can’t replicate the exact results running the same files on the DAVID web interface, though many of the same clusters do appear.

Issue (2) of the database is a larger problem. Annecdotal discussion on biostars [suggests][https://www.biostars.org/p/9394/#9401] this is a problem.

At this point - my thoughts are to give up on DAVID.

To get the main benefits of the DAVID analysis, clustering of related terms, I continued with clustering related GO terms using GOSemSim R/Bioconductor package as yesterday

Specifcally, I calculated the semantic similarity among all GO terms for an enriched category (e.g. High genes), calculated the distance among terms, and then plotted.

I was then able to assign a functional name to each cluster of related-GO terms. For example, here’s the clustering of A. picea High genes:

A. picea high cluster
A. picea high cluster

and here’s the clustering for A. picea Low genes:

A. picea low cluster
A. picea low cluster

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